Starting phenix.real_space_refine on Wed Mar 4 06:32:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sef_10154/03_2026/6sef_10154.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sef_10154/03_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_10154/03_2026/6sef_10154.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sef_10154/03_2026/6sef_10154.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6sef_10154/03_2026/6sef_10154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sef_10154/03_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 2.50, per 1000 atoms: 0.21 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: 0.94 Conformation dependent library (CDL) restraints added in 392.0 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: 1.92 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: 2.20 Time building geometry restraints manager: 1.32 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 1.422 1.504 -0.082 3.00e-02 1.11e+03 7.40e+00 bond pdb=" CG1 ILE B 66 " pdb=" CD1 ILE B 66 " ideal model delta sigma weight residual 1.513 1.441 0.072 3.90e-02 6.57e+02 3.44e+00 bond pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " ideal model delta sigma weight residual 1.422 1.477 -0.055 3.00e-02 1.11e+03 3.40e+00 bond pdb=" C3' DA J -38 " pdb=" O3' DA J -38 " ideal model delta sigma weight residual 1.422 1.476 -0.054 3.00e-02 1.11e+03 3.20e+00 bond pdb=" C3' DC J -58 " pdb=" O3' DC J -58 " ideal model delta sigma weight residual 1.422 1.476 -0.054 3.00e-02 1.11e+03 3.18e+00 ... (remaining 12725 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 17637 1.87 - 3.75: 704 3.75 - 5.62: 72 5.62 - 7.50: 12 7.50 - 9.37: 8 Bond angle restraints: 18433 Sorted by residual: angle pdb=" C ARG A 44 " pdb=" N GLN A 45 " pdb=" CA GLN A 45 " ideal model delta sigma weight residual 122.46 127.99 -5.53 1.41e+00 5.03e-01 1.54e+01 angle pdb=" C SER V 535 " pdb=" N GLU V 536 " pdb=" CA GLU V 536 " ideal model delta sigma weight residual 121.70 128.22 -6.52 1.80e+00 3.09e-01 1.31e+01 angle pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sigma weight residual 120.20 125.48 -5.28 1.50e+00 4.44e-01 1.24e+01 angle pdb=" N GLY H 104 " pdb=" CA GLY H 104 " pdb=" C GLY H 104 " ideal model delta sigma weight residual 112.49 116.53 -4.04 1.21e+00 6.83e-01 1.12e+01 angle pdb=" CG1 VAL H 39 " pdb=" CB VAL H 39 " pdb=" CG2 VAL H 39 " ideal model delta sigma weight residual 110.80 103.51 7.29 2.20e+00 2.07e-01 1.10e+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: 1326 0.045 - 0.090: 593 0.090 - 0.134: 128 0.134 - 0.179: 34 0.179 - 0.224: 5 Chirality restraints: 2086 Sorted by residual: 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=" 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 2.35 -2.56 -0.22 2.00e-01 2.50e+01 1.16e+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: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.130 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 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 : 0.007 0.082 12730 Z= 0.310 Angle : 0.851 9.370 18433 Z= 0.493 Chirality : 0.052 0.224 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 covalent geometry : bond 0.00692 (12730) covalent geometry : angle 0.85074 (18433) hydrogen bonds : bond 0.12583 ( 714) hydrogen bonds : angle 4.74211 ( 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 : 0.294 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: 0.8672 (mt-10) REVERT: A 52 ARG cc_start: 0.9226 (ttm170) cc_final: 0.8721 (mtm-85) REVERT: A 63 ARG cc_start: 0.8372 (mmp-170) cc_final: 0.8027 (mmm-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: 0.9267 (m-40) REVERT: A 95 GLN cc_start: 0.9069 (tt0) cc_final: 0.8821 (tt0) REVERT: A 96 GLU cc_start: 0.8979 (tp30) cc_final: 0.8649 (tp30) REVERT: A 108 ASP cc_start: 0.8669 (m-30) cc_final: 0.8328 (p0) REVERT: B 30 THR cc_start: 0.8763 (p) cc_final: 0.8427 (t) 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: 0.8429 (m-80) REVERT: B 79 LYS cc_start: 0.8954 (mtmm) cc_final: 0.8720 (ttmm) REVERT: B 81 VAL cc_start: 0.9389 (t) cc_final: 0.9163 (t) REVERT: C 32 ARG cc_start: 0.9247 (ttp80) cc_final: 0.9032 (ptm-80) 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: 0.7949 (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: 0.9052 (mt) REVERT: D 35 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7572 (mm-30) REVERT: D 37 TYR cc_start: 0.9280 (m-80) cc_final: 0.9053 (m-80) REVERT: D 71 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8198 (tm-30) REVERT: D 83 TYR cc_start: 0.8258 (m-10) cc_final: 0.7944 (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: 0.9188 (tp) REVERT: E 89 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8204 (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: 0.6945 (mm-30) REVERT: F 59 LYS cc_start: 0.8732 (tttm) cc_final: 0.8230 (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: 0.8110 (m-80) REVERT: G 25 PHE cc_start: 0.8452 (m-80) cc_final: 0.8220 (m-10) REVERT: G 36 LYS cc_start: 0.9228 (mmmt) cc_final: 0.8965 (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: 0.8586 (mtm110) REVERT: H 83 TYR cc_start: 0.8518 (m-10) cc_final: 0.7854 (m-10) REVERT: H 90 THR cc_start: 0.8840 (p) cc_final: 0.8267 (p) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.1561 time to fit residues: 63.8269 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 : 0.282 ------------------------------------------------------------------------------- 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: 4.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN B 64 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN C 73 ASN D 82 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS E 95 GLN G 94 ASN H 63 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.056967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.043090 restraints weight = 63954.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.044226 restraints weight = 31898.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.045133 restraints weight = 20721.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.045684 restraints weight = 15602.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.046015 restraints weight = 13106.247| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12730 Z= 0.175 Angle : 0.606 7.034 18433 Z= 0.355 Chirality : 0.034 0.216 2086 Planarity : 0.004 0.045 1322 Dihedral : 30.291 160.016 3997 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.89 % Allowed : 21.86 % Favored : 75.24 % 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: -0.13 (0.30), residues: 733 helix: 0.65 (0.23), residues: 512 sheet: None (None), residues: 0 loop : -1.75 (0.35), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 43 TYR 0.021 0.002 TYR E 110 PHE 0.019 0.001 PHE H 65 TRP 0.006 0.001 TRP E 47 HIS 0.007 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00382 (12730) covalent geometry : angle 0.60597 (18433) hydrogen bonds : bond 0.05672 ( 714) hydrogen bonds : angle 3.09394 ( 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 281 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 263 time to evaluate : 0.300 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: A 50 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8556 (mt-10) REVERT: A 85 ASN cc_start: 0.9521 (m-40) cc_final: 0.9165 (m-40) REVERT: A 87 GLN cc_start: 0.9168 (mt0) cc_final: 0.8943 (mt0) REVERT: A 104 HIS cc_start: 0.8504 (t70) cc_final: 0.7679 (t70) REVERT: A 107 GLU cc_start: 0.8758 (pp20) cc_final: 0.8026 (pp20) REVERT: A 108 ASP cc_start: 0.8695 (m-30) cc_final: 0.7738 (m-30) REVERT: A 127 GLN cc_start: 0.8749 (tm-30) cc_final: 0.8494 (tm-30) REVERT: B 30 THR cc_start: 0.8950 (p) cc_final: 0.8623 (t) REVERT: B 31 LYS cc_start: 0.9250 (mtpp) cc_final: 0.8824 (mtpp) REVERT: B 79 LYS cc_start: 0.8883 (mtmm) cc_final: 0.8616 (ttmm) REVERT: B 81 VAL cc_start: 0.9467 (t) cc_final: 0.9256 (t) REVERT: B 88 TYR cc_start: 0.8848 (m-10) cc_final: 0.8354 (m-80) REVERT: C 32 ARG cc_start: 0.9288 (ttp80) cc_final: 0.8788 (ptm160) REVERT: C 61 GLU cc_start: 0.9210 (tp30) cc_final: 0.8862 (tp30) REVERT: C 64 GLU cc_start: 0.8565 (tp30) cc_final: 0.8234 (tp30) REVERT: C 90 ASP cc_start: 0.8181 (t70) cc_final: 0.7247 (t70) REVERT: C 91 GLU cc_start: 0.8813 (pm20) cc_final: 0.7709 (pm20) REVERT: C 93 LEU cc_start: 0.9695 (OUTLIER) cc_final: 0.9470 (mm) REVERT: C 95 LYS cc_start: 0.9587 (ttmm) cc_final: 0.9206 (tptt) REVERT: D 37 TYR cc_start: 0.9454 (m-80) cc_final: 0.9045 (m-80) REVERT: D 62 MET cc_start: 0.9283 (mmm) cc_final: 0.9080 (mmm) REVERT: D 71 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8469 (tm-30) REVERT: D 83 TYR cc_start: 0.8399 (m-10) cc_final: 0.7686 (m-10) REVERT: D 95 GLN cc_start: 0.9272 (tt0) cc_final: 0.9051 (tm-30) REVERT: E 65 LEU cc_start: 0.9497 (tp) cc_final: 0.9256 (tp) REVERT: E 74 ILE cc_start: 0.9605 (tt) cc_final: 0.9371 (tt) REVERT: E 85 ASN cc_start: 0.8879 (m-40) cc_final: 0.8665 (m-40) REVERT: E 104 HIS cc_start: 0.8976 (t-90) cc_final: 0.8531 (t70) REVERT: E 107 GLU cc_start: 0.8371 (pt0) cc_final: 0.8097 (pt0) REVERT: E 130 ARG cc_start: 0.9649 (mtp180) cc_final: 0.9373 (ptm160) REVERT: F 55 ARG cc_start: 0.8257 (mpt-90) cc_final: 0.7966 (mpt-90) REVERT: F 74 GLU cc_start: 0.9031 (tp30) cc_final: 0.8798 (tp30) REVERT: F 84 MET cc_start: 0.8768 (tpp) cc_final: 0.8508 (tpp) REVERT: F 88 TYR cc_start: 0.8843 (m-10) cc_final: 0.7954 (m-80) REVERT: G 25 PHE cc_start: 0.8383 (m-80) cc_final: 0.8121 (m-10) REVERT: G 36 LYS cc_start: 0.9309 (mmmt) cc_final: 0.8952 (mmtt) REVERT: G 61 GLU cc_start: 0.8783 (tp30) cc_final: 0.8557 (tp30) REVERT: G 64 GLU cc_start: 0.8746 (tp30) cc_final: 0.8378 (tp30) REVERT: G 65 LEU cc_start: 0.9607 (mm) cc_final: 0.9315 (mm) REVERT: G 84 GLN cc_start: 0.9302 (tp-100) cc_final: 0.8242 (tp-100) REVERT: G 95 LYS cc_start: 0.9037 (ttpt) cc_final: 0.8709 (ttmm) REVERT: H 62 MET cc_start: 0.9160 (mmm) cc_final: 0.8941 (mmm) REVERT: H 83 TYR cc_start: 0.8470 (m-10) cc_final: 0.7838 (m-10) REVERT: H 100 LEU cc_start: 0.9334 (mt) cc_final: 0.9096 (mt) outliers start: 18 outliers final: 9 residues processed: 270 average time/residue: 0.1313 time to fit residues: 47.5214 Evaluate side-chains 239 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 229 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 82 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 94 ILE 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 56 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 97 optimal weight: 30.0000 chunk 78 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.055161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.041197 restraints weight = 65661.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.042346 restraints weight = 33290.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.043237 restraints weight = 21811.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.043771 restraints weight = 16460.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.044094 restraints weight = 13861.953| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12730 Z= 0.243 Angle : 0.621 6.912 18433 Z= 0.366 Chirality : 0.036 0.210 2086 Planarity : 0.004 0.044 1322 Dihedral : 30.460 159.610 3997 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.22 % Allowed : 25.40 % Favored : 71.38 % 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: 0.59 (0.30), residues: 733 helix: 1.17 (0.23), residues: 510 sheet: None (None), residues: 0 loop : -1.42 (0.36), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 79 TYR 0.016 0.002 TYR G 39 PHE 0.016 0.001 PHE F 61 TRP 0.006 0.001 TRP A 47 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00532 (12730) covalent geometry : angle 0.62094 (18433) hydrogen bonds : bond 0.06047 ( 714) hydrogen bonds : angle 3.17748 ( 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 270 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 250 time to evaluate : 0.302 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: A 50 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8603 (mt-10) REVERT: A 55 GLN cc_start: 0.9370 (mt0) cc_final: 0.9013 (tt0) REVERT: A 104 HIS cc_start: 0.8623 (t70) cc_final: 0.7624 (t70) REVERT: A 107 GLU cc_start: 0.8975 (pp20) cc_final: 0.8210 (pp20) REVERT: A 108 ASP cc_start: 0.8889 (m-30) cc_final: 0.7725 (m-30) REVERT: A 127 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8613 (tm-30) REVERT: B 24 ASP cc_start: 0.8358 (p0) cc_final: 0.7998 (p0) REVERT: B 30 THR cc_start: 0.9027 (p) cc_final: 0.8709 (t) REVERT: B 31 LYS cc_start: 0.9232 (mtpp) cc_final: 0.8818 (mtpp) REVERT: B 44 LYS cc_start: 0.9034 (tttm) cc_final: 0.8648 (mtpp) REVERT: B 74 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8161 (mt-10) REVERT: B 79 LYS cc_start: 0.8947 (mtmm) cc_final: 0.8689 (ttmm) REVERT: B 81 VAL cc_start: 0.9453 (t) cc_final: 0.9238 (t) REVERT: B 88 TYR cc_start: 0.8870 (m-10) cc_final: 0.8572 (m-10) REVERT: C 29 ARG cc_start: 0.8679 (mtp-110) cc_final: 0.8407 (mmm-85) REVERT: C 32 ARG cc_start: 0.9326 (ttp80) cc_final: 0.8841 (ptm160) REVERT: C 64 GLU cc_start: 0.8587 (tp30) cc_final: 0.8326 (tp30) REVERT: C 90 ASP cc_start: 0.8657 (t70) cc_final: 0.7641 (t70) REVERT: C 93 LEU cc_start: 0.9728 (OUTLIER) cc_final: 0.9458 (mm) REVERT: C 95 LYS cc_start: 0.9602 (ttmm) cc_final: 0.9202 (tptt) REVERT: C 104 GLN cc_start: 0.8309 (mm-40) cc_final: 0.8001 (tp-100) REVERT: D 35 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7433 (mm-30) REVERT: D 37 TYR cc_start: 0.9481 (m-80) cc_final: 0.9239 (m-80) REVERT: D 71 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8509 (tm-30) REVERT: D 83 TYR cc_start: 0.8495 (m-10) cc_final: 0.7812 (m-10) REVERT: D 95 GLN cc_start: 0.9261 (tt0) cc_final: 0.8948 (tm-30) REVERT: E 50 GLU cc_start: 0.8563 (pp20) cc_final: 0.8002 (pp20) REVERT: E 65 LEU cc_start: 0.9542 (tp) cc_final: 0.9281 (tp) REVERT: E 85 ASN cc_start: 0.8966 (m-40) cc_final: 0.8716 (m-40) REVERT: E 104 HIS cc_start: 0.9027 (t-90) cc_final: 0.8558 (t70) REVERT: E 107 GLU cc_start: 0.8398 (pt0) cc_final: 0.8181 (pt0) REVERT: E 110 TYR cc_start: 0.8583 (t80) cc_final: 0.8356 (t80) REVERT: E 122 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.8851 (m-80) REVERT: E 130 ARG cc_start: 0.9631 (mtp180) cc_final: 0.9345 (ptm160) REVERT: F 39 ARG cc_start: 0.9185 (mmt90) cc_final: 0.8982 (mmm-85) REVERT: F 52 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8797 (tp30) REVERT: F 74 GLU cc_start: 0.9054 (tp30) cc_final: 0.8741 (tp30) REVERT: F 88 TYR cc_start: 0.8812 (m-10) cc_final: 0.8552 (m-80) REVERT: G 36 LYS cc_start: 0.9260 (mmmt) cc_final: 0.8911 (mmtt) REVERT: G 65 LEU cc_start: 0.9531 (mm) cc_final: 0.8870 (mm) REVERT: G 84 GLN cc_start: 0.9338 (tp-100) cc_final: 0.9038 (tp40) REVERT: G 95 LYS cc_start: 0.9063 (ttpt) cc_final: 0.8757 (ttmm) REVERT: G 104 GLN cc_start: 0.8639 (mp10) cc_final: 0.7955 (mp10) REVERT: H 46 LYS cc_start: 0.9106 (tppt) cc_final: 0.8842 (tppt) REVERT: H 62 MET cc_start: 0.9336 (mmm) cc_final: 0.9122 (mmm) REVERT: H 105 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8595 (tm-30) outliers start: 20 outliers final: 15 residues processed: 258 average time/residue: 0.1268 time to fit residues: 43.8962 Evaluate side-chains 248 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 231 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 B residue 82 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 93 LEU 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 E residue 122 PHE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 13 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 104 HIS A 115 HIS ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.054612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.040623 restraints weight = 65832.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.041766 restraints weight = 33117.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.042666 restraints weight = 21597.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.043185 restraints weight = 16229.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.043520 restraints weight = 13691.894| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12730 Z= 0.243 Angle : 0.624 6.490 18433 Z= 0.367 Chirality : 0.036 0.171 2086 Planarity : 0.004 0.044 1322 Dihedral : 30.577 165.028 3997 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 4.66 % Allowed : 26.37 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.30), residues: 733 helix: 1.42 (0.23), residues: 508 sheet: None (None), residues: 0 loop : -1.28 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 71 TYR 0.020 0.002 TYR E 110 PHE 0.010 0.001 PHE H 65 TRP 0.010 0.001 TRP A 86 HIS 0.007 0.001 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00534 (12730) covalent geometry : angle 0.62436 (18433) hydrogen bonds : bond 0.06041 ( 714) hydrogen bonds : angle 3.13177 ( 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 275 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 246 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8590 (mt-10) REVERT: A 87 GLN cc_start: 0.9351 (mt0) cc_final: 0.9067 (mt0) REVERT: A 95 GLN cc_start: 0.9176 (tt0) cc_final: 0.8976 (tt0) REVERT: A 104 HIS cc_start: 0.8640 (t-90) cc_final: 0.7868 (t70) REVERT: A 107 GLU cc_start: 0.8989 (pp20) cc_final: 0.8243 (pp20) REVERT: A 108 ASP cc_start: 0.8731 (m-30) cc_final: 0.7633 (m-30) REVERT: A 127 GLN cc_start: 0.9085 (tm-30) cc_final: 0.8714 (tm-30) REVERT: B 30 THR cc_start: 0.9061 (p) cc_final: 0.8721 (t) REVERT: B 44 LYS cc_start: 0.9053 (tttm) cc_final: 0.8680 (mtpp) REVERT: B 74 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8310 (mt-10) REVERT: B 79 LYS cc_start: 0.8976 (mtmm) cc_final: 0.8715 (ttmm) REVERT: B 81 VAL cc_start: 0.9556 (t) cc_final: 0.9353 (t) REVERT: C 29 ARG cc_start: 0.8776 (mtp-110) cc_final: 0.8202 (mmm-85) REVERT: C 32 ARG cc_start: 0.9325 (ttp80) cc_final: 0.8854 (ptm160) REVERT: C 39 TYR cc_start: 0.8929 (m-80) cc_final: 0.8620 (m-80) REVERT: C 64 GLU cc_start: 0.8555 (tp30) cc_final: 0.8225 (tp30) REVERT: C 68 ASN cc_start: 0.8962 (m-40) cc_final: 0.8262 (m-40) REVERT: C 90 ASP cc_start: 0.8370 (t70) cc_final: 0.8078 (t70) REVERT: C 95 LYS cc_start: 0.9627 (ttmm) cc_final: 0.9204 (tptt) REVERT: C 104 GLN cc_start: 0.8283 (mm-40) cc_final: 0.8024 (tp-100) REVERT: D 35 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7293 (mm-30) REVERT: D 47 GLN cc_start: 0.9293 (tm-30) cc_final: 0.9044 (tm-30) REVERT: D 71 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8523 (tm-30) REVERT: D 95 GLN cc_start: 0.9224 (tt0) cc_final: 0.8979 (tm-30) REVERT: D 109 HIS cc_start: 0.8973 (m-70) cc_final: 0.8721 (m-70) REVERT: E 50 GLU cc_start: 0.8661 (pp20) cc_final: 0.8322 (pp20) REVERT: E 65 LEU cc_start: 0.9536 (tp) cc_final: 0.9272 (tp) REVERT: E 85 ASN cc_start: 0.8968 (m-40) cc_final: 0.8679 (m-40) REVERT: E 104 HIS cc_start: 0.9032 (t-90) cc_final: 0.8530 (t70) REVERT: E 122 PHE cc_start: 0.9127 (OUTLIER) cc_final: 0.8841 (m-80) REVERT: E 130 ARG cc_start: 0.9620 (mtp180) cc_final: 0.8823 (mtp85) REVERT: F 43 VAL cc_start: 0.9627 (OUTLIER) cc_final: 0.9424 (p) REVERT: F 52 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8757 (tp30) REVERT: F 74 GLU cc_start: 0.9087 (tp30) cc_final: 0.8823 (tp30) REVERT: F 84 MET cc_start: 0.8506 (tpp) cc_final: 0.8282 (tpp) REVERT: F 88 TYR cc_start: 0.8682 (m-10) cc_final: 0.7759 (m-80) REVERT: G 36 LYS cc_start: 0.9240 (mmmt) cc_final: 0.8868 (mmtt) REVERT: G 56 GLU cc_start: 0.8459 (tt0) cc_final: 0.8231 (mt-10) REVERT: G 64 GLU cc_start: 0.8838 (tp30) cc_final: 0.8574 (tp30) REVERT: G 65 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9365 (mm) REVERT: G 92 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7971 (tt0) REVERT: G 95 LYS cc_start: 0.9079 (ttpt) cc_final: 0.8745 (ttmm) REVERT: H 46 LYS cc_start: 0.9126 (tppt) cc_final: 0.8781 (tppt) REVERT: H 62 MET cc_start: 0.9372 (mmm) cc_final: 0.9059 (mmm) REVERT: H 83 TYR cc_start: 0.8612 (m-10) cc_final: 0.7706 (m-10) REVERT: H 105 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8088 (tm-30) REVERT: H 120 LYS cc_start: 0.9281 (tmtt) cc_final: 0.8927 (tmtt) outliers start: 29 outliers final: 21 residues processed: 258 average time/residue: 0.1349 time to fit residues: 46.5319 Evaluate side-chains 251 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 227 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 82 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 90 THR 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 E residue 122 PHE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 86 VAL 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 88 THR Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 71 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** D 84 ASN ** 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 = 0.3342 r_free = 0.3342 target = 0.054254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.040253 restraints weight = 66275.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.041377 restraints weight = 33227.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.042231 restraints weight = 21732.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.042756 restraints weight = 16513.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.043084 restraints weight = 13957.150| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 12730 Z= 0.252 Angle : 0.638 9.047 18433 Z= 0.372 Chirality : 0.037 0.167 2086 Planarity : 0.004 0.044 1322 Dihedral : 30.680 170.495 3997 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 4.66 % Allowed : 29.90 % Favored : 65.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.30), residues: 733 helix: 1.55 (0.23), residues: 508 sheet: None (None), residues: 0 loop : -1.27 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 86 TYR 0.023 0.002 TYR D 83 PHE 0.015 0.002 PHE A 78 TRP 0.006 0.001 TRP A 47 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00556 (12730) covalent geometry : angle 0.63757 (18433) hydrogen bonds : bond 0.06192 ( 714) hydrogen bonds : angle 3.22168 ( 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 266 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 237 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8538 (mt-10) REVERT: A 87 GLN cc_start: 0.9370 (mt0) cc_final: 0.9048 (mt0) REVERT: A 104 HIS cc_start: 0.8562 (t-90) cc_final: 0.7897 (t70) REVERT: A 107 GLU cc_start: 0.8944 (pp20) cc_final: 0.8394 (pp20) REVERT: A 108 ASP cc_start: 0.8573 (m-30) cc_final: 0.7544 (m-30) REVERT: A 127 GLN cc_start: 0.9089 (tm-30) cc_final: 0.8722 (tm-30) REVERT: B 30 THR cc_start: 0.9140 (p) cc_final: 0.8864 (t) REVERT: B 31 LYS cc_start: 0.9225 (ttmm) cc_final: 0.8883 (ttmm) REVERT: B 44 LYS cc_start: 0.9062 (tttm) cc_final: 0.8705 (mtpp) REVERT: B 51 TYR cc_start: 0.8961 (m-80) cc_final: 0.8542 (m-80) REVERT: B 74 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8345 (mt-10) REVERT: B 79 LYS cc_start: 0.8998 (mtmm) cc_final: 0.8751 (ttmm) REVERT: C 32 ARG cc_start: 0.9365 (ttp80) cc_final: 0.8841 (ptm-80) REVERT: C 64 GLU cc_start: 0.8590 (tp30) cc_final: 0.8315 (tp30) REVERT: C 71 ARG cc_start: 0.8865 (ttp80) cc_final: 0.8655 (ttp-110) REVERT: C 90 ASP cc_start: 0.8194 (t70) cc_final: 0.7838 (t70) REVERT: C 95 LYS cc_start: 0.9628 (ttmm) cc_final: 0.9218 (tptt) REVERT: C 104 GLN cc_start: 0.8295 (mm-40) cc_final: 0.8034 (tp-100) REVERT: D 47 GLN cc_start: 0.9278 (tm-30) cc_final: 0.8997 (tm-30) REVERT: D 71 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8536 (tm-30) REVERT: D 93 GLU cc_start: 0.8983 (mp0) cc_final: 0.8670 (mm-30) REVERT: D 95 GLN cc_start: 0.9260 (tt0) cc_final: 0.8998 (tm-30) REVERT: D 109 HIS cc_start: 0.8943 (m-70) cc_final: 0.8477 (m-70) REVERT: D 121 TYR cc_start: 0.9412 (t80) cc_final: 0.9109 (t80) REVERT: E 104 HIS cc_start: 0.9019 (t-90) cc_final: 0.8554 (t70) REVERT: E 122 PHE cc_start: 0.9070 (OUTLIER) cc_final: 0.8802 (m-80) REVERT: E 130 ARG cc_start: 0.9630 (mtp180) cc_final: 0.8890 (mtp85) REVERT: F 52 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8782 (tp30) REVERT: F 74 GLU cc_start: 0.9022 (tp30) cc_final: 0.8786 (tp30) REVERT: F 88 TYR cc_start: 0.8717 (m-10) cc_final: 0.7910 (m-80) REVERT: G 36 LYS cc_start: 0.9271 (mmmt) cc_final: 0.8870 (mmtt) REVERT: G 92 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7682 (tt0) REVERT: G 95 LYS cc_start: 0.9106 (ttpt) cc_final: 0.8772 (ttmm) REVERT: H 46 LYS cc_start: 0.9132 (tppt) cc_final: 0.8576 (tppt) REVERT: H 62 MET cc_start: 0.9347 (mmm) cc_final: 0.8999 (mmm) REVERT: H 83 TYR cc_start: 0.8642 (m-10) cc_final: 0.7534 (m-10) REVERT: H 105 GLU cc_start: 0.8480 (tm-30) cc_final: 0.7775 (tm-30) REVERT: H 120 LYS cc_start: 0.9325 (tmtt) cc_final: 0.9049 (tmtt) outliers start: 29 outliers final: 22 residues processed: 246 average time/residue: 0.1253 time to fit residues: 41.6056 Evaluate side-chains 244 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 221 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 30 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 90 THR 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 E residue 122 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 88 THR 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: 8.9990 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 chunk 61 optimal weight: 0.0570 chunk 39 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 overall best weight: 5.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS ** D 84 ASN ** 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 = 0.3317 r_free = 0.3317 target = 0.053409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.039664 restraints weight = 66793.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.040802 restraints weight = 33346.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.041634 restraints weight = 21708.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.042165 restraints weight = 16498.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.042514 restraints weight = 13877.859| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 12730 Z= 0.269 Angle : 0.657 9.522 18433 Z= 0.383 Chirality : 0.038 0.162 2086 Planarity : 0.004 0.044 1322 Dihedral : 30.800 176.690 3997 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.82 % Allowed : 31.67 % Favored : 63.50 % 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: 0.99 (0.30), residues: 733 helix: 1.51 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.36 (0.37), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 86 TYR 0.036 0.002 TYR D 83 PHE 0.013 0.001 PHE G 25 TRP 0.006 0.001 TRP A 86 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00594 (12730) covalent geometry : angle 0.65731 (18433) hydrogen bonds : bond 0.06385 ( 714) hydrogen bonds : angle 3.31951 ( 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 267 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 237 time to evaluate : 0.217 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: 0.8794 (mt-10) cc_final: 0.8538 (mt-10) REVERT: A 87 GLN cc_start: 0.9379 (mt0) cc_final: 0.9069 (mt0) REVERT: A 104 HIS cc_start: 0.8569 (t-90) cc_final: 0.7964 (t70) REVERT: A 107 GLU cc_start: 0.8949 (pp20) cc_final: 0.8438 (pp20) REVERT: A 108 ASP cc_start: 0.8672 (m-30) cc_final: 0.7825 (m-30) REVERT: A 122 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8355 (m-80) REVERT: A 127 GLN cc_start: 0.9131 (tm-30) cc_final: 0.8716 (tm-30) REVERT: B 30 THR cc_start: 0.9094 (p) cc_final: 0.8841 (t) REVERT: B 44 LYS cc_start: 0.9006 (tttm) cc_final: 0.8729 (mtpp) REVERT: B 74 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8441 (mt-10) REVERT: B 79 LYS cc_start: 0.9033 (mtmm) cc_final: 0.8765 (ttmm) REVERT: B 84 MET cc_start: 0.9154 (mmm) cc_final: 0.8813 (tpp) REVERT: C 32 ARG cc_start: 0.9377 (ttp80) cc_final: 0.9102 (ptm-80) REVERT: C 64 GLU cc_start: 0.8596 (tp30) cc_final: 0.8314 (tp30) REVERT: C 71 ARG cc_start: 0.8866 (ttp80) cc_final: 0.8641 (ttp-110) REVERT: C 90 ASP cc_start: 0.8223 (t70) cc_final: 0.7903 (t70) REVERT: C 95 LYS cc_start: 0.9632 (ttmm) cc_final: 0.9220 (tptt) REVERT: C 104 GLN cc_start: 0.8325 (mm-40) cc_final: 0.8042 (tp-100) REVERT: D 47 GLN cc_start: 0.9307 (tm-30) cc_final: 0.8991 (tm-30) REVERT: D 71 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8550 (tm-30) REVERT: D 93 GLU cc_start: 0.8943 (mp0) cc_final: 0.8646 (mm-30) REVERT: D 95 GLN cc_start: 0.9265 (tt0) cc_final: 0.8989 (tm-30) REVERT: D 105 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8257 (tm-30) REVERT: D 109 HIS cc_start: 0.9016 (m-70) cc_final: 0.8547 (m-70) REVERT: E 73 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8688 (tm-30) REVERT: E 104 HIS cc_start: 0.8987 (t-90) cc_final: 0.8571 (t70) REVERT: E 122 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.8800 (m-80) REVERT: E 130 ARG cc_start: 0.9633 (mtp180) cc_final: 0.8877 (mtp85) REVERT: F 52 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8795 (tp30) REVERT: F 88 TYR cc_start: 0.8731 (m-10) cc_final: 0.7757 (m-80) REVERT: G 36 LYS cc_start: 0.9242 (mmmt) cc_final: 0.8905 (mmtt) REVERT: G 39 TYR cc_start: 0.9123 (m-80) cc_final: 0.8713 (m-80) REVERT: G 92 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7875 (tt0) REVERT: G 95 LYS cc_start: 0.9114 (ttpt) cc_final: 0.8769 (ttmm) REVERT: G 99 LYS cc_start: 0.9111 (mmmm) cc_final: 0.8883 (mmmm) REVERT: H 62 MET cc_start: 0.9346 (mmm) cc_final: 0.8989 (mmm) REVERT: H 83 TYR cc_start: 0.8582 (m-10) cc_final: 0.7623 (m-10) REVERT: H 105 GLU cc_start: 0.8456 (tm-30) cc_final: 0.7991 (tm-30) REVERT: H 120 LYS cc_start: 0.9361 (tmtt) cc_final: 0.9060 (tmtt) outliers start: 30 outliers final: 22 residues processed: 250 average time/residue: 0.1223 time to fit residues: 41.4649 Evaluate side-chains 244 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 220 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 122 PHE 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 82 THR 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 112 LEU Chi-restraints excluded: chain E residue 122 PHE 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 F residue 86 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 88 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: 0.9990 chunk 68 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 78 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** 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 = 0.055511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.041731 restraints weight = 65530.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.042842 restraints weight = 33573.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.043678 restraints weight = 22148.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.044224 restraints weight = 17035.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.044493 restraints weight = 14394.767| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12730 Z= 0.176 Angle : 0.628 8.609 18433 Z= 0.365 Chirality : 0.035 0.219 2086 Planarity : 0.004 0.048 1322 Dihedral : 30.620 179.077 3997 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.22 % Allowed : 34.08 % Favored : 62.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.30), residues: 733 helix: 1.58 (0.23), residues: 510 sheet: None (None), residues: 0 loop : -1.34 (0.37), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 86 TYR 0.015 0.002 TYR B 51 PHE 0.011 0.001 PHE H 65 TRP 0.006 0.001 TRP A 47 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00386 (12730) covalent geometry : angle 0.62828 (18433) hydrogen bonds : bond 0.05471 ( 714) hydrogen bonds : angle 3.07243 ( 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: 20 poor density : 244 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8536 (mt-10) REVERT: A 74 ILE cc_start: 0.9582 (tt) cc_final: 0.9292 (tt) REVERT: A 85 ASN cc_start: 0.9568 (m-40) cc_final: 0.9255 (m-40) REVERT: A 104 HIS cc_start: 0.8630 (t-90) cc_final: 0.7905 (t70) REVERT: A 107 GLU cc_start: 0.8964 (pp20) cc_final: 0.8242 (pp20) REVERT: A 108 ASP cc_start: 0.8576 (m-30) cc_final: 0.7461 (m-30) REVERT: A 122 PHE cc_start: 0.9012 (OUTLIER) cc_final: 0.8253 (m-80) REVERT: A 127 GLN cc_start: 0.9099 (tm-30) cc_final: 0.8732 (tm-30) REVERT: B 31 LYS cc_start: 0.9203 (ttmm) cc_final: 0.8869 (ttmm) REVERT: B 51 TYR cc_start: 0.8828 (m-80) cc_final: 0.8557 (m-80) REVERT: B 74 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8372 (mt-10) REVERT: B 79 LYS cc_start: 0.8928 (mtmm) cc_final: 0.8645 (ttmm) REVERT: C 29 ARG cc_start: 0.8355 (mtp-110) cc_final: 0.7998 (ttp-170) REVERT: C 32 ARG cc_start: 0.9352 (ttp80) cc_final: 0.9067 (ptm-80) REVERT: C 64 GLU cc_start: 0.8620 (tp30) cc_final: 0.8328 (tp30) REVERT: C 71 ARG cc_start: 0.8878 (ttp80) cc_final: 0.8654 (ttp-110) REVERT: C 90 ASP cc_start: 0.8163 (t70) cc_final: 0.7932 (t70) REVERT: C 95 LYS cc_start: 0.9612 (ttmm) cc_final: 0.9197 (tptt) REVERT: C 104 GLN cc_start: 0.8283 (mm-40) cc_final: 0.7969 (tp-100) REVERT: D 42 TYR cc_start: 0.8378 (t80) cc_final: 0.8177 (t80) REVERT: D 47 GLN cc_start: 0.9338 (tm-30) cc_final: 0.9020 (tm-30) REVERT: D 71 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8571 (tm-30) REVERT: D 93 GLU cc_start: 0.8920 (mp0) cc_final: 0.8567 (mm-30) REVERT: D 95 GLN cc_start: 0.9246 (tt0) cc_final: 0.8999 (tm-30) REVERT: D 109 HIS cc_start: 0.8988 (m-70) cc_final: 0.8520 (m-70) REVERT: E 104 HIS cc_start: 0.9110 (t-90) cc_final: 0.8672 (t70) REVERT: E 112 LEU cc_start: 0.9644 (OUTLIER) cc_final: 0.9422 (tt) REVERT: E 130 ARG cc_start: 0.9627 (mtp180) cc_final: 0.9367 (ptm160) REVERT: F 52 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8789 (tp30) REVERT: F 88 TYR cc_start: 0.8560 (m-10) cc_final: 0.8210 (m-80) REVERT: G 36 LYS cc_start: 0.9212 (mmmt) cc_final: 0.8820 (mmtt) REVERT: G 39 TYR cc_start: 0.9112 (m-80) cc_final: 0.8738 (m-80) REVERT: G 92 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7575 (tt0) REVERT: G 95 LYS cc_start: 0.9096 (ttpt) cc_final: 0.8737 (ttmm) REVERT: H 46 LYS cc_start: 0.9197 (tppt) cc_final: 0.8684 (tppt) REVERT: H 62 MET cc_start: 0.9272 (mmm) cc_final: 0.8926 (mmm) REVERT: H 76 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8346 (tp30) REVERT: H 83 TYR cc_start: 0.8334 (m-10) cc_final: 0.7914 (m-10) REVERT: H 105 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8178 (tm-30) REVERT: H 120 LYS cc_start: 0.9307 (tmtt) cc_final: 0.8992 (tmtt) outliers start: 20 outliers final: 12 residues processed: 252 average time/residue: 0.1355 time to fit residues: 45.8154 Evaluate side-chains 245 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 231 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 122 PHE 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 30 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 71 THR 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: 10.0000 chunk 44 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 14 optimal weight: 0.0370 overall best weight: 3.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.054917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.041139 restraints weight = 65907.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.042237 restraints weight = 34081.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.043080 restraints weight = 22600.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.043594 restraints weight = 17220.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.043752 restraints weight = 14609.450| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12730 Z= 0.210 Angle : 0.656 10.070 18433 Z= 0.377 Chirality : 0.036 0.244 2086 Planarity : 0.004 0.046 1322 Dihedral : 30.662 178.114 3997 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.54 % Allowed : 34.57 % Favored : 61.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.30), residues: 733 helix: 1.57 (0.23), residues: 511 sheet: None (None), residues: 0 loop : -1.46 (0.36), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.016 0.002 TYR H 37 PHE 0.010 0.001 PHE F 61 TRP 0.015 0.001 TRP A 86 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00465 (12730) covalent geometry : angle 0.65613 (18433) hydrogen bonds : bond 0.05758 ( 714) hydrogen bonds : angle 3.18164 ( 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 255 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 233 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8510 (mt-10) REVERT: A 74 ILE cc_start: 0.9577 (tt) cc_final: 0.9307 (tt) REVERT: A 78 PHE cc_start: 0.8961 (m-10) cc_final: 0.8703 (m-80) REVERT: A 87 GLN cc_start: 0.9124 (mt0) cc_final: 0.8895 (mt0) REVERT: A 104 HIS cc_start: 0.8610 (t-90) cc_final: 0.7980 (t70) REVERT: A 107 GLU cc_start: 0.8982 (pp20) cc_final: 0.8501 (pp20) REVERT: A 108 ASP cc_start: 0.8637 (m-30) cc_final: 0.7756 (m-30) REVERT: A 122 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8342 (m-80) REVERT: A 127 GLN cc_start: 0.9084 (tm-30) cc_final: 0.8685 (tm-30) REVERT: B 79 LYS cc_start: 0.8960 (mtmm) cc_final: 0.8671 (ttmm) REVERT: B 84 MET cc_start: 0.8812 (tpp) cc_final: 0.8097 (tpp) REVERT: C 29 ARG cc_start: 0.8523 (mtp-110) cc_final: 0.7964 (ttt180) REVERT: C 32 ARG cc_start: 0.9375 (ttp80) cc_final: 0.9085 (ptm-80) REVERT: C 56 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8658 (mm-30) REVERT: C 64 GLU cc_start: 0.8607 (tp30) cc_final: 0.8052 (tp30) REVERT: C 68 ASN cc_start: 0.8923 (m-40) cc_final: 0.8117 (m-40) REVERT: C 90 ASP cc_start: 0.8175 (t70) cc_final: 0.7941 (t70) REVERT: C 95 LYS cc_start: 0.9620 (ttmm) cc_final: 0.9207 (tptt) REVERT: C 104 GLN cc_start: 0.8282 (mm-40) cc_final: 0.7969 (tp-100) REVERT: D 47 GLN cc_start: 0.9288 (tm-30) cc_final: 0.8976 (tm-30) REVERT: D 71 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8602 (tm-30) REVERT: D 93 GLU cc_start: 0.8920 (mp0) cc_final: 0.8616 (mm-30) REVERT: D 95 GLN cc_start: 0.9251 (tt0) cc_final: 0.9001 (tm-30) REVERT: D 105 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8238 (tm-30) REVERT: D 109 HIS cc_start: 0.8992 (m-70) cc_final: 0.8362 (m-70) REVERT: E 104 HIS cc_start: 0.9011 (t-90) cc_final: 0.8585 (t70) REVERT: E 110 TYR cc_start: 0.8486 (t80) cc_final: 0.8228 (t80) REVERT: E 112 LEU cc_start: 0.9664 (OUTLIER) cc_final: 0.9456 (tt) REVERT: E 122 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8823 (m-80) REVERT: E 130 ARG cc_start: 0.9629 (mtp180) cc_final: 0.9366 (ptm160) REVERT: F 52 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8662 (tp30) REVERT: G 36 LYS cc_start: 0.9223 (mmmt) cc_final: 0.8710 (mmmt) REVERT: G 39 TYR cc_start: 0.9063 (m-80) cc_final: 0.8593 (m-80) REVERT: G 84 GLN cc_start: 0.9281 (tp-100) cc_final: 0.8273 (tp-100) REVERT: G 92 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7513 (tt0) REVERT: G 95 LYS cc_start: 0.9093 (ttpt) cc_final: 0.8727 (ttmm) REVERT: H 46 LYS cc_start: 0.9055 (tppt) cc_final: 0.8457 (tppt) REVERT: H 62 MET cc_start: 0.9321 (mmm) cc_final: 0.8966 (mmm) REVERT: H 83 TYR cc_start: 0.8263 (m-10) cc_final: 0.7947 (m-10) REVERT: H 105 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7996 (tm-30) REVERT: H 120 LYS cc_start: 0.9341 (tmtt) cc_final: 0.9032 (tmtt) outliers start: 22 outliers final: 16 residues processed: 242 average time/residue: 0.1259 time to fit residues: 41.4949 Evaluate side-chains 242 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 223 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 122 PHE 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 30 VAL Chi-restraints excluded: chain C residue 54 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 112 LEU Chi-restraints excluded: chain E residue 122 PHE 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 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: 3.9990 chunk 86 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.055203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.041443 restraints weight = 65739.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.042506 restraints weight = 33906.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.043339 restraints weight = 22548.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.043869 restraints weight = 17305.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.044199 restraints weight = 14670.642| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12730 Z= 0.199 Angle : 0.667 9.172 18433 Z= 0.382 Chirality : 0.036 0.246 2086 Planarity : 0.004 0.047 1322 Dihedral : 30.646 174.738 3997 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.02 % Allowed : 35.05 % Favored : 60.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.30), residues: 733 helix: 1.53 (0.23), residues: 512 sheet: None (None), residues: 0 loop : -1.44 (0.36), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 71 TYR 0.027 0.002 TYR F 88 PHE 0.012 0.001 PHE H 65 TRP 0.011 0.001 TRP A 86 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00441 (12730) covalent geometry : angle 0.66723 (18433) hydrogen bonds : bond 0.05576 ( 714) hydrogen bonds : angle 3.16668 ( 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 256 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 231 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8445 (mt-10) REVERT: A 74 ILE cc_start: 0.9592 (tt) cc_final: 0.9339 (tt) REVERT: A 87 GLN cc_start: 0.9110 (mt0) cc_final: 0.8896 (mt0) REVERT: A 104 HIS cc_start: 0.8619 (t-90) cc_final: 0.7891 (t70) REVERT: A 107 GLU cc_start: 0.8985 (pp20) cc_final: 0.8267 (pp20) REVERT: A 108 ASP cc_start: 0.8648 (m-30) cc_final: 0.7721 (m-30) REVERT: A 122 PHE cc_start: 0.9020 (OUTLIER) cc_final: 0.8310 (m-80) REVERT: A 127 GLN cc_start: 0.9089 (tm-30) cc_final: 0.8696 (tm-30) REVERT: B 31 LYS cc_start: 0.9166 (ttmm) cc_final: 0.8897 (ttmm) REVERT: B 79 LYS cc_start: 0.8980 (mtmm) cc_final: 0.8699 (ttmm) REVERT: B 84 MET cc_start: 0.8797 (tpp) cc_final: 0.8058 (tpp) REVERT: C 32 ARG cc_start: 0.9377 (ttp80) cc_final: 0.9100 (ptm-80) REVERT: C 56 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8619 (mm-30) REVERT: C 64 GLU cc_start: 0.8612 (tp30) cc_final: 0.8327 (tp30) REVERT: C 90 ASP cc_start: 0.8231 (t70) cc_final: 0.8003 (t70) REVERT: C 95 LYS cc_start: 0.9614 (ttmm) cc_final: 0.9204 (tptt) REVERT: C 104 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7927 (tp-100) REVERT: D 47 GLN cc_start: 0.9323 (tm-30) cc_final: 0.9007 (tm-30) REVERT: D 71 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8592 (tm-30) REVERT: D 93 GLU cc_start: 0.8856 (mp0) cc_final: 0.8604 (mm-30) REVERT: D 95 GLN cc_start: 0.9255 (tt0) cc_final: 0.8977 (tm-30) REVERT: D 105 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8282 (tm-30) REVERT: D 109 HIS cc_start: 0.8972 (m-70) cc_final: 0.8345 (m-70) REVERT: E 104 HIS cc_start: 0.9063 (t-90) cc_final: 0.8674 (t70) REVERT: E 112 LEU cc_start: 0.9665 (OUTLIER) cc_final: 0.9449 (tt) REVERT: E 122 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8795 (m-80) REVERT: E 130 ARG cc_start: 0.9630 (mtp180) cc_final: 0.9293 (ptm160) REVERT: F 52 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8654 (tp30) REVERT: F 88 TYR cc_start: 0.8773 (m-80) cc_final: 0.8469 (m-80) REVERT: G 36 LYS cc_start: 0.9232 (mmmt) cc_final: 0.8710 (mmmt) REVERT: G 39 TYR cc_start: 0.9052 (m-80) cc_final: 0.8669 (m-80) REVERT: G 51 MET cc_start: 0.9158 (mmm) cc_final: 0.8842 (mmm) REVERT: G 84 GLN cc_start: 0.9175 (tp-100) cc_final: 0.8245 (tp-100) REVERT: G 92 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7534 (tt0) REVERT: G 95 LYS cc_start: 0.9090 (ttpt) cc_final: 0.8789 (tppt) REVERT: H 46 LYS cc_start: 0.9108 (tppt) cc_final: 0.8567 (tppt) REVERT: H 62 MET cc_start: 0.9304 (mmm) cc_final: 0.8951 (mmm) REVERT: H 83 TYR cc_start: 0.8085 (m-10) cc_final: 0.7871 (m-10) REVERT: H 105 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7885 (tm-30) REVERT: H 120 LYS cc_start: 0.9296 (tmtt) cc_final: 0.9062 (tmtt) outliers start: 25 outliers final: 17 residues processed: 242 average time/residue: 0.1174 time to fit residues: 38.9770 Evaluate side-chains 243 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 223 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 122 PHE 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 82 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 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 112 LEU Chi-restraints excluded: chain E residue 122 PHE 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 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: 10.0000 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 17 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 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 = 0.056457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.042798 restraints weight = 65408.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.043892 restraints weight = 33513.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.044778 restraints weight = 22075.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.045323 restraints weight = 16677.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.045671 restraints weight = 14067.066| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12730 Z= 0.170 Angle : 0.667 9.788 18433 Z= 0.378 Chirality : 0.036 0.260 2086 Planarity : 0.004 0.049 1322 Dihedral : 30.501 170.609 3997 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.57 % Allowed : 36.33 % Favored : 61.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.30), residues: 733 helix: 1.56 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.47 (0.36), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 86 TYR 0.027 0.002 TYR F 88 PHE 0.012 0.001 PHE H 65 TRP 0.011 0.001 TRP A 86 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00377 (12730) covalent geometry : angle 0.66652 (18433) hydrogen bonds : bond 0.05355 ( 714) hydrogen bonds : angle 3.10900 ( 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 254 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 238 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8341 (mt-10) REVERT: A 74 ILE cc_start: 0.9573 (tt) cc_final: 0.9324 (tt) REVERT: A 104 HIS cc_start: 0.8534 (t-90) cc_final: 0.7770 (t70) REVERT: A 107 GLU cc_start: 0.8967 (pp20) cc_final: 0.8241 (pp20) REVERT: A 108 ASP cc_start: 0.8660 (m-30) cc_final: 0.7690 (m-30) REVERT: A 122 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8135 (m-80) REVERT: A 127 GLN cc_start: 0.9089 (tm-30) cc_final: 0.8722 (tm-30) REVERT: B 64 ASN cc_start: 0.9266 (m-40) cc_final: 0.8907 (t0) REVERT: B 79 LYS cc_start: 0.8948 (mtmm) cc_final: 0.8575 (ttmm) REVERT: C 32 ARG cc_start: 0.9367 (ttp80) cc_final: 0.9075 (ptm-80) REVERT: C 56 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8672 (mm-30) REVERT: C 64 GLU cc_start: 0.8601 (tp30) cc_final: 0.8067 (tp30) REVERT: C 68 ASN cc_start: 0.9005 (m-40) cc_final: 0.7943 (m-40) REVERT: C 90 ASP cc_start: 0.8231 (t70) cc_final: 0.8025 (t70) REVERT: C 95 LYS cc_start: 0.9611 (ttmm) cc_final: 0.9191 (tptt) REVERT: C 104 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7882 (tp-100) REVERT: D 47 GLN cc_start: 0.9286 (tm-30) cc_final: 0.8982 (tm-30) REVERT: D 71 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8562 (tm-30) REVERT: D 93 GLU cc_start: 0.8846 (mp0) cc_final: 0.8575 (mm-30) REVERT: D 95 GLN cc_start: 0.9254 (tt0) cc_final: 0.8990 (tm-30) REVERT: D 109 HIS cc_start: 0.8967 (m-70) cc_final: 0.8378 (m-70) REVERT: E 104 HIS cc_start: 0.9090 (t-90) cc_final: 0.8647 (t70) REVERT: E 122 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8796 (m-80) REVERT: E 130 ARG cc_start: 0.9589 (mtp180) cc_final: 0.9366 (ptm160) REVERT: F 52 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8660 (tp30) REVERT: F 88 TYR cc_start: 0.8840 (m-80) cc_final: 0.8410 (m-80) REVERT: G 36 LYS cc_start: 0.9227 (mmmt) cc_final: 0.8680 (mmmt) REVERT: G 39 TYR cc_start: 0.8974 (m-80) cc_final: 0.8651 (m-80) REVERT: G 51 MET cc_start: 0.9237 (mmm) cc_final: 0.8872 (mmm) REVERT: G 92 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7632 (tt0) REVERT: G 95 LYS cc_start: 0.9077 (ttpt) cc_final: 0.8701 (ttmm) REVERT: H 46 LYS cc_start: 0.9194 (tppt) cc_final: 0.8678 (tppt) REVERT: H 62 MET cc_start: 0.9320 (mmm) cc_final: 0.8954 (mmm) REVERT: H 100 LEU cc_start: 0.8944 (mm) cc_final: 0.8743 (mt) REVERT: H 105 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7949 (tm-30) REVERT: H 120 LYS cc_start: 0.9249 (tmtt) cc_final: 0.9006 (tmtt) outliers start: 16 outliers final: 10 residues processed: 245 average time/residue: 0.1220 time to fit residues: 40.6434 Evaluate side-chains 235 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 223 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 122 PHE 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 82 THR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain F residue 58 LEU 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: 7.9990 chunk 41 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 17 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN D 82 HIS ** D 84 ASN ** 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 = 0.3348 r_free = 0.3348 target = 0.054887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.041204 restraints weight = 67097.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.042292 restraints weight = 34826.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.043155 restraints weight = 23284.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.043675 restraints weight = 17732.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.043990 restraints weight = 15054.092| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12730 Z= 0.232 Angle : 0.699 11.370 18433 Z= 0.394 Chirality : 0.038 0.261 2086 Planarity : 0.004 0.046 1322 Dihedral : 30.673 164.614 3997 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.05 % Allowed : 37.62 % Favored : 59.32 % 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: 0.91 (0.30), residues: 733 helix: 1.49 (0.23), residues: 511 sheet: None (None), residues: 0 loop : -1.52 (0.36), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 71 TYR 0.038 0.003 TYR F 88 PHE 0.012 0.001 PHE A 67 TRP 0.016 0.001 TRP A 86 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00516 (12730) covalent geometry : angle 0.69865 (18433) hydrogen bonds : bond 0.05899 ( 714) hydrogen bonds : angle 3.30441 ( 1758) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1832.04 seconds wall clock time: 32 minutes 19.48 seconds (1939.48 seconds total)