Starting phenix.real_space_refine on Fri Sep 11 20:42:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sef_10154/09_2026/6sef_10154.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sef_10154/09_2026/6sef_10154.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6sef_10154/09_2026/6sef_10154.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sef_10154/09_2026/6sef_10154.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6sef_10154/09_2026/6sef_10154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sef_10154/09_2026/6sef_10154.map" } resolution = 3.7 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= 0.003 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 288 5.49 5 S 10 5.16 5 C 6608 2.51 5 N 2235 2.21 5 O 2778 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11919 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 812 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "B" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 629 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 739 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 812 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "F" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 618 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 792 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "H" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "V" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 160 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 1, 'TRANS': 16} Time building chain proxies: 2.57, per 1000 atoms: 0.22 Number of scatterers: 11919 At special positions: 0 Unit cell: (79.3, 120.9, 115.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 288 15.00 O 2778 8.00 N 2235 7.00 C 6608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 400.8 milliseconds 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1394 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 9 sheets defined 70.8% alpha, 2.7% beta 143 base pairs and 246 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 46 through 57 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 87 through 116 removed outlier: 3.663A pdb=" N LEU A 91 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.625A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 139 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.588A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.529A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 removed outlier: 4.113A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.559A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.713A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.721A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 122 removed outlier: 3.866A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 removed outlier: 3.603A pdb=" N GLU E 50 " --> pdb=" O GLY E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.792A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR E 79 " --> pdb=" O CYS E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 117 removed outlier: 3.751A pdb=" N LEU E 91 " --> pdb=" O GLN E 87 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU E 112 " --> pdb=" O ASP E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 134 removed outlier: 4.075A pdb=" N GLY E 134 " --> pdb=" O ARG E 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.683A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 25 through 29' Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 52 removed outlier: 3.878A pdb=" N GLU F 52 " --> pdb=" O LEU F 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 49 through 52' Processing helix chain 'F' and resid 53 through 76 removed outlier: 3.667A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.861A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 72 removed outlier: 4.079A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 removed outlier: 3.530A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 38 through 49 removed outlier: 3.703A pdb=" N TYR H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.537A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.691A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 122 removed outlier: 3.716A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR H 119 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 7.106A pdb=" N ASN A 85 " --> 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 120 through 121 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.861A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 removed outlier: 7.038A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 85 through 86 removed outlier: 6.712A pdb=" N ASN E 85 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 120 through 121 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.809A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 354 hydrogen bonds defined for protein. 1062 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 360 hydrogen bonds 696 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 246 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1964 1.33 - 1.45: 4370 1.45 - 1.56: 5801 1.56 - 1.68: 577 1.68 - 1.80: 18 Bond restraints: 12730 Sorted by residual: bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.435 1.504 -0.069 1.30e-02 5.92e+03 2.79e+01 bond pdb=" C5' DG I -68 " pdb=" C4' DG I -68 " ideal model delta sigma weight residual 1.512 1.547 -0.035 7.00e-03 2.04e+04 2.50e+01 bond pdb=" C5' DA I -69 " pdb=" C4' DA I -69 " ideal model delta sigma weight residual 1.512 1.542 -0.030 7.00e-03 2.04e+04 1.79e+01 bond pdb=" C5' DA I 46 " pdb=" C4' DA I 46 " ideal model delta sigma weight residual 1.512 1.539 -0.027 7.00e-03 2.04e+04 1.51e+01 bond pdb=" C3' DC J 34 " pdb=" C2' DC J 34 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.44e+01 ... (remaining 12725 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 17180 1.87 - 3.75: 1149 3.75 - 5.62: 81 5.62 - 7.50: 15 7.50 - 9.37: 8 Bond angle restraints: 18433 Sorted by residual: angle pdb=" O5' DA I -35 " pdb=" C5' DA I -35 " pdb=" C4' DA I -35 " ideal model delta sigma weight residual 109.40 113.57 -4.17 8.00e-01 1.56e+00 2.71e+01 angle pdb=" O5' DG I -68 " pdb=" C5' DG I -68 " pdb=" C4' DG I -68 " ideal model delta sigma weight residual 109.40 113.52 -4.12 8.00e-01 1.56e+00 2.65e+01 angle pdb=" O5' DA I -5 " pdb=" C5' DA I -5 " pdb=" C4' DA I -5 " ideal model delta sigma weight residual 109.40 113.50 -4.10 8.00e-01 1.56e+00 2.63e+01 angle pdb=" O5' DA I 57 " pdb=" C5' DA I 57 " pdb=" C4' DA I 57 " ideal model delta sigma weight residual 109.40 113.46 -4.06 8.00e-01 1.56e+00 2.57e+01 angle pdb=" O5' DC I -46 " pdb=" C5' DC I -46 " pdb=" C4' DC I -46 " ideal model delta sigma weight residual 109.40 113.38 -3.98 8.00e-01 1.56e+00 2.47e+01 ... (remaining 18428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.21: 5352 32.21 - 64.41: 1481 64.41 - 96.62: 25 96.62 - 128.83: 2 128.83 - 161.03: 4 Dihedral angle restraints: 6864 sinusoidal: 4702 harmonic: 2162 Sorted by residual: dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 58.97 161.03 1 3.50e+01 8.16e-04 1.52e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 66.60 153.40 1 3.50e+01 8.16e-04 1.48e+01 dihedral pdb=" C4' DC J -58 " pdb=" C3' DC J -58 " pdb=" O3' DC J -58 " pdb=" P DT J -57 " ideal model delta sinusoidal sigma weight residual 220.00 86.54 133.46 1 3.50e+01 8.16e-04 1.32e+01 ... (remaining 6861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1141 0.045 - 0.090: 666 0.090 - 0.136: 223 0.136 - 0.181: 50 0.181 - 0.226: 6 Chirality restraints: 2086 Sorted by residual: chirality pdb=" P DT J -16 " pdb=" OP1 DT J -16 " pdb=" OP2 DT J -16 " pdb=" O5' DT J -16 " both_signs ideal model delta sigma weight residual True 2.34 -2.56 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ASP E 108 " pdb=" N ASP E 108 " pdb=" C ASP E 108 " pdb=" CB ASP E 108 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB VAL H 48 " pdb=" CA VAL H 48 " pdb=" CG1 VAL H 48 " pdb=" CG2 VAL H 48 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.45e-01 ... (remaining 2083 not shown) Planarity restraints: 1322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG V 522 " -0.011 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" C ARG V 522 " 0.040 2.00e-02 2.50e+03 pdb=" O ARG V 522 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE V 523 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 98 " 0.017 2.00e-02 2.50e+03 1.60e-02 5.11e+00 pdb=" CG TYR F 98 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR F 98 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR F 98 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR F 98 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR F 98 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR F 98 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 98 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -69 " -0.028 2.00e-02 2.50e+03 1.34e-02 4.91e+00 pdb=" N9 DA I -69 " 0.033 2.00e-02 2.50e+03 pdb=" C8 DA I -69 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA I -69 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA I -69 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I -69 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I -69 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DA I -69 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I -69 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA I -69 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DA I -69 " 0.002 2.00e-02 2.50e+03 ... (remaining 1319 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1777 2.76 - 3.29: 10088 3.29 - 3.83: 24215 3.83 - 4.36: 26986 4.36 - 4.90: 38283 Nonbonded interactions: 101349 Sorted by model distance: nonbonded pdb=" O2 DC I -64 " pdb=" N2 DG J 64 " model vdw 2.225 2.496 nonbonded pdb=" N2 DG I -58 " pdb=" O2 DC J 58 " model vdw 2.250 2.496 nonbonded pdb=" O2 DC I -56 " pdb=" N2 DG J 56 " model vdw 2.270 2.496 nonbonded pdb=" N2 DG I -60 " pdb=" O2 DC J 60 " model vdw 2.275 2.496 nonbonded pdb=" O2 DC I 5 " pdb=" N2 DG J -5 " model vdw 2.283 2.496 ... (remaining 101344 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' } ncs_group { reference = (chain 'B' and resid 25 through 100) selection = (chain 'F' and resid 25 through 100) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 111) } ncs_group { reference = (chain 'D' and resid 35 through 124) selection = chain 'H' } 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=1.00 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: 0.340 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.800 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 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 : 0.008 0.072 12730 Z= 0.696 Angle : 0.970 9.370 18433 Z= 0.771 Chirality : 0.060 0.226 2086 Planarity : 0.005 0.032 1322 Dihedral : 27.687 161.032 5470 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 16.08 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.26), residues: 733 helix: -0.93 (0.20), residues: 495 sheet: None (None), residues: 0 loop : -2.17 (0.33), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 133 TYR 0.038 0.003 TYR F 98 PHE 0.011 0.002 PHE H 65 TRP 0.013 0.002 TRP V 530 HIS 0.009 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00797 / 0.70 (12730) covalent geometry : angle 0.97029 / 0.77 (18433) hydrogen bonds : bond 0.12583 / 8.15 ( 714) hydrogen bonds : angle 4.74211 / 3.64 ( 1758) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8670 (mt-10) REVERT: A 52 ARG cc_start: 0.9226 (ttm170) cc_final: 0.8721 (mtm-85) REVERT: A 77 LYS cc_start: 0.9121 (ttmm) cc_final: 0.8862 (ttmm) REVERT: A 78 PHE cc_start: 0.8862 (m-80) cc_final: 0.7841 (m-80) REVERT: A 85 ASN cc_start: 0.9507 (m-40) cc_final: 0.9280 (m-40) REVERT: A 95 GLN cc_start: 0.9069 (tt0) cc_final: 0.8823 (tt0) REVERT: A 96 GLU cc_start: 0.8979 (tp30) cc_final: 0.8651 (tp30) REVERT: A 108 ASP cc_start: 0.8669 (m-30) cc_final: 0.8327 (p0) REVERT: B 44 LYS cc_start: 0.9098 (tttm) cc_final: 0.8690 (mtpp) REVERT: B 51 TYR cc_start: 0.8980 (m-80) cc_final: 0.8425 (m-80) REVERT: B 79 LYS cc_start: 0.8954 (mtmm) cc_final: 0.8716 (ttmm) REVERT: B 81 VAL cc_start: 0.9389 (t) cc_final: 0.9165 (t) REVERT: C 32 ARG cc_start: 0.9247 (ttp80) cc_final: 0.8575 (ttp80) REVERT: C 36 LYS cc_start: 0.9609 (mptt) cc_final: 0.9365 (mmmm) REVERT: C 61 GLU cc_start: 0.9063 (tp30) cc_final: 0.8729 (tp30) REVERT: C 64 GLU cc_start: 0.8377 (tp30) cc_final: 0.7950 (tp30) REVERT: C 68 ASN cc_start: 0.8803 (m110) cc_final: 0.8171 (m110) REVERT: C 95 LYS cc_start: 0.9579 (ttmm) cc_final: 0.9179 (tptt) REVERT: C 102 ILE cc_start: 0.9319 (mm) cc_final: 0.9051 (mt) REVERT: D 35 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7558 (mm-30) REVERT: D 37 TYR cc_start: 0.9280 (m-80) cc_final: 0.9058 (m-80) REVERT: D 71 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8201 (tm-30) REVERT: D 83 TYR cc_start: 0.8258 (m-10) cc_final: 0.7947 (m-10) REVERT: D 95 GLN cc_start: 0.9197 (tt0) cc_final: 0.8928 (tm-30) REVERT: D 120 LYS cc_start: 0.9556 (tttt) cc_final: 0.9290 (ttmm) REVERT: E 53 LYS cc_start: 0.9442 (ttpt) cc_final: 0.8998 (pttp) REVERT: E 65 LEU cc_start: 0.9463 (tp) cc_final: 0.9189 (tp) REVERT: E 89 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8203 (mm-40) REVERT: E 107 GLU cc_start: 0.8419 (pt0) cc_final: 0.8026 (pt0) REVERT: E 130 ARG cc_start: 0.9576 (mtp180) cc_final: 0.9265 (mtp85) REVERT: E 137 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6946 (mm-30) REVERT: F 59 LYS cc_start: 0.8732 (tttm) cc_final: 0.8231 (tttm) REVERT: F 64 ASN cc_start: 0.9217 (t0) cc_final: 0.8753 (t0) REVERT: F 68 ASP cc_start: 0.8721 (m-30) cc_final: 0.7357 (m-30) REVERT: F 88 TYR cc_start: 0.8753 (m-10) cc_final: 0.8111 (m-80) REVERT: G 25 PHE cc_start: 0.8452 (m-80) cc_final: 0.8221 (m-10) REVERT: G 36 LYS cc_start: 0.9228 (mmmt) cc_final: 0.8964 (mmtt) REVERT: G 56 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8329 (tt0) REVERT: G 64 GLU cc_start: 0.8778 (tp30) cc_final: 0.7861 (tp30) REVERT: G 65 LEU cc_start: 0.9499 (mm) cc_final: 0.9258 (mm) REVERT: G 68 ASN cc_start: 0.8259 (m110) cc_final: 0.7177 (m110) REVERT: G 84 GLN cc_start: 0.9318 (tp-100) cc_final: 0.8391 (tp-100) REVERT: H 79 ARG cc_start: 0.8958 (ptp90) cc_final: 0.8585 (mtm110) REVERT: H 83 TYR cc_start: 0.8518 (m-10) cc_final: 0.7851 (m-10) REVERT: H 90 THR cc_start: 0.8840 (p) cc_final: 0.8265 (p) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.1495 time to fit residues: 61.9633 Evaluate side-chains 239 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.0040 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN C 68 ASN C 73 ASN D 82 HIS D 84 ASN E 95 GLN G 94 ASN H 63 ASN H 109 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.056920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.042960 restraints weight = 65207.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.044083 restraints weight = 33262.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.044940 restraints weight = 21931.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.045508 restraints weight = 16823.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.045786 restraints weight = 14203.173| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12730 Z= 0.166 Angle : 0.704 7.323 18433 Z= 0.411 Chirality : 0.046 0.229 2086 Planarity : 0.005 0.058 1322 Dihedral : 30.610 164.423 3997 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.73 % Allowed : 22.19 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.29), residues: 733 helix: 0.30 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -1.84 (0.34), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 33 TYR 0.022 0.002 TYR E 110 PHE 0.018 0.001 PHE H 65 TRP 0.007 0.001 TRP E 47 HIS 0.010 0.002 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.17 (12730) covalent geometry : angle 0.70442 / 0.41 (18433) hydrogen bonds : bond 0.06878 / 4.28 ( 714) hydrogen bonds : angle 3.37226 / 2.59 ( 1758) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 262 time to evaluate : 0.314 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: symmetry clash REVERT: A 50 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8634 (mt-10) REVERT: A 77 LYS cc_start: 0.9206 (ttmm) cc_final: 0.8880 (ttmm) REVERT: A 78 PHE cc_start: 0.9017 (m-80) cc_final: 0.8394 (m-80) REVERT: A 85 ASN cc_start: 0.9491 (m-40) cc_final: 0.9250 (m-40) REVERT: A 96 GLU cc_start: 0.8908 (tp30) cc_final: 0.8674 (tp30) REVERT: A 104 HIS cc_start: 0.8483 (t70) cc_final: 0.7719 (t70) REVERT: A 107 GLU cc_start: 0.8706 (pp20) cc_final: 0.8074 (pp20) REVERT: A 108 ASP cc_start: 0.8732 (m-30) cc_final: 0.7887 (m-30) REVERT: A 127 GLN cc_start: 0.8702 (tm-30) cc_final: 0.8479 (tm-30) REVERT: B 27 GLN cc_start: 0.8848 (tp40) cc_final: 0.8559 (mm-40) REVERT: B 79 LYS cc_start: 0.8898 (mtmm) cc_final: 0.8526 (mtpp) REVERT: B 81 VAL cc_start: 0.9406 (t) cc_final: 0.9196 (t) REVERT: B 88 TYR cc_start: 0.8954 (m-10) cc_final: 0.8293 (m-10) REVERT: C 32 ARG cc_start: 0.9328 (ttp80) cc_final: 0.9081 (ptm-80) REVERT: C 36 LYS cc_start: 0.9549 (mptt) cc_final: 0.9343 (mmmm) REVERT: C 64 GLU cc_start: 0.8539 (tp30) cc_final: 0.8084 (tp30) REVERT: C 68 ASN cc_start: 0.9065 (m-40) cc_final: 0.7975 (m110) REVERT: C 95 LYS cc_start: 0.9595 (ttmm) cc_final: 0.9191 (tptt) REVERT: C 99 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8115 (mmmm) REVERT: D 35 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7843 (mm-30) REVERT: D 37 TYR cc_start: 0.9412 (m-80) cc_final: 0.9124 (m-80) REVERT: D 71 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8501 (tm-30) REVERT: D 83 TYR cc_start: 0.8307 (m-10) cc_final: 0.7641 (m-10) REVERT: D 95 GLN cc_start: 0.9255 (tt0) cc_final: 0.8931 (tm-30) REVERT: D 108 LYS cc_start: 0.8886 (mtmm) cc_final: 0.8639 (ptpt) REVERT: E 65 LEU cc_start: 0.9474 (tp) cc_final: 0.9216 (tp) REVERT: E 73 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8496 (tm-30) REVERT: E 89 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8275 (mm-40) REVERT: E 104 HIS cc_start: 0.8549 (t-90) cc_final: 0.8159 (t-170) REVERT: E 130 ARG cc_start: 0.9647 (mtp180) cc_final: 0.9354 (ptm160) REVERT: F 88 TYR cc_start: 0.8868 (m-10) cc_final: 0.8185 (m-80) REVERT: G 25 PHE cc_start: 0.8402 (m-80) cc_final: 0.8081 (m-10) REVERT: G 36 LYS cc_start: 0.9327 (mmmt) cc_final: 0.8954 (mmtt) REVERT: G 61 GLU cc_start: 0.8791 (tp30) cc_final: 0.8586 (tp30) REVERT: G 64 GLU cc_start: 0.8817 (tp30) cc_final: 0.8401 (tp30) REVERT: G 65 LEU cc_start: 0.9590 (mm) cc_final: 0.9322 (mm) REVERT: G 68 ASN cc_start: 0.8103 (m110) cc_final: 0.7870 (m110) REVERT: G 84 GLN cc_start: 0.9273 (tp-100) cc_final: 0.8553 (tp-100) REVERT: G 95 LYS cc_start: 0.8945 (ttpt) cc_final: 0.8652 (tppt) REVERT: G 99 LYS cc_start: 0.8865 (mmmt) cc_final: 0.8650 (mmtm) REVERT: G 102 ILE cc_start: 0.9485 (mp) cc_final: 0.9275 (mp) REVERT: H 59 MET cc_start: 0.9197 (tpp) cc_final: 0.8938 (tpp) REVERT: H 83 TYR cc_start: 0.8513 (m-10) cc_final: 0.7894 (m-10) REVERT: H 100 LEU cc_start: 0.9404 (mt) cc_final: 0.9183 (mt) REVERT: H 102 LEU cc_start: 0.8896 (tp) cc_final: 0.8657 (tp) outliers start: 17 outliers final: 9 residues processed: 268 average time/residue: 0.1239 time to fit residues: 45.0130 Evaluate side-chains 245 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 235 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 118 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 56 optimal weight: 0.9990 chunk 61 optimal weight: 0.1980 chunk 25 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 97 optimal weight: 30.0000 chunk 78 optimal weight: 40.0000 chunk 7 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 GLN A 87 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.056677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.042805 restraints weight = 64452.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.043987 restraints weight = 31560.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.044873 restraints weight = 20356.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.045422 restraints weight = 15301.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.045806 restraints weight = 12830.080| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 12730 Z= 0.159 Angle : 0.661 6.815 18433 Z= 0.391 Chirality : 0.044 0.252 2086 Planarity : 0.004 0.045 1322 Dihedral : 30.678 163.606 3997 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.05 % Allowed : 24.92 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.30), residues: 733 helix: 0.72 (0.23), residues: 513 sheet: None (None), residues: 0 loop : -1.74 (0.35), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 79 TYR 0.019 0.002 TYR D 83 PHE 0.022 0.001 PHE F 61 TRP 0.005 0.001 TRP V 530 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.16 (12730) covalent geometry : angle 0.66085 / 0.39 (18433) hydrogen bonds : bond 0.06419 / 4.02 ( 714) hydrogen bonds : angle 3.14013 / 2.40 ( 1758) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 249 time to evaluate : 0.265 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: A 50 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8589 (mt-10) REVERT: A 77 LYS cc_start: 0.9233 (ttmm) cc_final: 0.8897 (ttmm) REVERT: A 78 PHE cc_start: 0.9011 (m-80) cc_final: 0.8465 (m-80) REVERT: A 85 ASN cc_start: 0.9505 (m-40) cc_final: 0.9283 (m-40) REVERT: A 104 HIS cc_start: 0.8521 (t70) cc_final: 0.7714 (t70) REVERT: A 107 GLU cc_start: 0.8770 (pp20) cc_final: 0.8122 (pp20) REVERT: A 108 ASP cc_start: 0.8800 (m-30) cc_final: 0.7871 (m-30) REVERT: A 127 GLN cc_start: 0.8771 (tm-30) cc_final: 0.8476 (tm-30) REVERT: B 30 THR cc_start: 0.8905 (p) cc_final: 0.8589 (t) REVERT: B 31 LYS cc_start: 0.9235 (mtpp) cc_final: 0.8767 (mtpp) REVERT: B 79 LYS cc_start: 0.8883 (mtmm) cc_final: 0.8517 (mtpp) REVERT: C 32 ARG cc_start: 0.9313 (ttp80) cc_final: 0.8646 (ttp80) REVERT: C 64 GLU cc_start: 0.8569 (tp30) cc_final: 0.8063 (tp30) REVERT: C 68 ASN cc_start: 0.8914 (m-40) cc_final: 0.7933 (m110) REVERT: C 95 LYS cc_start: 0.9591 (ttmm) cc_final: 0.9179 (tptt) REVERT: C 104 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7646 (tp-100) REVERT: D 35 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7948 (mm-30) REVERT: D 37 TYR cc_start: 0.9422 (m-80) cc_final: 0.9100 (m-80) REVERT: D 71 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8503 (tm-30) REVERT: D 95 GLN cc_start: 0.9259 (tt0) cc_final: 0.9012 (tm-30) REVERT: E 65 LEU cc_start: 0.9492 (tp) cc_final: 0.9240 (tp) REVERT: E 73 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8455 (tm-30) REVERT: E 74 ILE cc_start: 0.9583 (tt) cc_final: 0.9266 (tt) REVERT: E 104 HIS cc_start: 0.8836 (t-90) cc_final: 0.8549 (t-170) REVERT: E 130 ARG cc_start: 0.9606 (mtp180) cc_final: 0.9327 (ptm160) REVERT: F 88 TYR cc_start: 0.8866 (m-10) cc_final: 0.8141 (m-80) REVERT: G 25 PHE cc_start: 0.8403 (m-80) cc_final: 0.8084 (m-10) REVERT: G 36 LYS cc_start: 0.9249 (mmmt) cc_final: 0.8856 (mmtt) REVERT: G 64 GLU cc_start: 0.8792 (tp30) cc_final: 0.8382 (tp30) REVERT: G 65 LEU cc_start: 0.9612 (mm) cc_final: 0.9308 (mm) REVERT: G 84 GLN cc_start: 0.9285 (tp-100) cc_final: 0.8725 (tp-100) REVERT: G 95 LYS cc_start: 0.8907 (ttpt) cc_final: 0.8629 (tppt) REVERT: H 83 TYR cc_start: 0.8522 (m-10) cc_final: 0.7762 (m-10) REVERT: H 102 LEU cc_start: 0.8965 (tp) cc_final: 0.8736 (tp) outliers start: 19 outliers final: 12 residues processed: 258 average time/residue: 0.1105 time to fit residues: 39.1547 Evaluate side-chains 241 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 229 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 94 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 13 optimal weight: 0.6980 chunk 79 optimal weight: 30.0000 chunk 12 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 87 optimal weight: 40.0000 chunk 84 optimal weight: 50.0000 chunk 85 optimal weight: 30.0000 chunk 70 optimal weight: 40.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 GLN A 95 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.056345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.042433 restraints weight = 64617.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.043606 restraints weight = 31905.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.044515 restraints weight = 20626.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.045061 restraints weight = 15457.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.045385 restraints weight = 12999.382| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12730 Z= 0.166 Angle : 0.651 9.180 18433 Z= 0.384 Chirality : 0.043 0.247 2086 Planarity : 0.004 0.045 1322 Dihedral : 30.746 163.292 3997 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.89 % Allowed : 27.01 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.30), residues: 733 helix: 1.03 (0.23), residues: 508 sheet: None (None), residues: 0 loop : -1.55 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 71 TYR 0.024 0.002 TYR D 83 PHE 0.015 0.001 PHE H 65 TRP 0.006 0.001 TRP E 86 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.17 (12730) covalent geometry : angle 0.65060 / 0.38 (18433) hydrogen bonds : bond 0.06286 / 3.95 ( 714) hydrogen bonds : angle 3.12333 / 2.37 ( 1758) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 249 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8578 (mt-10) REVERT: A 77 LYS cc_start: 0.9285 (ttmm) cc_final: 0.8957 (ttmm) REVERT: A 78 PHE cc_start: 0.9007 (m-80) cc_final: 0.8622 (m-80) REVERT: A 85 ASN cc_start: 0.9524 (m-40) cc_final: 0.9314 (m-40) REVERT: A 87 GLN cc_start: 0.9400 (mt0) cc_final: 0.9150 (mt0) REVERT: A 104 HIS cc_start: 0.8645 (t70) cc_final: 0.7816 (t70) REVERT: A 107 GLU cc_start: 0.8867 (pp20) cc_final: 0.8046 (pp20) REVERT: A 108 ASP cc_start: 0.8860 (m-30) cc_final: 0.7773 (m-30) REVERT: A 127 GLN cc_start: 0.8855 (tm-30) cc_final: 0.8528 (tm-30) REVERT: B 30 THR cc_start: 0.8924 (p) cc_final: 0.8625 (t) REVERT: B 31 LYS cc_start: 0.9212 (mtpp) cc_final: 0.8837 (mtpp) REVERT: B 79 LYS cc_start: 0.8894 (mtmm) cc_final: 0.8526 (mtpp) REVERT: B 88 TYR cc_start: 0.8786 (m-10) cc_final: 0.8474 (m-80) REVERT: C 32 ARG cc_start: 0.9324 (ttp80) cc_final: 0.8660 (ttp80) REVERT: C 64 GLU cc_start: 0.8587 (tp30) cc_final: 0.8238 (tp30) REVERT: C 91 GLU cc_start: 0.8752 (pm20) cc_final: 0.7723 (pm20) REVERT: C 95 LYS cc_start: 0.9603 (ttmm) cc_final: 0.9178 (tptt) REVERT: C 104 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7479 (mm-40) REVERT: D 35 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7878 (mm-30) REVERT: D 37 TYR cc_start: 0.9459 (m-80) cc_final: 0.9151 (m-80) REVERT: D 71 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8532 (tm-30) REVERT: D 83 TYR cc_start: 0.7763 (m-80) cc_final: 0.7531 (m-80) REVERT: D 95 GLN cc_start: 0.9288 (tt0) cc_final: 0.9034 (tm-30) REVERT: D 105 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8487 (tm-30) REVERT: E 50 GLU cc_start: 0.8556 (pp20) cc_final: 0.8349 (pp20) REVERT: E 65 LEU cc_start: 0.9508 (tp) cc_final: 0.9258 (tp) REVERT: E 104 HIS cc_start: 0.8853 (t-90) cc_final: 0.8558 (t70) REVERT: E 110 TYR cc_start: 0.8593 (t80) cc_final: 0.8186 (t80) REVERT: E 130 ARG cc_start: 0.9603 (mtp180) cc_final: 0.9324 (ptm160) REVERT: F 88 TYR cc_start: 0.8790 (m-10) cc_final: 0.8076 (m-80) REVERT: G 36 LYS cc_start: 0.9239 (mmmt) cc_final: 0.8850 (mmtt) REVERT: G 56 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8398 (mt-10) REVERT: G 61 GLU cc_start: 0.8738 (tp30) cc_final: 0.8443 (tp30) REVERT: G 65 LEU cc_start: 0.9634 (mm) cc_final: 0.9122 (mm) REVERT: G 68 ASN cc_start: 0.7935 (m110) cc_final: 0.7679 (p0) REVERT: G 84 GLN cc_start: 0.9260 (tp-100) cc_final: 0.8943 (tp40) REVERT: G 92 GLU cc_start: 0.8134 (tt0) cc_final: 0.7865 (tt0) REVERT: G 95 LYS cc_start: 0.9005 (ttpt) cc_final: 0.8771 (tppt) REVERT: G 99 LYS cc_start: 0.8988 (mmmm) cc_final: 0.8650 (mmtm) REVERT: H 83 TYR cc_start: 0.8523 (m-10) cc_final: 0.7615 (m-10) REVERT: H 120 LYS cc_start: 0.9681 (ttmm) cc_final: 0.9455 (tmtt) outliers start: 18 outliers final: 14 residues processed: 257 average time/residue: 0.1168 time to fit residues: 40.9094 Evaluate side-chains 240 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 226 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 94 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 71 optimal weight: 30.0000 chunk 28 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 70 optimal weight: 40.0000 chunk 79 optimal weight: 30.0000 chunk 61 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 11 optimal weight: 0.4980 chunk 24 optimal weight: 5.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.055060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.040958 restraints weight = 66492.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.042059 restraints weight = 33829.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.042879 restraints weight = 22409.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.043417 restraints weight = 17228.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.043747 restraints weight = 14601.272| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12730 Z= 0.221 Angle : 0.687 6.712 18433 Z= 0.399 Chirality : 0.044 0.237 2086 Planarity : 0.005 0.044 1322 Dihedral : 30.913 162.887 3997 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.66 % Allowed : 25.56 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.30), residues: 733 helix: 1.31 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.49 (0.36), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 79 TYR 0.017 0.002 TYR G 39 PHE 0.012 0.002 PHE H 65 TRP 0.006 0.001 TRP V 531 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.22 (12730) covalent geometry : angle 0.68745 / 0.40 (18433) hydrogen bonds : bond 0.06884 / 4.37 ( 714) hydrogen bonds : angle 3.24584 / 2.44 ( 1758) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 239 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8596 (mt-10) REVERT: A 77 LYS cc_start: 0.9311 (ttmm) cc_final: 0.9020 (ttmm) REVERT: A 85 ASN cc_start: 0.9567 (m-40) cc_final: 0.9349 (m-40) REVERT: A 87 GLN cc_start: 0.9430 (mt0) cc_final: 0.9215 (mt0) REVERT: A 104 HIS cc_start: 0.8676 (t70) cc_final: 0.7838 (t70) REVERT: A 107 GLU cc_start: 0.8911 (pp20) cc_final: 0.8098 (pp20) REVERT: A 108 ASP cc_start: 0.8904 (m-30) cc_final: 0.7826 (m-30) REVERT: A 127 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8551 (tm-30) REVERT: B 30 THR cc_start: 0.9071 (p) cc_final: 0.8784 (t) REVERT: B 31 LYS cc_start: 0.9266 (mtpp) cc_final: 0.8911 (mtpp) REVERT: B 44 LYS cc_start: 0.8991 (tttm) cc_final: 0.8759 (mtpp) REVERT: B 79 LYS cc_start: 0.8937 (mtmm) cc_final: 0.8560 (mtpp) REVERT: B 84 MET cc_start: 0.9164 (mmp) cc_final: 0.8916 (tpp) REVERT: C 32 ARG cc_start: 0.9345 (ttp80) cc_final: 0.8740 (ttp80) REVERT: C 64 GLU cc_start: 0.8609 (tp30) cc_final: 0.8116 (tp30) REVERT: C 68 ASN cc_start: 0.8825 (m-40) cc_final: 0.7955 (m110) REVERT: C 92 GLU cc_start: 0.8675 (mp0) cc_final: 0.8386 (pm20) REVERT: C 95 LYS cc_start: 0.9617 (ttmm) cc_final: 0.9181 (tptt) REVERT: C 104 GLN cc_start: 0.8272 (mm-40) cc_final: 0.7600 (mm-40) REVERT: D 35 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7894 (mm-30) REVERT: D 37 TYR cc_start: 0.9482 (m-80) cc_final: 0.9279 (m-80) REVERT: D 71 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8579 (tm-30) REVERT: D 83 TYR cc_start: 0.8345 (m-80) cc_final: 0.7672 (m-80) REVERT: D 95 GLN cc_start: 0.9289 (tt0) cc_final: 0.9004 (tm-30) REVERT: E 65 LEU cc_start: 0.9544 (tp) cc_final: 0.9286 (tp) REVERT: E 73 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8439 (tm-30) REVERT: E 104 HIS cc_start: 0.9026 (t-90) cc_final: 0.8668 (t70) REVERT: E 130 ARG cc_start: 0.9610 (mtp180) cc_final: 0.9327 (ptm160) REVERT: F 52 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8781 (tp30) REVERT: F 88 TYR cc_start: 0.8755 (m-10) cc_final: 0.8396 (m-80) REVERT: G 36 LYS cc_start: 0.9290 (mmmt) cc_final: 0.8902 (mmtt) REVERT: G 65 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.9323 (mm) REVERT: G 95 LYS cc_start: 0.9047 (ttpt) cc_final: 0.8712 (ttmm) REVERT: G 104 GLN cc_start: 0.8500 (mp10) cc_final: 0.8152 (mp10) REVERT: H 46 LYS cc_start: 0.9129 (tppt) cc_final: 0.8852 (tppt) REVERT: H 62 MET cc_start: 0.9242 (mmm) cc_final: 0.8945 (mmm) outliers start: 29 outliers final: 20 residues processed: 250 average time/residue: 0.1174 time to fit residues: 40.5311 Evaluate side-chains 248 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 227 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 79 optimal weight: 30.0000 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 83 optimal weight: 50.0000 chunk 61 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 82 optimal weight: 50.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 GLN A 95 GLN A 104 HIS ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.054892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.040890 restraints weight = 66668.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.041991 restraints weight = 34031.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.042840 restraints weight = 22469.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.043373 restraints weight = 17214.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.043698 restraints weight = 14578.345| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12730 Z= 0.217 Angle : 0.685 7.948 18433 Z= 0.398 Chirality : 0.044 0.238 2086 Planarity : 0.004 0.045 1322 Dihedral : 30.998 161.331 3997 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.66 % Allowed : 29.42 % Favored : 65.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.30), residues: 733 helix: 1.39 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.51 (0.37), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 71 TYR 0.017 0.002 TYR D 83 PHE 0.013 0.001 PHE H 65 TRP 0.006 0.001 TRP V 531 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.22 (12730) covalent geometry : angle 0.68484 / 0.40 (18433) hydrogen bonds : bond 0.06638 / 4.20 ( 714) hydrogen bonds : angle 3.25228 / 2.43 ( 1758) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 230 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8576 (mt-10) REVERT: A 87 GLN cc_start: 0.9455 (mt0) cc_final: 0.9205 (mt0) REVERT: A 104 HIS cc_start: 0.8521 (t-90) cc_final: 0.7694 (t70) REVERT: A 107 GLU cc_start: 0.8905 (pp20) cc_final: 0.8055 (pp20) REVERT: A 108 ASP cc_start: 0.8699 (m-30) cc_final: 0.7816 (m-30) REVERT: A 127 GLN cc_start: 0.8956 (tm-30) cc_final: 0.8580 (tm-30) REVERT: B 30 THR cc_start: 0.9051 (p) cc_final: 0.8756 (t) REVERT: B 31 LYS cc_start: 0.9245 (mtpp) cc_final: 0.8819 (mtpp) REVERT: B 44 LYS cc_start: 0.9015 (tttm) cc_final: 0.8772 (mtpp) REVERT: B 79 LYS cc_start: 0.8949 (mtmm) cc_final: 0.8677 (ttmm) REVERT: C 64 GLU cc_start: 0.8662 (tp30) cc_final: 0.8253 (tp30) REVERT: C 68 ASN cc_start: 0.8963 (m-40) cc_final: 0.8096 (m-40) REVERT: C 92 GLU cc_start: 0.8595 (mp0) cc_final: 0.8345 (pm20) REVERT: C 95 LYS cc_start: 0.9621 (ttmm) cc_final: 0.9173 (tptt) REVERT: C 104 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7550 (mm-40) REVERT: D 71 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8563 (tm-30) REVERT: D 95 GLN cc_start: 0.9301 (tt0) cc_final: 0.8387 (tt0) REVERT: E 73 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8549 (tm-30) REVERT: E 104 HIS cc_start: 0.9026 (t-90) cc_final: 0.8637 (t70) REVERT: E 110 TYR cc_start: 0.8659 (t80) cc_final: 0.8395 (t80) REVERT: E 130 ARG cc_start: 0.9621 (mtp180) cc_final: 0.9328 (ptm160) REVERT: F 52 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8768 (tp30) REVERT: F 88 TYR cc_start: 0.8711 (m-10) cc_final: 0.7549 (m-80) REVERT: G 36 LYS cc_start: 0.9295 (mmmt) cc_final: 0.8915 (mmtt) REVERT: G 65 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9344 (mm) REVERT: G 95 LYS cc_start: 0.9013 (ttpt) cc_final: 0.8708 (ttmm) REVERT: H 46 LYS cc_start: 0.9133 (tppt) cc_final: 0.8827 (tppt) REVERT: H 62 MET cc_start: 0.9308 (mmm) cc_final: 0.9076 (mmm) REVERT: H 83 TYR cc_start: 0.8508 (m-10) cc_final: 0.7590 (m-10) outliers start: 29 outliers final: 23 residues processed: 240 average time/residue: 0.1222 time to fit residues: 40.1193 Evaluate side-chains 242 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 218 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.0060 chunk 68 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 15 optimal weight: 0.1980 chunk 78 optimal weight: 40.0000 chunk 88 optimal weight: 40.0000 chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.8402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.055924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.041898 restraints weight = 65053.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.043041 restraints weight = 32935.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.043899 restraints weight = 21652.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.044419 restraints weight = 16577.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.044753 restraints weight = 14059.369| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12730 Z= 0.157 Angle : 0.661 7.960 18433 Z= 0.385 Chirality : 0.043 0.246 2086 Planarity : 0.004 0.045 1322 Dihedral : 30.927 161.418 3997 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.86 % Allowed : 30.39 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.31), residues: 733 helix: 1.52 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.47 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 71 TYR 0.038 0.002 TYR D 83 PHE 0.015 0.001 PHE H 65 TRP 0.006 0.001 TRP A 47 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.16 (12730) covalent geometry : angle 0.66056 / 0.38 (18433) hydrogen bonds : bond 0.05977 / 3.77 ( 714) hydrogen bonds : angle 3.05338 / 2.29 ( 1758) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 240 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8566 (mt-10) REVERT: A 80 ARG cc_start: 0.8092 (ptp90) cc_final: 0.7884 (ptt-90) REVERT: A 95 GLN cc_start: 0.9025 (tt0) cc_final: 0.8616 (tp40) REVERT: A 104 HIS cc_start: 0.8596 (t-90) cc_final: 0.7719 (t70) REVERT: A 107 GLU cc_start: 0.8916 (pp20) cc_final: 0.8143 (pp20) REVERT: A 108 ASP cc_start: 0.8666 (m-30) cc_final: 0.7839 (m-30) REVERT: A 127 GLN cc_start: 0.9007 (tm-30) cc_final: 0.8638 (tm-30) REVERT: B 30 THR cc_start: 0.9046 (p) cc_final: 0.8746 (t) REVERT: B 79 LYS cc_start: 0.8951 (mtmm) cc_final: 0.8690 (ttmm) REVERT: C 32 ARG cc_start: 0.9369 (ptm-80) cc_final: 0.8752 (ttp80) REVERT: C 64 GLU cc_start: 0.8648 (tp30) cc_final: 0.8150 (tp30) REVERT: C 68 ASN cc_start: 0.8947 (m-40) cc_final: 0.7870 (m110) REVERT: C 92 GLU cc_start: 0.8555 (mp0) cc_final: 0.8333 (pm20) REVERT: C 95 LYS cc_start: 0.9603 (ttmm) cc_final: 0.9143 (tptt) REVERT: C 99 LYS cc_start: 0.8555 (mmmm) cc_final: 0.8283 (mmmm) REVERT: C 104 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7542 (mm-40) REVERT: D 71 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8541 (tm-30) REVERT: D 83 TYR cc_start: 0.8069 (m-80) cc_final: 0.7564 (m-80) REVERT: D 95 GLN cc_start: 0.9249 (tt0) cc_final: 0.8952 (tm-30) REVERT: E 73 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8515 (tm-30) REVERT: E 104 HIS cc_start: 0.9012 (t-90) cc_final: 0.8621 (t70) REVERT: E 110 TYR cc_start: 0.8628 (t80) cc_final: 0.8189 (t80) REVERT: F 43 VAL cc_start: 0.9580 (p) cc_final: 0.9160 (p) REVERT: F 52 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8728 (tp30) REVERT: F 84 MET cc_start: 0.8097 (tpp) cc_final: 0.7796 (tpp) REVERT: F 88 TYR cc_start: 0.8681 (m-10) cc_final: 0.7529 (m-80) REVERT: G 36 LYS cc_start: 0.9279 (mmmt) cc_final: 0.8883 (mmtt) REVERT: G 65 LEU cc_start: 0.9632 (OUTLIER) cc_final: 0.9406 (mm) REVERT: G 95 LYS cc_start: 0.8949 (ttpt) cc_final: 0.8638 (ttmm) REVERT: G 104 GLN cc_start: 0.8601 (mp10) cc_final: 0.8397 (mp10) REVERT: H 46 LYS cc_start: 0.9211 (tppt) cc_final: 0.8897 (tppt) REVERT: H 62 MET cc_start: 0.9287 (mmm) cc_final: 0.8897 (mmm) REVERT: H 83 TYR cc_start: 0.8459 (m-10) cc_final: 0.7817 (m-10) outliers start: 24 outliers final: 18 residues processed: 250 average time/residue: 0.1211 time to fit residues: 41.6402 Evaluate side-chains 245 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 226 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain H residue 94 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 96 optimal weight: 50.0000 chunk 44 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 92 optimal weight: 40.0000 chunk 77 optimal weight: 30.0000 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 50.0000 chunk 8 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.055359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.041434 restraints weight = 65698.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.042551 restraints weight = 33344.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.043387 restraints weight = 22053.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.043858 restraints weight = 16893.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.044251 restraints weight = 14387.672| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12730 Z= 0.182 Angle : 0.687 12.165 18433 Z= 0.394 Chirality : 0.043 0.251 2086 Planarity : 0.004 0.045 1322 Dihedral : 30.976 163.017 3997 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.70 % Allowed : 31.67 % Favored : 64.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.31), residues: 733 helix: 1.46 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.49 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 29 TYR 0.019 0.002 TYR D 83 PHE 0.012 0.001 PHE H 65 TRP 0.011 0.001 TRP A 86 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.18 (12730) covalent geometry : angle 0.68685 / 0.39 (18433) hydrogen bonds : bond 0.06272 / 3.98 ( 714) hydrogen bonds : angle 3.16175 / 2.36 ( 1758) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 230 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8580 (mt-10) REVERT: A 104 HIS cc_start: 0.8629 (t-90) cc_final: 0.7813 (t70) REVERT: A 107 GLU cc_start: 0.8929 (pp20) cc_final: 0.8168 (pp20) REVERT: A 108 ASP cc_start: 0.8635 (m-30) cc_final: 0.7730 (m-30) REVERT: A 110 TYR cc_start: 0.9027 (t80) cc_final: 0.8825 (t80) REVERT: A 127 GLN cc_start: 0.9057 (tm-30) cc_final: 0.8661 (tm-30) REVERT: B 30 THR cc_start: 0.9011 (p) cc_final: 0.8731 (t) REVERT: B 44 LYS cc_start: 0.9013 (tttm) cc_final: 0.8696 (mtpp) REVERT: B 51 TYR cc_start: 0.8710 (m-80) cc_final: 0.8364 (m-80) REVERT: B 79 LYS cc_start: 0.8968 (mtmm) cc_final: 0.8719 (ttmm) REVERT: C 32 ARG cc_start: 0.9376 (ptm-80) cc_final: 0.8754 (ttp80) REVERT: C 64 GLU cc_start: 0.8655 (tp30) cc_final: 0.8191 (tp30) REVERT: C 68 ASN cc_start: 0.8863 (m-40) cc_final: 0.8235 (m110) REVERT: C 92 GLU cc_start: 0.8599 (mp0) cc_final: 0.8363 (pm20) REVERT: C 95 LYS cc_start: 0.9612 (ttmm) cc_final: 0.9180 (tptt) REVERT: C 104 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7581 (mm-40) REVERT: D 71 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8544 (tm-30) REVERT: D 95 GLN cc_start: 0.9246 (tt0) cc_final: 0.8946 (tm-30) REVERT: D 105 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8405 (tm-30) REVERT: E 73 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8541 (tm-30) REVERT: E 104 HIS cc_start: 0.9031 (t-90) cc_final: 0.8614 (t70) REVERT: F 43 VAL cc_start: 0.9586 (OUTLIER) cc_final: 0.9377 (p) REVERT: F 52 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8738 (tp30) REVERT: F 84 MET cc_start: 0.8071 (tpp) cc_final: 0.7829 (tpp) REVERT: F 88 TYR cc_start: 0.8665 (m-10) cc_final: 0.7594 (m-80) REVERT: G 36 LYS cc_start: 0.9274 (mmmt) cc_final: 0.8850 (mmtt) REVERT: G 95 LYS cc_start: 0.8980 (ttpt) cc_final: 0.8702 (ttmm) REVERT: G 104 GLN cc_start: 0.8717 (mp10) cc_final: 0.8443 (mp10) REVERT: H 46 LYS cc_start: 0.9169 (tppt) cc_final: 0.8704 (tppt) REVERT: H 62 MET cc_start: 0.9295 (mmm) cc_final: 0.8890 (mmm) REVERT: H 83 TYR cc_start: 0.8483 (m-10) cc_final: 0.7739 (m-10) outliers start: 23 outliers final: 18 residues processed: 239 average time/residue: 0.1147 time to fit residues: 37.8792 Evaluate side-chains 243 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 224 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 94 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 17 optimal weight: 0.4980 chunk 86 optimal weight: 30.0000 chunk 9 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.055177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.041389 restraints weight = 64569.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.042518 restraints weight = 32085.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.043352 restraints weight = 20855.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.043885 restraints weight = 15864.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.044186 restraints weight = 13342.173| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12730 Z= 0.184 Angle : 0.693 11.146 18433 Z= 0.397 Chirality : 0.043 0.264 2086 Planarity : 0.004 0.049 1322 Dihedral : 31.008 163.893 3997 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.86 % Allowed : 31.99 % Favored : 64.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.31), residues: 733 helix: 1.46 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.46 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 80 TYR 0.039 0.002 TYR D 83 PHE 0.012 0.001 PHE H 65 TRP 0.012 0.001 TRP A 86 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.18 (12730) covalent geometry : angle 0.69287 / 0.40 (18433) hydrogen bonds : bond 0.06187 / 3.91 ( 714) hydrogen bonds : angle 3.18510 / 2.37 ( 1758) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 225 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8575 (mt-10) REVERT: A 95 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8566 (tp40) REVERT: A 104 HIS cc_start: 0.8630 (t-90) cc_final: 0.7794 (t70) REVERT: A 107 GLU cc_start: 0.8926 (pp20) cc_final: 0.8179 (pp20) REVERT: A 108 ASP cc_start: 0.8633 (m-30) cc_final: 0.7741 (m-30) REVERT: A 110 TYR cc_start: 0.9009 (t80) cc_final: 0.8799 (t80) REVERT: A 127 GLN cc_start: 0.9069 (tm-30) cc_final: 0.8655 (tm-30) REVERT: B 30 THR cc_start: 0.9012 (p) cc_final: 0.8734 (t) REVERT: B 44 LYS cc_start: 0.9036 (tttm) cc_final: 0.8689 (mtpp) REVERT: B 79 LYS cc_start: 0.8973 (mtmm) cc_final: 0.8731 (ttmm) REVERT: C 32 ARG cc_start: 0.9380 (ptm-80) cc_final: 0.8750 (ttp80) REVERT: C 56 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8299 (mm-30) REVERT: C 64 GLU cc_start: 0.8658 (tp30) cc_final: 0.8171 (tp30) REVERT: C 68 ASN cc_start: 0.8986 (m-40) cc_final: 0.7974 (m110) REVERT: C 92 GLU cc_start: 0.8527 (mp0) cc_final: 0.8315 (pm20) REVERT: C 95 LYS cc_start: 0.9613 (ttmm) cc_final: 0.9183 (tptt) REVERT: C 99 LYS cc_start: 0.8633 (mmmm) cc_final: 0.8317 (mmmm) REVERT: C 104 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7509 (mm-40) REVERT: D 71 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8549 (tm-30) REVERT: D 93 GLU cc_start: 0.8942 (mp0) cc_final: 0.8523 (mp0) REVERT: D 95 GLN cc_start: 0.9257 (tt0) cc_final: 0.8999 (tm-30) REVERT: E 73 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8592 (tm-30) REVERT: E 104 HIS cc_start: 0.8972 (t-90) cc_final: 0.8521 (t70) REVERT: E 110 TYR cc_start: 0.8599 (t80) cc_final: 0.8364 (t80) REVERT: F 43 VAL cc_start: 0.9523 (OUTLIER) cc_final: 0.9300 (p) REVERT: F 52 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8730 (tp30) REVERT: F 84 MET cc_start: 0.8207 (tpp) cc_final: 0.7925 (tpp) REVERT: F 88 TYR cc_start: 0.8571 (m-10) cc_final: 0.7520 (m-80) REVERT: G 36 LYS cc_start: 0.9269 (mmmt) cc_final: 0.8842 (mmtt) REVERT: G 56 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8567 (mt-10) REVERT: G 95 LYS cc_start: 0.8984 (ttpt) cc_final: 0.8702 (ttmm) REVERT: G 104 GLN cc_start: 0.8559 (mp10) cc_final: 0.8286 (mp10) REVERT: H 46 LYS cc_start: 0.9190 (tppt) cc_final: 0.8746 (tppt) REVERT: H 62 MET cc_start: 0.9292 (mmm) cc_final: 0.8890 (mmm) REVERT: H 83 TYR cc_start: 0.8536 (m-10) cc_final: 0.7798 (m-10) outliers start: 24 outliers final: 18 residues processed: 235 average time/residue: 0.1215 time to fit residues: 39.2630 Evaluate side-chains 243 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 222 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 94 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 77 optimal weight: 30.0000 chunk 24 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 17 optimal weight: 0.2980 chunk 42 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN H 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.055515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.041417 restraints weight = 65836.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.042571 restraints weight = 33593.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.043453 restraints weight = 22270.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.043964 restraints weight = 16937.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.044307 restraints weight = 14393.582| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12730 Z= 0.169 Angle : 0.695 11.791 18433 Z= 0.397 Chirality : 0.043 0.274 2086 Planarity : 0.004 0.045 1322 Dihedral : 31.006 164.645 3997 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 4.18 % Allowed : 31.99 % Favored : 63.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.30), residues: 733 helix: 1.41 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.43 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 29 TYR 0.057 0.002 TYR D 83 PHE 0.013 0.001 PHE H 70 TRP 0.011 0.001 TRP A 86 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.17 (12730) covalent geometry : angle 0.69486 / 0.40 (18433) hydrogen bonds : bond 0.06060 / 3.83 ( 714) hydrogen bonds : angle 3.16845 / 2.35 ( 1758) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8578 (mt-10) REVERT: A 95 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8663 (tp40) REVERT: A 104 HIS cc_start: 0.8622 (t-90) cc_final: 0.7827 (t70) REVERT: A 107 GLU cc_start: 0.8917 (pp20) cc_final: 0.8160 (pp20) REVERT: A 108 ASP cc_start: 0.8620 (m-30) cc_final: 0.7744 (m-30) REVERT: A 110 TYR cc_start: 0.8994 (t80) cc_final: 0.8790 (t80) REVERT: A 127 GLN cc_start: 0.9040 (tm-30) cc_final: 0.8658 (tm-30) REVERT: B 30 THR cc_start: 0.8927 (p) cc_final: 0.8662 (t) REVERT: B 44 LYS cc_start: 0.9041 (tttm) cc_final: 0.8683 (mtpp) REVERT: B 79 LYS cc_start: 0.8963 (mtmm) cc_final: 0.8724 (ttmm) REVERT: C 32 ARG cc_start: 0.9328 (ptm-80) cc_final: 0.8763 (ttp80) REVERT: C 64 GLU cc_start: 0.8646 (tp30) cc_final: 0.8211 (tp30) REVERT: C 68 ASN cc_start: 0.8905 (m-40) cc_final: 0.8183 (m110) REVERT: C 95 LYS cc_start: 0.9608 (ttmm) cc_final: 0.9178 (tptt) REVERT: C 99 LYS cc_start: 0.8628 (mmmm) cc_final: 0.8296 (mmmm) REVERT: C 104 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7494 (mm-40) REVERT: D 71 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8537 (tm-30) REVERT: D 93 GLU cc_start: 0.8928 (mp0) cc_final: 0.8528 (mp0) REVERT: D 95 GLN cc_start: 0.9248 (tt0) cc_final: 0.8991 (tm-30) REVERT: E 73 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8588 (tm-30) REVERT: E 104 HIS cc_start: 0.9034 (t-90) cc_final: 0.8614 (t70) REVERT: E 110 TYR cc_start: 0.8580 (t80) cc_final: 0.8330 (t80) REVERT: F 43 VAL cc_start: 0.9537 (OUTLIER) cc_final: 0.9292 (p) REVERT: F 52 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8697 (tp30) REVERT: F 84 MET cc_start: 0.8152 (tpp) cc_final: 0.7884 (tpp) REVERT: F 88 TYR cc_start: 0.8552 (m-10) cc_final: 0.7511 (m-80) REVERT: G 36 LYS cc_start: 0.9261 (mmmt) cc_final: 0.8835 (mmtt) REVERT: G 56 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8444 (mt-10) REVERT: G 95 LYS cc_start: 0.8993 (ttpt) cc_final: 0.8690 (ttmm) REVERT: G 104 GLN cc_start: 0.8459 (mp10) cc_final: 0.8200 (mp10) REVERT: H 46 LYS cc_start: 0.9186 (tppt) cc_final: 0.8751 (tppt) REVERT: H 62 MET cc_start: 0.9285 (mmm) cc_final: 0.8889 (mmm) REVERT: H 83 TYR cc_start: 0.8529 (m-10) cc_final: 0.7793 (m-10) outliers start: 26 outliers final: 19 residues processed: 236 average time/residue: 0.1153 time to fit residues: 37.0766 Evaluate side-chains 243 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 222 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 94 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 57 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 76 optimal weight: 30.0000 chunk 79 optimal weight: 30.0000 chunk 39 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 27 optimal weight: 0.0270 chunk 17 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 84 optimal weight: 40.0000 overall best weight: 4.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 GLN A 115 HIS ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.054928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.041005 restraints weight = 66230.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.042126 restraints weight = 33831.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.042948 restraints weight = 22462.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.043458 restraints weight = 17288.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.043810 restraints weight = 14654.043| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12730 Z= 0.203 Angle : 0.707 10.972 18433 Z= 0.404 Chirality : 0.044 0.285 2086 Planarity : 0.004 0.045 1322 Dihedral : 31.064 166.109 3997 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.02 % Allowed : 32.80 % Favored : 63.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.30), residues: 733 helix: 1.44 (0.23), residues: 511 sheet: None (None), residues: 0 loop : -1.50 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 71 TYR 0.053 0.002 TYR D 83 PHE 0.011 0.001 PHE H 65 TRP 0.011 0.001 TRP A 86 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.20 (12730) covalent geometry : angle 0.70680 / 0.40 (18433) hydrogen bonds : bond 0.06368 / 4.05 ( 714) hydrogen bonds : angle 3.28046 / 2.44 ( 1758) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1798.64 seconds wall clock time: 31 minutes 41.01 seconds (1901.01 seconds total)