Starting phenix.real_space_refine on Tue Jul 29 17:35:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sef_10154/07_2025/6sef_10154.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sef_10154/07_2025/6sef_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6sef_10154/07_2025/6sef_10154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sef_10154/07_2025/6sef_10154.map" model { file = "/net/cci-nas-00/data/ceres_data/6sef_10154/07_2025/6sef_10154.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sef_10154/07_2025/6sef_10154.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.20, per 1000 atoms: 0.69 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: 2.77 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 6.46 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: 4.83 Time building geometry restraints manager: 3.41 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: 0.320 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: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 36.360 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.690 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.013 0.002 TRP V 530 HIS 0.009 0.002 HIS F 75 PHE 0.011 0.002 PHE H 65 TYR 0.038 0.003 TYR F 98 ARG 0.004 0.001 ARG E 133 Details of bonding type rmsd hydrogen bonds : bond 0.12583 ( 714) hydrogen bonds : angle 4.74211 ( 1758) covalent geometry : bond 0.00692 (12730) covalent geometry : angle 0.85074 (18433) *********************** 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 : 0.800 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: 0.8973 (mt-10) cc_final: 0.8673 (mt-10) REVERT: A 52 ARG cc_start: 0.9226 (ttm170) cc_final: 0.8720 (mtm-85) REVERT: A 63 ARG cc_start: 0.8372 (mmp-170) cc_final: 0.8031 (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: 0.9272 (m-40) REVERT: A 95 GLN cc_start: 0.9069 (tt0) cc_final: 0.8820 (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: 0.8428 (t) REVERT: B 44 LYS cc_start: 0.9099 (tttm) cc_final: 0.8690 (mtpp) REVERT: B 51 TYR cc_start: 0.8980 (m-80) cc_final: 0.8429 (m-80) REVERT: B 64 ASN cc_start: 0.8608 (m-40) cc_final: 0.8407 (m110) REVERT: B 79 LYS cc_start: 0.8954 (mtmm) cc_final: 0.8603 (mtpp) REVERT: B 81 VAL cc_start: 0.9388 (t) cc_final: 0.9167 (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: 0.9367 (mmmm) REVERT: C 39 TYR cc_start: 0.8755 (m-80) cc_final: 0.8545 (m-80) REVERT: C 61 GLU cc_start: 0.9063 (tp30) cc_final: 0.8729 (tp30) REVERT: C 64 GLU cc_start: 0.8377 (tp30) cc_final: 0.7950 (tp30) REVERT: C 68 ASN cc_start: 0.8803 (m110) cc_final: 0.8171 (m110) REVERT: C 95 LYS cc_start: 0.9579 (ttmm) cc_final: 0.9179 (tptt) REVERT: C 102 ILE cc_start: 0.9320 (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: 0.8197 (tm-30) REVERT: D 83 TYR cc_start: 0.8258 (m-10) cc_final: 0.7946 (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: 0.8203 (mm-40) REVERT: E 107 GLU cc_start: 0.8419 (pt0) cc_final: 0.8025 (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: 0.8229 (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: 0.7358 (m-30) REVERT: F 88 TYR cc_start: 0.8753 (m-10) cc_final: 0.8112 (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: 0.8946 (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: 0.7860 (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: 0.8266 (p) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.3493 time to fit residues: 141.8051 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 : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 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 38 ASN G 94 ASN H 63 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.055507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.041688 restraints weight = 64804.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.042845 restraints weight = 32382.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.043710 restraints weight = 21050.669| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12730 Z= 0.234 Angle : 0.635 7.060 18433 Z= 0.371 Chirality : 0.036 0.209 2086 Planarity : 0.004 0.046 1322 Dihedral : 30.429 159.659 3997 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 3.38 % Allowed : 22.19 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.29), residues: 733 helix: 0.66 (0.22), residues: 512 sheet: None (None), residues: 0 loop : -1.73 (0.35), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 47 HIS 0.007 0.002 HIS D 82 PHE 0.019 0.001 PHE H 65 TYR 0.022 0.002 TYR E 110 ARG 0.005 0.001 ARG D 33 Details of bonding type rmsd hydrogen bonds : bond 0.06173 ( 714) hydrogen bonds : angle 3.22171 ( 1758) covalent geometry : bond 0.00515 (12730) covalent geometry : angle 0.63487 (18433) *********************** 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: 21 poor density : 260 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8637 (mt-10) REVERT: A 77 LYS cc_start: 0.9294 (ttmm) cc_final: 0.9081 (ttmm) REVERT: A 78 PHE cc_start: 0.9004 (m-80) cc_final: 0.8744 (m-80) REVERT: A 85 ASN cc_start: 0.9552 (m-40) cc_final: 0.9188 (m-40) REVERT: A 87 GLN cc_start: 0.9288 (mt0) cc_final: 0.9029 (mt0) REVERT: A 95 GLN cc_start: 0.9117 (tt0) cc_final: 0.8901 (tt0) REVERT: A 104 HIS cc_start: 0.8559 (t70) cc_final: 0.7736 (t70) REVERT: A 107 GLU cc_start: 0.8806 (pp20) cc_final: 0.8124 (pp20) REVERT: A 108 ASP cc_start: 0.8795 (m-30) cc_final: 0.7879 (m-30) REVERT: A 127 GLN cc_start: 0.8828 (tm-30) cc_final: 0.8570 (tm-30) REVERT: B 30 THR cc_start: 0.9014 (p) cc_final: 0.8676 (t) REVERT: B 31 LYS cc_start: 0.9257 (mtpp) cc_final: 0.8821 (mtpp) REVERT: B 44 LYS cc_start: 0.9089 (tttm) cc_final: 0.8680 (mtpp) REVERT: B 79 LYS cc_start: 0.8909 (mtmm) cc_final: 0.8540 (mtpp) REVERT: B 81 VAL cc_start: 0.9466 (t) cc_final: 0.9261 (t) REVERT: B 88 TYR cc_start: 0.8894 (m-10) cc_final: 0.8425 (m-80) REVERT: C 32 ARG cc_start: 0.9344 (ttp80) cc_final: 0.8856 (ptm160) REVERT: C 36 LYS cc_start: 0.9587 (mptt) cc_final: 0.9382 (mmmm) REVERT: C 64 GLU cc_start: 0.8622 (tp30) cc_final: 0.8320 (tp30) REVERT: C 90 ASP cc_start: 0.8148 (t70) cc_final: 0.7487 (t70) REVERT: C 91 GLU cc_start: 0.8911 (pm20) cc_final: 0.7844 (pm20) REVERT: C 95 LYS cc_start: 0.9615 (ttmm) cc_final: 0.9228 (tptt) REVERT: D 35 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7875 (mm-30) REVERT: D 37 TYR cc_start: 0.9466 (m-80) cc_final: 0.9160 (m-80) REVERT: D 71 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8605 (tm-30) REVERT: D 83 TYR cc_start: 0.8472 (m-10) cc_final: 0.7465 (m-10) REVERT: E 53 LYS cc_start: 0.9375 (ttpt) cc_final: 0.9036 (pttp) REVERT: E 65 LEU cc_start: 0.9529 (tp) cc_final: 0.9292 (tp) REVERT: E 73 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8688 (tm-30) REVERT: E 85 ASN cc_start: 0.8952 (m-40) cc_final: 0.8707 (m-40) REVERT: E 89 GLN cc_start: 0.8698 (mm-40) cc_final: 0.8277 (mm-40) REVERT: E 104 HIS cc_start: 0.9037 (t-90) cc_final: 0.8595 (t70) REVERT: E 107 GLU cc_start: 0.8384 (pt0) cc_final: 0.8105 (pt0) REVERT: E 130 ARG cc_start: 0.9652 (mtp180) cc_final: 0.9223 (mtp85) REVERT: F 52 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8486 (tp30) REVERT: F 55 ARG cc_start: 0.8296 (mpt-90) cc_final: 0.8075 (mpt-90) REVERT: F 88 TYR cc_start: 0.8867 (m-10) cc_final: 0.8014 (m-80) REVERT: G 25 PHE cc_start: 0.8460 (m-80) cc_final: 0.8188 (m-10) REVERT: G 36 LYS cc_start: 0.9272 (mmmt) cc_final: 0.8941 (mmtt) REVERT: G 61 GLU cc_start: 0.8878 (tp30) cc_final: 0.8647 (tp30) REVERT: G 64 GLU cc_start: 0.8738 (tp30) cc_final: 0.8351 (tp30) REVERT: G 65 LEU cc_start: 0.9604 (mm) cc_final: 0.9317 (mm) REVERT: G 84 GLN cc_start: 0.9321 (tp-100) cc_final: 0.8754 (tp-100) REVERT: G 95 LYS cc_start: 0.9071 (ttpt) cc_final: 0.8722 (ttmm) REVERT: H 62 MET cc_start: 0.9229 (mmm) cc_final: 0.9027 (mmm) REVERT: H 83 TYR cc_start: 0.8538 (m-10) cc_final: 0.7712 (m-10) REVERT: H 100 LEU cc_start: 0.9360 (mt) cc_final: 0.9109 (mt) REVERT: H 105 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8410 (tm-30) REVERT: H 120 LYS cc_start: 0.9701 (ttmm) cc_final: 0.9477 (tmtt) outliers start: 21 outliers final: 11 residues processed: 269 average time/residue: 0.2986 time to fit residues: 107.3618 Evaluate side-chains 239 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 228 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 30 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain 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 64 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.054743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.040563 restraints weight = 66104.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.041719 restraints weight = 33487.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.042567 restraints weight = 22025.877| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 12730 Z= 0.254 Angle : 0.631 8.751 18433 Z= 0.371 Chirality : 0.036 0.172 2086 Planarity : 0.004 0.043 1322 Dihedral : 30.557 161.586 3997 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.02 % Allowed : 24.28 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.30), residues: 733 helix: 1.24 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.47 (0.37), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 86 HIS 0.006 0.001 HIS F 75 PHE 0.017 0.002 PHE F 61 TYR 0.018 0.002 TYR B 88 ARG 0.005 0.001 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.06221 ( 714) hydrogen bonds : angle 3.19208 ( 1758) covalent geometry : bond 0.00557 (12730) covalent geometry : angle 0.63091 (18433) *********************** 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 276 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 251 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8585 (mt-10) REVERT: A 55 GLN cc_start: 0.9381 (mt0) cc_final: 0.9045 (tt0) REVERT: A 95 GLN cc_start: 0.9117 (tt0) cc_final: 0.8844 (tt0) REVERT: A 104 HIS cc_start: 0.8674 (t70) cc_final: 0.7744 (t70) REVERT: A 107 GLU cc_start: 0.8899 (pp20) cc_final: 0.8088 (pp20) REVERT: A 108 ASP cc_start: 0.8953 (m-30) cc_final: 0.7832 (m-30) REVERT: A 127 GLN cc_start: 0.8972 (tm-30) cc_final: 0.8622 (tm-30) REVERT: B 30 THR cc_start: 0.9070 (p) cc_final: 0.8742 (t) REVERT: B 31 LYS cc_start: 0.9230 (mtpp) cc_final: 0.9006 (ttmm) REVERT: B 44 LYS cc_start: 0.9103 (tttm) cc_final: 0.8723 (mtpp) REVERT: B 51 TYR cc_start: 0.9055 (m-80) cc_final: 0.8796 (m-80) REVERT: B 79 LYS cc_start: 0.8973 (mtmm) cc_final: 0.8737 (ttmm) REVERT: B 88 TYR cc_start: 0.8910 (m-10) cc_final: 0.8647 (m-10) REVERT: C 32 ARG cc_start: 0.9324 (ttp80) cc_final: 0.8933 (ptm-80) REVERT: C 64 GLU cc_start: 0.8618 (tp30) cc_final: 0.8331 (tp30) REVERT: C 90 ASP cc_start: 0.8710 (t70) cc_final: 0.7904 (t70) REVERT: C 95 LYS cc_start: 0.9622 (ttmm) cc_final: 0.9215 (tptt) REVERT: C 104 GLN cc_start: 0.8277 (mm-40) cc_final: 0.8030 (tp-100) REVERT: D 47 GLN cc_start: 0.9292 (tm-30) cc_final: 0.9034 (tm-30) REVERT: D 71 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8547 (tm-30) REVERT: D 83 TYR cc_start: 0.8462 (m-10) cc_final: 0.7826 (m-10) REVERT: D 95 GLN cc_start: 0.9271 (tt0) cc_final: 0.8948 (tm-30) REVERT: D 121 TYR cc_start: 0.9421 (t80) cc_final: 0.9093 (t80) REVERT: E 53 LYS cc_start: 0.9384 (ttpt) cc_final: 0.9073 (pttp) REVERT: E 65 LEU cc_start: 0.9543 (tp) cc_final: 0.9288 (tp) REVERT: E 73 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8681 (tm-30) REVERT: E 85 ASN cc_start: 0.8929 (m-40) cc_final: 0.8661 (m-40) REVERT: E 89 GLN cc_start: 0.8695 (mm-40) cc_final: 0.8263 (mm-40) REVERT: E 104 HIS cc_start: 0.9102 (t-90) cc_final: 0.8602 (t70) REVERT: E 107 GLU cc_start: 0.8305 (pt0) cc_final: 0.8088 (pt0) REVERT: E 122 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.8800 (m-80) REVERT: E 130 ARG cc_start: 0.9622 (mtp180) cc_final: 0.9268 (ptm160) REVERT: F 52 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8434 (tp30) REVERT: F 68 ASP cc_start: 0.8400 (t0) cc_final: 0.8138 (t0) REVERT: F 88 TYR cc_start: 0.8746 (m-10) cc_final: 0.8412 (m-80) REVERT: G 25 PHE cc_start: 0.8550 (m-80) cc_final: 0.8340 (m-10) REVERT: G 36 LYS cc_start: 0.9270 (mmmt) cc_final: 0.8890 (mmtt) REVERT: G 65 LEU cc_start: 0.9536 (mm) cc_final: 0.8874 (mm) REVERT: G 84 GLN cc_start: 0.9388 (tp-100) cc_final: 0.9080 (tp40) REVERT: G 92 GLU cc_start: 0.8304 (tt0) cc_final: 0.7747 (tt0) REVERT: G 95 LYS cc_start: 0.9080 (ttpt) cc_final: 0.8785 (ttmm) REVERT: H 46 LYS cc_start: 0.9126 (tppt) cc_final: 0.8824 (tppt) REVERT: H 62 MET cc_start: 0.9341 (mmm) cc_final: 0.9131 (mmm) REVERT: H 105 GLU cc_start: 0.8362 (tm-30) cc_final: 0.7502 (tm-30) outliers start: 25 outliers final: 18 residues processed: 261 average time/residue: 0.2965 time to fit residues: 102.9154 Evaluate side-chains 250 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 231 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain F residue 58 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 111 VAL 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 97 optimal weight: 0.0000 chunk 18 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 chunk 33 optimal weight: 10.0000 overall best weight: 5.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.053576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.039730 restraints weight = 65584.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.040847 restraints weight = 33068.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.041659 restraints weight = 21700.441| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 12730 Z= 0.279 Angle : 0.648 7.772 18433 Z= 0.379 Chirality : 0.037 0.165 2086 Planarity : 0.004 0.042 1322 Dihedral : 30.728 167.372 3997 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.18 % Allowed : 27.49 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.30), residues: 733 helix: 1.46 (0.23), residues: 508 sheet: None (None), residues: 0 loop : -1.34 (0.38), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 86 HIS 0.006 0.001 HIS H 49 PHE 0.010 0.002 PHE H 65 TYR 0.024 0.002 TYR E 110 ARG 0.005 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.06490 ( 714) hydrogen bonds : angle 3.22732 ( 1758) covalent geometry : bond 0.00613 (12730) covalent geometry : angle 0.64837 (18433) *********************** 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 264 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 238 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8564 (mt-10) REVERT: A 87 GLN cc_start: 0.9393 (mt0) cc_final: 0.9119 (mt0) REVERT: A 95 GLN cc_start: 0.9139 (tt0) cc_final: 0.8837 (tt0) REVERT: A 104 HIS cc_start: 0.8630 (t-90) cc_final: 0.7859 (t70) REVERT: A 107 GLU cc_start: 0.8958 (pp20) cc_final: 0.8246 (pp20) REVERT: A 108 ASP cc_start: 0.8714 (m-30) cc_final: 0.7688 (m-30) REVERT: A 127 GLN cc_start: 0.9174 (tm-30) cc_final: 0.8841 (tm-30) REVERT: B 30 THR cc_start: 0.9093 (p) cc_final: 0.8776 (t) REVERT: B 44 LYS cc_start: 0.9128 (tttm) cc_final: 0.8771 (mtpp) REVERT: B 79 LYS cc_start: 0.8984 (mtmm) cc_final: 0.8731 (ttmm) REVERT: C 32 ARG cc_start: 0.9353 (ttp80) cc_final: 0.8981 (ptm-80) REVERT: C 38 ASN cc_start: 0.8965 (m-40) cc_final: 0.8720 (p0) REVERT: C 64 GLU cc_start: 0.8602 (tp30) cc_final: 0.8231 (tp30) REVERT: C 68 ASN cc_start: 0.8995 (m-40) cc_final: 0.8315 (m-40) REVERT: C 90 ASP cc_start: 0.8354 (t70) cc_final: 0.8071 (t70) REVERT: C 95 LYS cc_start: 0.9646 (ttmm) cc_final: 0.9238 (tptt) REVERT: C 104 GLN cc_start: 0.8282 (mm-40) cc_final: 0.7873 (tp-100) REVERT: D 35 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7740 (tp30) REVERT: D 47 GLN cc_start: 0.9320 (tm-30) cc_final: 0.8999 (tm-30) REVERT: D 71 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8553 (tm-30) REVERT: D 83 TYR cc_start: 0.8469 (m-10) cc_final: 0.8257 (m-10) REVERT: D 95 GLN cc_start: 0.9283 (tt0) cc_final: 0.8955 (tm-30) REVERT: D 121 TYR cc_start: 0.9472 (t80) cc_final: 0.9270 (t80) REVERT: E 53 LYS cc_start: 0.9391 (ttpt) cc_final: 0.9064 (pttp) REVERT: E 73 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8797 (tm-30) REVERT: E 104 HIS cc_start: 0.9098 (t-90) cc_final: 0.8561 (t70) REVERT: E 107 GLU cc_start: 0.8430 (pt0) cc_final: 0.8160 (pt0) REVERT: E 122 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8783 (m-80) REVERT: E 130 ARG cc_start: 0.9648 (mtp180) cc_final: 0.9163 (mtp85) REVERT: F 43 VAL cc_start: 0.9615 (OUTLIER) cc_final: 0.9337 (p) REVERT: F 52 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8451 (tp30) REVERT: F 88 TYR cc_start: 0.8778 (m-10) cc_final: 0.8002 (m-10) REVERT: F 95 ARG cc_start: 0.8348 (mtt-85) cc_final: 0.7919 (mmt180) REVERT: G 36 LYS cc_start: 0.9261 (mmmt) cc_final: 0.8873 (mmtt) REVERT: G 64 GLU cc_start: 0.8795 (tp30) cc_final: 0.8572 (tp30) REVERT: G 92 GLU cc_start: 0.8261 (tt0) cc_final: 0.7826 (tt0) REVERT: G 95 LYS cc_start: 0.9071 (ttpt) cc_final: 0.8776 (ttmm) REVERT: H 46 LYS cc_start: 0.9091 (tppt) cc_final: 0.8512 (tppt) REVERT: H 62 MET cc_start: 0.9373 (mmm) cc_final: 0.9164 (mmm) REVERT: H 83 TYR cc_start: 0.8660 (m-10) cc_final: 0.7553 (m-10) REVERT: H 105 GLU cc_start: 0.8436 (tm-30) cc_final: 0.7815 (tm-30) outliers start: 26 outliers final: 19 residues processed: 246 average time/residue: 0.2938 time to fit residues: 95.9598 Evaluate side-chains 244 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 223 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 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 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 111 VAL 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 57 optimal weight: 0.9980 chunk 93 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.055867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.041779 restraints weight = 64488.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.042930 restraints weight = 32088.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.043798 restraints weight = 20994.924| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3263 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= 0.172 Angle : 0.609 8.553 18433 Z= 0.356 Chirality : 0.034 0.158 2086 Planarity : 0.004 0.046 1322 Dihedral : 30.527 171.920 3997 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.73 % Allowed : 30.71 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.31), residues: 733 helix: 1.64 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.19 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.004 0.001 HIS H 49 PHE 0.012 0.001 PHE A 78 TYR 0.015 0.002 TYR G 39 ARG 0.006 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.05453 ( 714) hydrogen bonds : angle 2.92305 ( 1758) covalent geometry : bond 0.00379 (12730) covalent geometry : angle 0.60885 (18433) *********************** 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 269 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 252 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8521 (mt-10) REVERT: A 55 GLN cc_start: 0.9363 (mt0) cc_final: 0.9149 (tt0) REVERT: A 85 ASN cc_start: 0.9561 (m-40) cc_final: 0.9229 (m-40) REVERT: A 87 GLN cc_start: 0.9327 (mt0) cc_final: 0.9027 (mt0) REVERT: A 104 HIS cc_start: 0.8566 (t-90) cc_final: 0.7838 (t70) REVERT: A 107 GLU cc_start: 0.8962 (pp20) cc_final: 0.8244 (pp20) REVERT: A 108 ASP cc_start: 0.8525 (m-30) cc_final: 0.7432 (m-30) REVERT: A 127 GLN cc_start: 0.9069 (tm-30) cc_final: 0.8712 (tm-30) REVERT: B 30 THR cc_start: 0.9129 (p) cc_final: 0.8905 (t) REVERT: B 31 LYS cc_start: 0.9182 (ttmm) cc_final: 0.8864 (ttmm) REVERT: B 51 TYR cc_start: 0.8955 (m-80) cc_final: 0.8590 (m-80) REVERT: B 79 LYS cc_start: 0.8920 (mtmm) cc_final: 0.8669 (ttmm) REVERT: C 32 ARG cc_start: 0.9326 (ttp80) cc_final: 0.8824 (ptm-80) REVERT: C 39 TYR cc_start: 0.8821 (m-80) cc_final: 0.8453 (m-80) REVERT: C 64 GLU cc_start: 0.8652 (tp30) cc_final: 0.8387 (tp30) REVERT: C 71 ARG cc_start: 0.8917 (ttp80) cc_final: 0.8669 (ttp-110) REVERT: C 90 ASP cc_start: 0.8530 (t70) cc_final: 0.8151 (t70) REVERT: C 95 LYS cc_start: 0.9620 (ttmm) cc_final: 0.9204 (tptt) REVERT: C 104 GLN cc_start: 0.8271 (mm-40) cc_final: 0.8039 (tp-100) REVERT: D 47 GLN cc_start: 0.9313 (tm-30) cc_final: 0.8959 (tm-30) REVERT: D 71 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8515 (tm-30) REVERT: D 86 ARG cc_start: 0.8697 (tpp-160) cc_final: 0.8253 (tpp80) REVERT: D 93 GLU cc_start: 0.8891 (mp0) cc_final: 0.8423 (mp0) REVERT: D 95 GLN cc_start: 0.9234 (tt0) cc_final: 0.8982 (tm-30) REVERT: D 121 TYR cc_start: 0.9424 (t80) cc_final: 0.9171 (t80) REVERT: E 73 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8598 (tm-30) REVERT: E 104 HIS cc_start: 0.9079 (t-90) cc_final: 0.8528 (t70) REVERT: E 107 GLU cc_start: 0.8371 (pt0) cc_final: 0.8100 (pt0) REVERT: E 122 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.8847 (m-80) REVERT: E 130 ARG cc_start: 0.9626 (mtp180) cc_final: 0.8882 (mtp85) REVERT: F 52 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8267 (tp30) REVERT: F 88 TYR cc_start: 0.8711 (m-10) cc_final: 0.7918 (m-10) REVERT: G 36 LYS cc_start: 0.9259 (mmmt) cc_final: 0.8846 (mmtt) REVERT: G 95 LYS cc_start: 0.9058 (ttpt) cc_final: 0.8710 (ttmm) REVERT: H 46 LYS cc_start: 0.9187 (tppt) cc_final: 0.8665 (tppt) REVERT: H 62 MET cc_start: 0.9329 (mmm) cc_final: 0.8939 (mmm) REVERT: H 83 TYR cc_start: 0.8536 (m-10) cc_final: 0.7223 (m-10) outliers start: 17 outliers final: 12 residues processed: 258 average time/residue: 0.2853 time to fit residues: 98.9767 Evaluate side-chains 243 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 230 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 60 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 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 H residue 94 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 96 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 115 HIS ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS H 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.054151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.040173 restraints weight = 66600.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.041262 restraints weight = 33963.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.042070 restraints weight = 22581.734| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12730 Z= 0.248 Angle : 0.643 9.563 18433 Z= 0.374 Chirality : 0.037 0.158 2086 Planarity : 0.004 0.045 1322 Dihedral : 30.697 175.181 3997 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.98 % Allowed : 30.87 % Favored : 64.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.31), residues: 733 helix: 1.70 (0.23), residues: 502 sheet: None (None), residues: 0 loop : -1.13 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 86 HIS 0.006 0.001 HIS F 75 PHE 0.014 0.002 PHE A 78 TYR 0.023 0.002 TYR B 88 ARG 0.007 0.001 ARG A 80 Details of bonding type rmsd hydrogen bonds : bond 0.06154 ( 714) hydrogen bonds : angle 3.17411 ( 1758) covalent geometry : bond 0.00549 (12730) covalent geometry : angle 0.64285 (18433) *********************** 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 260 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 229 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8509 (mt-10) REVERT: A 74 ILE cc_start: 0.9613 (tt) cc_final: 0.9339 (tt) REVERT: A 87 GLN cc_start: 0.9389 (mt0) cc_final: 0.9113 (mt0) REVERT: A 104 HIS cc_start: 0.8552 (t-90) cc_final: 0.7901 (t70) REVERT: A 107 GLU cc_start: 0.8940 (pp20) cc_final: 0.8408 (pp20) REVERT: A 108 ASP cc_start: 0.8563 (m-30) cc_final: 0.7565 (m-30) REVERT: A 127 GLN cc_start: 0.9123 (tm-30) cc_final: 0.8723 (tm-30) REVERT: B 27 GLN cc_start: 0.9222 (tp40) cc_final: 0.8628 (tp-100) REVERT: B 44 LYS cc_start: 0.9022 (tttm) cc_final: 0.8759 (mtpp) REVERT: B 79 LYS cc_start: 0.8959 (mtmm) cc_final: 0.8694 (ttmm) REVERT: C 32 ARG cc_start: 0.9379 (ttp80) cc_final: 0.8952 (ptm-80) REVERT: C 38 ASN cc_start: 0.8934 (m-40) cc_final: 0.8719 (p0) REVERT: C 64 GLU cc_start: 0.8564 (tp30) cc_final: 0.8300 (tp30) REVERT: C 71 ARG cc_start: 0.8987 (ttp80) cc_final: 0.8701 (ttp-110) REVERT: C 90 ASP cc_start: 0.8304 (t70) cc_final: 0.7992 (t70) REVERT: C 95 LYS cc_start: 0.9638 (ttmm) cc_final: 0.9228 (tptt) REVERT: C 99 LYS cc_start: 0.8639 (mmmm) cc_final: 0.8373 (mmmm) REVERT: C 104 GLN cc_start: 0.8303 (mm-40) cc_final: 0.8057 (tp-100) REVERT: D 47 GLN cc_start: 0.9357 (tm-30) cc_final: 0.8991 (tm-30) REVERT: D 71 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8566 (tm-30) REVERT: D 93 GLU cc_start: 0.8935 (mp0) cc_final: 0.8649 (mm-30) REVERT: D 95 GLN cc_start: 0.9273 (tt0) cc_final: 0.8974 (tm-30) REVERT: D 121 TYR cc_start: 0.9466 (t80) cc_final: 0.9254 (t80) REVERT: E 73 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8663 (tm-30) REVERT: E 104 HIS cc_start: 0.9079 (t-90) cc_final: 0.8539 (t70) REVERT: E 107 GLU cc_start: 0.8398 (pt0) cc_final: 0.8131 (pt0) REVERT: E 112 LEU cc_start: 0.9656 (OUTLIER) cc_final: 0.9417 (tt) REVERT: E 122 PHE cc_start: 0.9132 (OUTLIER) cc_final: 0.8834 (m-80) REVERT: E 130 ARG cc_start: 0.9651 (mtp180) cc_final: 0.8879 (mtp85) REVERT: F 52 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8396 (tp30) REVERT: F 88 TYR cc_start: 0.8769 (m-10) cc_final: 0.7836 (m-10) REVERT: F 95 ARG cc_start: 0.8148 (mmt90) cc_final: 0.7914 (mmt180) REVERT: G 36 LYS cc_start: 0.9263 (mmmt) cc_final: 0.8852 (mmtt) REVERT: G 95 LYS cc_start: 0.8954 (ttpt) cc_final: 0.8579 (ttmm) REVERT: G 99 LYS cc_start: 0.9071 (mmmm) cc_final: 0.8702 (mmmm) REVERT: H 46 LYS cc_start: 0.9089 (tppt) cc_final: 0.8469 (tppt) REVERT: H 62 MET cc_start: 0.9361 (mmm) cc_final: 0.8987 (mmm) REVERT: H 83 TYR cc_start: 0.8628 (m-10) cc_final: 0.7201 (m-10) outliers start: 31 outliers final: 17 residues processed: 245 average time/residue: 0.2888 time to fit residues: 94.8550 Evaluate side-chains 237 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 218 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 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 46 ILE Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 94 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 84 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 69 optimal weight: 20.0000 chunk 76 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 95 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.054977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.041164 restraints weight = 65947.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.042262 restraints weight = 33661.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.043095 restraints weight = 22243.802| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3608 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= 0.198 Angle : 0.640 10.024 18433 Z= 0.369 Chirality : 0.036 0.158 2086 Planarity : 0.004 0.047 1322 Dihedral : 30.628 177.927 3997 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.18 % Allowed : 32.96 % Favored : 62.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.31), residues: 733 helix: 1.67 (0.23), residues: 501 sheet: None (None), residues: 0 loop : -1.13 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.003 0.001 HIS F 75 PHE 0.014 0.001 PHE A 78 TYR 0.029 0.002 TYR D 83 ARG 0.006 0.000 ARG A 80 Details of bonding type rmsd hydrogen bonds : bond 0.05605 ( 714) hydrogen bonds : angle 3.07750 ( 1758) covalent geometry : bond 0.00439 (12730) covalent geometry : angle 0.63981 (18433) *********************** 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 261 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 235 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8523 (mt-10) REVERT: A 74 ILE cc_start: 0.9598 (tt) cc_final: 0.9296 (tt) REVERT: A 85 ASN cc_start: 0.9564 (m-40) cc_final: 0.9261 (m-40) REVERT: A 87 GLN cc_start: 0.9392 (mt0) cc_final: 0.9098 (mt0) REVERT: A 95 GLN cc_start: 0.9130 (tt0) cc_final: 0.8848 (tp40) REVERT: A 104 HIS cc_start: 0.8558 (t-90) cc_final: 0.7761 (t70) REVERT: A 107 GLU cc_start: 0.8970 (pp20) cc_final: 0.8233 (pp20) REVERT: A 108 ASP cc_start: 0.8564 (m-30) cc_final: 0.7426 (m-30) REVERT: A 122 PHE cc_start: 0.9048 (OUTLIER) cc_final: 0.8256 (m-80) REVERT: A 127 GLN cc_start: 0.9097 (tm-30) cc_final: 0.8728 (tm-30) REVERT: B 27 GLN cc_start: 0.9190 (tp40) cc_final: 0.8624 (tp-100) REVERT: B 31 LYS cc_start: 0.9218 (ttmm) cc_final: 0.8857 (ttmm) REVERT: B 51 TYR cc_start: 0.8893 (m-80) cc_final: 0.8610 (m-80) REVERT: B 64 ASN cc_start: 0.9234 (m-40) cc_final: 0.8992 (t0) REVERT: B 79 LYS cc_start: 0.8950 (mtmm) cc_final: 0.8690 (ttmm) REVERT: C 32 ARG cc_start: 0.9366 (ttp80) cc_final: 0.9113 (ptm-80) REVERT: C 64 GLU cc_start: 0.8637 (tp30) cc_final: 0.8382 (tp30) REVERT: C 71 ARG cc_start: 0.8993 (ttp80) cc_final: 0.8679 (ttp-110) REVERT: C 90 ASP cc_start: 0.8212 (t70) cc_final: 0.7983 (t70) REVERT: C 95 LYS cc_start: 0.9633 (ttmm) cc_final: 0.9220 (tptt) REVERT: C 99 LYS cc_start: 0.8580 (mmmm) cc_final: 0.8367 (mmmm) REVERT: C 104 GLN cc_start: 0.8270 (mm-40) cc_final: 0.8001 (tp-100) REVERT: D 37 TYR cc_start: 0.9489 (m-80) cc_final: 0.9120 (m-80) REVERT: D 47 GLN cc_start: 0.9343 (tm-30) cc_final: 0.8971 (tm-30) REVERT: D 71 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8541 (tm-30) REVERT: D 93 GLU cc_start: 0.8999 (mp0) cc_final: 0.8659 (mm-30) REVERT: D 95 GLN cc_start: 0.9267 (tt0) cc_final: 0.8982 (tm-30) REVERT: E 73 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8604 (tm-30) REVERT: E 104 HIS cc_start: 0.9057 (t-90) cc_final: 0.8494 (t70) REVERT: E 107 GLU cc_start: 0.8373 (pt0) cc_final: 0.8102 (pt0) REVERT: E 112 LEU cc_start: 0.9665 (OUTLIER) cc_final: 0.9435 (tt) REVERT: E 122 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8860 (m-80) REVERT: E 130 ARG cc_start: 0.9643 (mtp180) cc_final: 0.8877 (mtp85) REVERT: F 52 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8408 (tp30) REVERT: F 88 TYR cc_start: 0.8597 (m-10) cc_final: 0.7692 (m-80) REVERT: F 95 ARG cc_start: 0.8121 (mmt90) cc_final: 0.7853 (mmt180) REVERT: G 36 LYS cc_start: 0.9277 (mmmt) cc_final: 0.8862 (mmtt) REVERT: G 95 LYS cc_start: 0.8974 (ttpt) cc_final: 0.8597 (ttmm) REVERT: H 46 LYS cc_start: 0.9164 (tppt) cc_final: 0.8582 (tppt) REVERT: H 62 MET cc_start: 0.9297 (mmm) cc_final: 0.8935 (mmm) REVERT: H 83 TYR cc_start: 0.8533 (m-10) cc_final: 0.7499 (m-10) REVERT: H 86 ARG cc_start: 0.8933 (tpp80) cc_final: 0.8666 (tpp80) outliers start: 26 outliers final: 17 residues processed: 247 average time/residue: 0.2889 time to fit residues: 95.4546 Evaluate side-chains 249 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 229 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 119 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 111 ILE Chi-restraints excluded: chain D residue 39 VAL 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 26 ILE Chi-restraints excluded: chain F residue 58 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 79 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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** D 82 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS H 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.055263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.041377 restraints weight = 67031.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.042492 restraints weight = 34390.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.043373 restraints weight = 22824.202| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3764 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= 0.190 Angle : 0.640 10.365 18433 Z= 0.370 Chirality : 0.036 0.162 2086 Planarity : 0.004 0.047 1322 Dihedral : 30.599 179.623 3997 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.18 % Allowed : 33.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.31), residues: 733 helix: 1.50 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.17 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.004 0.001 HIS F 75 PHE 0.017 0.002 PHE A 78 TYR 0.023 0.002 TYR D 83 ARG 0.006 0.000 ARG A 80 Details of bonding type rmsd hydrogen bonds : bond 0.05547 ( 714) hydrogen bonds : angle 3.09920 ( 1758) covalent geometry : bond 0.00421 (12730) covalent geometry : angle 0.63993 (18433) *********************** 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 259 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 233 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8509 (mt-10) REVERT: A 74 ILE cc_start: 0.9556 (tt) cc_final: 0.9308 (tt) REVERT: A 85 ASN cc_start: 0.9545 (m-40) cc_final: 0.9273 (m-40) REVERT: A 104 HIS cc_start: 0.8608 (t-90) cc_final: 0.7844 (t70) REVERT: A 107 GLU cc_start: 0.8970 (pp20) cc_final: 0.8221 (pp20) REVERT: A 108 ASP cc_start: 0.8530 (m-30) cc_final: 0.7387 (m-30) REVERT: A 122 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8351 (m-80) REVERT: A 127 GLN cc_start: 0.9054 (tm-30) cc_final: 0.8657 (tm-30) REVERT: B 27 GLN cc_start: 0.9201 (tp40) cc_final: 0.8652 (tp-100) REVERT: B 31 LYS cc_start: 0.9180 (ttmm) cc_final: 0.8951 (ttmm) REVERT: B 64 ASN cc_start: 0.9273 (m-40) cc_final: 0.9019 (t0) REVERT: B 79 LYS cc_start: 0.8964 (mtmm) cc_final: 0.8690 (ttmm) REVERT: B 84 MET cc_start: 0.9004 (mmm) cc_final: 0.8467 (tpp) REVERT: C 32 ARG cc_start: 0.9346 (ttp80) cc_final: 0.9082 (ptm-80) REVERT: C 56 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8337 (mm-30) REVERT: C 64 GLU cc_start: 0.8615 (tp30) cc_final: 0.8370 (tp30) REVERT: C 71 ARG cc_start: 0.8975 (ttp80) cc_final: 0.8654 (ttp-110) REVERT: C 90 ASP cc_start: 0.8245 (t70) cc_final: 0.8002 (t70) REVERT: C 95 LYS cc_start: 0.9629 (ttmm) cc_final: 0.9221 (tptt) REVERT: C 104 GLN cc_start: 0.8275 (mm-40) cc_final: 0.8030 (tp-100) REVERT: D 37 TYR cc_start: 0.9469 (m-80) cc_final: 0.9113 (m-80) REVERT: D 47 GLN cc_start: 0.9353 (tm-30) cc_final: 0.9020 (tm-30) REVERT: D 71 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8499 (tm-30) REVERT: D 93 GLU cc_start: 0.8904 (mp0) cc_final: 0.8548 (mm-30) REVERT: D 95 GLN cc_start: 0.9249 (tt0) cc_final: 0.8971 (tm-30) REVERT: E 73 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8619 (tm-30) REVERT: E 104 HIS cc_start: 0.9072 (t-90) cc_final: 0.8445 (t70) REVERT: E 107 GLU cc_start: 0.8354 (pt0) cc_final: 0.8077 (pt0) REVERT: E 112 LEU cc_start: 0.9660 (OUTLIER) cc_final: 0.9448 (tt) REVERT: E 122 PHE cc_start: 0.9120 (OUTLIER) cc_final: 0.8884 (m-80) REVERT: E 130 ARG cc_start: 0.9644 (mtp180) cc_final: 0.9306 (ptm160) REVERT: F 39 ARG cc_start: 0.9393 (mtt-85) cc_final: 0.9088 (mtt90) REVERT: F 52 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8336 (tp30) REVERT: F 88 TYR cc_start: 0.8667 (m-10) cc_final: 0.8213 (m-10) REVERT: F 95 ARG cc_start: 0.8152 (mmt90) cc_final: 0.7944 (mmt180) REVERT: G 23 LEU cc_start: 0.9094 (mm) cc_final: 0.8792 (mm) REVERT: G 36 LYS cc_start: 0.9246 (mmmt) cc_final: 0.8807 (mmtt) REVERT: G 95 LYS cc_start: 0.8936 (ttpt) cc_final: 0.8554 (ttmm) REVERT: G 99 LYS cc_start: 0.9009 (mmmm) cc_final: 0.8649 (mmmm) REVERT: H 46 LYS cc_start: 0.9159 (tppt) cc_final: 0.8565 (tppt) REVERT: H 62 MET cc_start: 0.9321 (mmm) cc_final: 0.8965 (mmm) REVERT: H 83 TYR cc_start: 0.8380 (m-10) cc_final: 0.7645 (m-10) outliers start: 26 outliers final: 20 residues processed: 246 average time/residue: 0.3047 time to fit residues: 102.1433 Evaluate side-chains 251 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 228 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 119 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 111 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 44 VAL 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 26 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain 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 27 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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** D 109 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.055926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.041979 restraints weight = 65782.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.043161 restraints weight = 34025.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.044009 restraints weight = 22520.404| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3872 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= 0.181 Angle : 0.651 9.879 18433 Z= 0.373 Chirality : 0.036 0.245 2086 Planarity : 0.004 0.048 1322 Dihedral : 30.563 177.309 3997 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.54 % Allowed : 35.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.30), residues: 733 helix: 1.48 (0.23), residues: 508 sheet: None (None), residues: 0 loop : -1.15 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 86 HIS 0.004 0.001 HIS F 75 PHE 0.012 0.001 PHE A 67 TYR 0.014 0.002 TYR F 88 ARG 0.007 0.000 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.05438 ( 714) hydrogen bonds : angle 3.09263 ( 1758) covalent geometry : bond 0.00400 (12730) covalent geometry : angle 0.65069 (18433) *********************** 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: 22 poor density : 234 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8435 (mt-10) REVERT: A 67 PHE cc_start: 0.9105 (t80) cc_final: 0.8882 (t80) REVERT: A 74 ILE cc_start: 0.9608 (tt) cc_final: 0.9379 (tt) REVERT: A 87 GLN cc_start: 0.9069 (mt0) cc_final: 0.8819 (mt0) REVERT: A 95 GLN cc_start: 0.9140 (tp40) cc_final: 0.8802 (tp40) REVERT: A 104 HIS cc_start: 0.8605 (t-90) cc_final: 0.7943 (t70) REVERT: A 107 GLU cc_start: 0.8971 (pp20) cc_final: 0.8348 (pp20) REVERT: A 108 ASP cc_start: 0.8534 (m-30) cc_final: 0.7608 (m-30) REVERT: A 122 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.8253 (m-80) REVERT: A 127 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8673 (tm-30) REVERT: B 31 LYS cc_start: 0.9198 (ttmm) cc_final: 0.8961 (ttmm) REVERT: B 64 ASN cc_start: 0.9284 (m-40) cc_final: 0.8987 (t0) REVERT: B 79 LYS cc_start: 0.8952 (mtmm) cc_final: 0.8671 (ttmm) REVERT: B 84 MET cc_start: 0.8809 (mmm) cc_final: 0.8515 (tpp) REVERT: C 32 ARG cc_start: 0.9357 (ttp80) cc_final: 0.9089 (ptm-80) REVERT: C 38 ASN cc_start: 0.8865 (m-40) cc_final: 0.8477 (p0) REVERT: C 56 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8305 (mm-30) REVERT: C 64 GLU cc_start: 0.8602 (tp30) cc_final: 0.8350 (tp30) REVERT: C 71 ARG cc_start: 0.8943 (ttp80) cc_final: 0.8629 (ttp-110) REVERT: C 95 LYS cc_start: 0.9631 (ttmm) cc_final: 0.9235 (tptt) REVERT: C 104 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7990 (tp-100) REVERT: D 37 TYR cc_start: 0.9455 (m-80) cc_final: 0.9037 (m-80) REVERT: D 47 GLN cc_start: 0.9372 (tm-30) cc_final: 0.9049 (tm-30) REVERT: D 71 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8544 (tm-30) REVERT: D 93 GLU cc_start: 0.8922 (mp0) cc_final: 0.8613 (mm-30) REVERT: D 95 GLN cc_start: 0.9246 (tt0) cc_final: 0.8972 (tm-30) REVERT: E 73 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8544 (tm-30) REVERT: E 104 HIS cc_start: 0.9125 (t-90) cc_final: 0.8565 (t70) REVERT: E 107 GLU cc_start: 0.8305 (pt0) cc_final: 0.8079 (pt0) REVERT: E 112 LEU cc_start: 0.9667 (OUTLIER) cc_final: 0.9459 (tt) REVERT: E 122 PHE cc_start: 0.9106 (OUTLIER) cc_final: 0.8882 (m-80) REVERT: E 130 ARG cc_start: 0.9646 (mtp180) cc_final: 0.9314 (ptm160) REVERT: F 39 ARG cc_start: 0.9395 (mtt-85) cc_final: 0.9124 (mtt90) REVERT: F 52 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8341 (tp30) REVERT: F 95 ARG cc_start: 0.8095 (mmt90) cc_final: 0.7850 (mmt180) REVERT: G 13 LYS cc_start: 0.7684 (tptp) cc_final: 0.7364 (tptp) REVERT: G 36 LYS cc_start: 0.9250 (mmmt) cc_final: 0.8647 (mmmt) REVERT: G 95 LYS cc_start: 0.8953 (ttpt) cc_final: 0.8563 (ttmm) REVERT: G 99 LYS cc_start: 0.9013 (mmmm) cc_final: 0.8640 (mmmm) REVERT: H 46 LYS cc_start: 0.9160 (tppt) cc_final: 0.8579 (tppt) REVERT: H 62 MET cc_start: 0.9307 (mmm) cc_final: 0.8950 (mmm) outliers start: 22 outliers final: 17 residues processed: 245 average time/residue: 0.3501 time to fit residues: 114.9916 Evaluate side-chains 245 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 225 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 119 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 111 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 44 VAL 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 26 ILE Chi-restraints excluded: chain F residue 58 LEU 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 3 optimal weight: 0.0980 chunk 72 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 16 optimal weight: 0.3980 chunk 88 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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** D 109 HIS H 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.055718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.041848 restraints weight = 66062.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.042963 restraints weight = 34044.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.043808 restraints weight = 22592.124| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12730 Z= 0.188 Angle : 0.658 9.756 18433 Z= 0.376 Chirality : 0.036 0.261 2086 Planarity : 0.004 0.047 1322 Dihedral : 30.570 175.401 3997 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.38 % Allowed : 35.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.30), residues: 733 helix: 1.42 (0.23), residues: 510 sheet: None (None), residues: 0 loop : -1.12 (0.38), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 86 HIS 0.004 0.001 HIS F 75 PHE 0.014 0.001 PHE A 67 TYR 0.057 0.003 TYR F 88 ARG 0.006 0.000 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.05513 ( 714) hydrogen bonds : angle 3.11725 ( 1758) covalent geometry : bond 0.00417 (12730) covalent geometry : angle 0.65839 (18433) ********************** 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 251 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 230 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8433 (mt-10) REVERT: A 74 ILE cc_start: 0.9613 (tt) cc_final: 0.9361 (tt) REVERT: A 87 GLN cc_start: 0.9088 (mt0) cc_final: 0.8718 (mp10) REVERT: A 95 GLN cc_start: 0.9185 (tp40) cc_final: 0.8917 (mm-40) REVERT: A 104 HIS cc_start: 0.8600 (t-90) cc_final: 0.7941 (t70) REVERT: A 107 GLU cc_start: 0.8975 (pp20) cc_final: 0.8357 (pp20) REVERT: A 108 ASP cc_start: 0.8534 (m-30) cc_final: 0.7559 (m-30) REVERT: A 122 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.8349 (m-80) REVERT: A 127 GLN cc_start: 0.9063 (tm-30) cc_final: 0.8665 (tm-30) REVERT: B 31 LYS cc_start: 0.9209 (ttmm) cc_final: 0.8970 (ttmm) REVERT: B 63 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8514 (tm-30) REVERT: B 64 ASN cc_start: 0.9302 (m-40) cc_final: 0.8903 (t0) REVERT: B 79 LYS cc_start: 0.8967 (mtmm) cc_final: 0.8587 (ttmm) REVERT: B 84 MET cc_start: 0.8690 (mmm) cc_final: 0.8330 (tpp) REVERT: C 32 ARG cc_start: 0.9359 (ttp80) cc_final: 0.9089 (ptm-80) REVERT: C 38 ASN cc_start: 0.8872 (m-40) cc_final: 0.8501 (p0) REVERT: C 56 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8347 (mm-30) REVERT: C 64 GLU cc_start: 0.8601 (tp30) cc_final: 0.8352 (tp30) REVERT: C 71 ARG cc_start: 0.8940 (ttp80) cc_final: 0.8721 (ttp-110) REVERT: C 92 GLU cc_start: 0.8419 (pm20) cc_final: 0.8159 (pm20) REVERT: C 95 LYS cc_start: 0.9632 (ttmm) cc_final: 0.9195 (tptt) REVERT: C 104 GLN cc_start: 0.8272 (mm-40) cc_final: 0.8018 (tp-100) REVERT: D 37 TYR cc_start: 0.9464 (m-80) cc_final: 0.9167 (m-80) REVERT: D 47 GLN cc_start: 0.9335 (tm-30) cc_final: 0.9024 (tm-30) REVERT: D 71 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8573 (tm-30) REVERT: D 93 GLU cc_start: 0.8935 (mp0) cc_final: 0.8652 (mm-30) REVERT: D 95 GLN cc_start: 0.9250 (tt0) cc_final: 0.8971 (tm-30) REVERT: E 73 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8557 (tm-30) REVERT: E 104 HIS cc_start: 0.9118 (t-90) cc_final: 0.8540 (t70) REVERT: E 107 GLU cc_start: 0.8400 (pt0) cc_final: 0.8112 (pt0) REVERT: E 112 LEU cc_start: 0.9666 (OUTLIER) cc_final: 0.9456 (tt) REVERT: E 122 PHE cc_start: 0.9112 (OUTLIER) cc_final: 0.8881 (m-80) REVERT: E 130 ARG cc_start: 0.9628 (mtp180) cc_final: 0.9304 (ptm160) REVERT: F 39 ARG cc_start: 0.9394 (mtt-85) cc_final: 0.9138 (mtt90) REVERT: F 52 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8337 (tp30) REVERT: F 88 TYR cc_start: 0.8834 (m-80) cc_final: 0.8495 (m-80) REVERT: F 95 ARG cc_start: 0.8114 (mmt90) cc_final: 0.7862 (mmt180) REVERT: G 13 LYS cc_start: 0.7690 (tptp) cc_final: 0.7358 (tptp) REVERT: G 36 LYS cc_start: 0.9249 (mmmt) cc_final: 0.8647 (mmmt) REVERT: G 95 LYS cc_start: 0.8962 (ttpt) cc_final: 0.8570 (ttmm) REVERT: H 46 LYS cc_start: 0.9159 (tppt) cc_final: 0.8568 (tppt) REVERT: H 62 MET cc_start: 0.9312 (mmm) cc_final: 0.8956 (mmm) outliers start: 21 outliers final: 17 residues processed: 241 average time/residue: 0.3620 time to fit residues: 119.1723 Evaluate side-chains 246 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 226 time to evaluate : 2.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 119 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 111 ILE Chi-restraints excluded: chain D residue 39 VAL 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 26 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain 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 11 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 83 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** D 109 HIS H 63 ASN H 109 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.054028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.039980 restraints weight = 67426.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.041048 restraints weight = 35460.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.041858 restraints weight = 23868.472| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 12730 Z= 0.263 Angle : 0.696 9.907 18433 Z= 0.398 Chirality : 0.038 0.242 2086 Planarity : 0.004 0.045 1322 Dihedral : 30.854 165.680 3997 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.54 % Allowed : 35.69 % Favored : 60.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.30), residues: 733 helix: 1.33 (0.23), residues: 513 sheet: None (None), residues: 0 loop : -1.19 (0.38), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 86 HIS 0.005 0.001 HIS D 109 PHE 0.010 0.002 PHE H 70 TYR 0.053 0.003 TYR F 88 ARG 0.006 0.001 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.06224 ( 714) hydrogen bonds : angle 3.35429 ( 1758) covalent geometry : bond 0.00581 (12730) covalent geometry : angle 0.69645 (18433) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4429.61 seconds wall clock time: 81 minutes 9.13 seconds (4869.13 seconds total)