Starting phenix.real_space_refine on Sat Jan 20 00:16:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0w_7326/01_2024/6c0w_7326_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0w_7326/01_2024/6c0w_7326.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0w_7326/01_2024/6c0w_7326.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0w_7326/01_2024/6c0w_7326.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0w_7326/01_2024/6c0w_7326_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0w_7326/01_2024/6c0w_7326_neut.pdb" } resolution = 4.0 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= 0.001 sd= 0.011 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 278 5.49 5 S 16 5.16 5 C 7427 2.51 5 N 2429 2.21 5 O 2972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K ARG 134": "NH1" <-> "NH2" Residue "K ARG 196": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13122 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 732 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "B" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 634 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 764 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} 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: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 749 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "F" Number of atoms: 623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 623 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 771 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "H" 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: "I" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2835 Classifications: {'DNA': 139} Link IDs: {'rna3p': 138} Chain: "J" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2864 Classifications: {'DNA': 139} Link IDs: {'rna3p': 138} Chain: "K" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1712 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 5, 'TRANS': 199} Chain breaks: 1 Time building chain proxies: 7.26, per 1000 atoms: 0.55 Number of scatterers: 13122 At special positions: 0 Unit cell: (100.98, 131.58, 118.32, 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 16 16.00 P 278 15.00 O 2972 8.00 N 2429 7.00 C 7427 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 - 3.50 Amino acid : False - 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: 7.01 Conformation dependent library (CDL) restraints added in 1.4 seconds 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1740 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 10 sheets defined 65.4% alpha, 6.1% beta 138 base pairs and 237 stacking pairs defined. Time for finding SS restraints: 6.12 Creating SS restraints... Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.787A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.784A pdb=" N VAL A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 114 Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.801A pdb=" N VAL A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN A 127 " --> pdb=" O PRO A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 127' Processing helix chain 'B' and resid 32 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.322A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.743A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.669A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.766A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.993A 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 removed outlier: 3.589A pdb=" N VAL D 41 " --> pdb=" O TYR D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 67 Processing helix chain 'D' and resid 68 through 80 removed outlier: 4.361A pdb=" N SER D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.656A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.726A pdb=" N THR D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 removed outlier: 3.678A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 78 removed outlier: 3.808A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 110 removed outlier: 3.714A pdb=" N LEU E 91 " --> pdb=" O GLN E 87 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 113 No H-bonds generated for 'chain 'E' and resid 111 through 113' Processing helix chain 'E' and resid 122 through 134 removed outlier: 3.710A pdb=" N ARG E 133 " --> pdb=" O ALA E 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 removed outlier: 3.688A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.565A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N TYR F 72 " --> pdb=" O ASP F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.675A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.707A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.936A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.580A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 removed outlier: 3.515A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.589A pdb=" N VAL H 41 " --> pdb=" O TYR H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 67 Processing helix chain 'H' and resid 68 through 84 removed outlier: 4.362A pdb=" N SER H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.657A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.726A pdb=" N THR H 115 " --> pdb=" O VAL H 111 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 16 removed outlier: 3.528A pdb=" N PHE K 8 " --> pdb=" O THR K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 29 removed outlier: 3.726A pdb=" N ASP K 29 " --> pdb=" O LEU K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 32 through 39 removed outlier: 3.531A pdb=" N VAL K 39 " --> pdb=" O GLN K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 59 removed outlier: 3.549A pdb=" N VAL K 48 " --> pdb=" O ARG K 44 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL K 49 " --> pdb=" O LYS K 45 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLN K 50 " --> pdb=" O GLU K 46 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU K 58 " --> pdb=" O HIS K 54 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS K 59 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 75 Processing helix chain 'K' and resid 100 through 116 removed outlier: 3.986A pdb=" N PHE K 104 " --> pdb=" O ASP K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 183 Processing helix chain 'K' and resid 197 through 210 removed outlier: 3.983A pdb=" N LEU K 201 " --> pdb=" O TYR K 197 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLN K 208 " --> pdb=" O ILE K 204 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.798A 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 'B' and resid 96 through 97 removed outlier: 6.401A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA6, first strand: chain 'E' and resid 85 through 86 removed outlier: 6.926A 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 'G' and resid 42 through 43 removed outlier: 7.699A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'K' and resid 120 through 122 Processing sheet with id=AB1, first strand: chain 'K' and resid 120 through 122 removed outlier: 4.757A pdb=" N TYR K 151 " --> pdb=" O SER K 164 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR K 155 " --> pdb=" O TYR K 160 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N TYR K 160 " --> pdb=" O TYR K 155 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LEU K 193 " --> pdb=" O VAL K 85 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N GLN K 87 " --> pdb=" O MET K 191 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N MET K 191 " --> pdb=" O GLN K 87 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N SER K 89 " --> pdb=" O VAL K 189 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N VAL K 189 " --> pdb=" O SER K 89 " (cutoff:3.500A) 400 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 670 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 237 stacking parallelities Total time for adding SS restraints: 5.24 Time building geometry restraints manager: 7.34 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: 2466 1.33 - 1.45: 4461 1.45 - 1.57: 6426 1.57 - 1.69: 554 1.69 - 1.81: 29 Bond restraints: 13936 Sorted by residual: bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.497 -0.075 3.00e-02 1.11e+03 6.17e+00 bond pdb=" C3' DT J -61 " pdb=" O3' DT J -61 " ideal model delta sigma weight residual 1.422 1.489 -0.067 3.00e-02 1.11e+03 4.96e+00 bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.480 -0.058 3.00e-02 1.11e+03 3.73e+00 bond pdb=" C3' DA J -38 " pdb=" O3' DA J -38 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.24e+00 bond pdb=" C3' DC I 4 " pdb=" O3' DC I 4 " ideal model delta sigma weight residual 1.422 1.465 -0.043 3.00e-02 1.11e+03 2.01e+00 ... (remaining 13931 not shown) Histogram of bond angle deviations from ideal: 96.96 - 104.37: 1078 104.37 - 111.78: 7283 111.78 - 119.19: 4443 119.19 - 126.60: 6348 126.60 - 134.02: 864 Bond angle restraints: 20016 Sorted by residual: angle pdb=" C ARG K 169 " pdb=" N ARG K 170 " pdb=" CA ARG K 170 " ideal model delta sigma weight residual 121.54 130.57 -9.03 1.91e+00 2.74e-01 2.23e+01 angle pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sigma weight residual 120.20 125.68 -5.48 1.50e+00 4.44e-01 1.34e+01 angle pdb=" C3' DT J -61 " pdb=" O3' DT J -61 " pdb=" P DA J -60 " ideal model delta sigma weight residual 120.20 125.31 -5.11 1.50e+00 4.44e-01 1.16e+01 angle pdb=" N GLY B 99 " pdb=" CA GLY B 99 " pdb=" C GLY B 99 " ideal model delta sigma weight residual 113.18 121.03 -7.85 2.37e+00 1.78e-01 1.10e+01 angle pdb=" N GLY H 104 " pdb=" CA GLY H 104 " pdb=" C GLY H 104 " ideal model delta sigma weight residual 113.18 120.87 -7.69 2.37e+00 1.78e-01 1.05e+01 ... (remaining 20011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 6158 35.97 - 71.94: 1421 71.94 - 107.91: 33 107.91 - 143.87: 5 143.87 - 179.84: 3 Dihedral angle restraints: 7620 sinusoidal: 4930 harmonic: 2690 Sorted by residual: dihedral pdb=" CA VAL D 66 " pdb=" C VAL D 66 " pdb=" N ASN D 67 " pdb=" CA ASN D 67 " ideal model delta harmonic sigma weight residual 180.00 153.03 26.97 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA VAL H 66 " pdb=" C VAL H 66 " pdb=" N ASN H 67 " pdb=" CA ASN H 67 " ideal model delta harmonic sigma weight residual 180.00 153.05 26.95 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA TYR B 98 " pdb=" C TYR B 98 " pdb=" N GLY B 99 " pdb=" CA GLY B 99 " ideal model delta harmonic sigma weight residual -180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 7617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1965 0.066 - 0.132: 269 0.132 - 0.198: 34 0.198 - 0.264: 0 0.264 - 0.330: 2 Chirality restraints: 2270 Sorted by residual: chirality pdb=" CB VAL H 66 " pdb=" CA VAL H 66 " pdb=" CG1 VAL H 66 " pdb=" CG2 VAL H 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CB VAL D 66 " pdb=" CA VAL D 66 " pdb=" CG1 VAL D 66 " pdb=" CG2 VAL D 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.67e+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 -2.54 -0.19 2.00e-01 2.50e+01 9.08e-01 ... (remaining 2267 not shown) Planarity restraints: 1559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 63 " -0.017 2.00e-02 2.50e+03 3.43e-02 1.17e+01 pdb=" C GLU B 63 " 0.059 2.00e-02 2.50e+03 pdb=" O GLU B 63 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN B 64 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " 0.051 5.00e-02 4.00e+02 7.67e-02 9.41e+00 pdb=" N PRO B 32 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 57 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.81e+00 pdb=" C VAL F 57 " 0.048 2.00e-02 2.50e+03 pdb=" O VAL F 57 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU F 58 " -0.016 2.00e-02 2.50e+03 ... (remaining 1556 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 403 2.67 - 3.22: 10868 3.22 - 3.78: 23903 3.78 - 4.34: 29972 4.34 - 4.90: 42476 Nonbonded interactions: 107622 Sorted by model distance: nonbonded pdb=" O TYR B 51 " pdb=" NH1 ARG B 55 " model vdw 2.107 2.520 nonbonded pdb=" NH1 ARG F 39 " pdb=" O LYS F 44 " model vdw 2.145 2.520 nonbonded pdb=" OD2 ASP K 70 " pdb=" OH TYR K 151 " model vdw 2.162 2.440 nonbonded pdb=" OH TYR H 42 " pdb=" NZ LYS H 46 " model vdw 2.190 2.520 nonbonded pdb=" OH TYR D 42 " pdb=" NZ LYS D 46 " model vdw 2.190 2.520 ... (remaining 107617 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 46 through 134) } ncs_group { reference = (chain 'B' and resid 24 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 15 through 112) selection = (chain 'G' and resid 15 through 112) } ncs_group { reference = chain 'D' 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: 0.130 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: 1.460 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 43.110 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 : 0.006 0.075 13936 Z= 0.337 Angle : 0.810 9.028 20016 Z= 0.473 Chirality : 0.047 0.330 2270 Planarity : 0.006 0.077 1559 Dihedral : 27.862 179.844 5880 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % 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: -4.19 (0.20), residues: 905 helix: -2.61 (0.14), residues: 605 sheet: -1.52 (0.80), residues: 38 loop : -2.86 (0.32), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP K 28 HIS 0.005 0.001 HIS F 75 PHE 0.026 0.002 PHE F 100 TYR 0.014 0.002 TYR F 88 ARG 0.006 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLN cc_start: 0.8295 (mt0) cc_final: 0.8001 (mt0) REVERT: A 133 ARG cc_start: 0.8017 (ttm170) cc_final: 0.7795 (mtp85) REVERT: B 44 LYS cc_start: 0.8028 (mttt) cc_final: 0.7744 (mttt) REVERT: B 88 TYR cc_start: 0.8530 (m-10) cc_final: 0.8254 (m-10) REVERT: C 23 LEU cc_start: 0.9074 (mt) cc_final: 0.8688 (mp) REVERT: C 79 ILE cc_start: 0.9316 (pt) cc_final: 0.9053 (mt) REVERT: D 105 GLU cc_start: 0.7384 (tp30) cc_final: 0.7167 (tp30) REVERT: E 58 THR cc_start: 0.9151 (p) cc_final: 0.8545 (t) REVERT: G 42 ARG cc_start: 0.7681 (mtp-110) cc_final: 0.7056 (mtp85) REVERT: G 111 ILE cc_start: 0.8253 (mt) cc_final: 0.7882 (mt) REVERT: H 36 SER cc_start: 0.8774 (t) cc_final: 0.8458 (t) REVERT: H 52 THR cc_start: 0.9145 (m) cc_final: 0.8926 (m) REVERT: H 101 LEU cc_start: 0.8376 (mm) cc_final: 0.7948 (mt) REVERT: K 5 VAL cc_start: 0.8963 (m) cc_final: 0.8655 (t) REVERT: K 70 ASP cc_start: 0.8059 (t70) cc_final: 0.7579 (t0) REVERT: K 106 ASN cc_start: 0.9100 (m110) cc_final: 0.8612 (m-40) REVERT: K 135 ILE cc_start: 0.9027 (mp) cc_final: 0.8715 (tt) REVERT: K 150 THR cc_start: 0.9140 (m) cc_final: 0.8939 (m) REVERT: K 158 THR cc_start: 0.7579 (p) cc_final: 0.7281 (p) REVERT: K 191 MET cc_start: 0.6136 (mtt) cc_final: 0.5671 (ttm) outliers start: 0 outliers final: 0 residues processed: 385 average time/residue: 0.3624 time to fit residues: 180.3217 Evaluate side-chains 279 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 34 optimal weight: 0.4980 chunk 54 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 HIS C 68 ASN C 89 ASN C 110 ASN F 64 ASN G 31 HIS G 38 ASN G 73 ASN G 94 ASN H 47 GLN H 67 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 GLN K 106 ASN K 145 ASN K 146 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13936 Z= 0.197 Angle : 0.615 6.740 20016 Z= 0.359 Chirality : 0.036 0.172 2270 Planarity : 0.004 0.054 1559 Dihedral : 31.548 179.345 4054 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.06 % Allowed : 15.94 % Favored : 80.99 % 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: -1.68 (0.25), residues: 905 helix: -0.49 (0.19), residues: 603 sheet: -0.63 (0.75), residues: 38 loop : -2.44 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 132 HIS 0.006 0.001 HIS E 59 PHE 0.013 0.001 PHE K 108 TYR 0.016 0.002 TYR H 121 ARG 0.006 0.001 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 324 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ARG cc_start: 0.8153 (ttm170) cc_final: 0.7950 (mtp85) REVERT: B 84 MET cc_start: 0.8011 (mmm) cc_final: 0.7662 (mmm) REVERT: B 88 TYR cc_start: 0.8724 (m-10) cc_final: 0.8402 (m-80) REVERT: C 39 TYR cc_start: 0.8295 (m-80) cc_final: 0.7879 (m-80) REVERT: C 95 LYS cc_start: 0.8985 (tptt) cc_final: 0.8771 (tptt) REVERT: D 43 LYS cc_start: 0.8670 (ttpt) cc_final: 0.8446 (ttpt) REVERT: D 51 ASP cc_start: 0.7778 (p0) cc_final: 0.7572 (p0) REVERT: F 29 ILE cc_start: 0.8965 (mm) cc_final: 0.8709 (mp) REVERT: F 92 ARG cc_start: 0.8032 (ttp80) cc_final: 0.7799 (ttp80) REVERT: G 39 TYR cc_start: 0.8764 (m-10) cc_final: 0.8330 (m-80) REVERT: H 101 LEU cc_start: 0.8312 (mm) cc_final: 0.7719 (mt) REVERT: H 116 LYS cc_start: 0.9075 (ttmm) cc_final: 0.8773 (tttp) REVERT: K 5 VAL cc_start: 0.8942 (m) cc_final: 0.8549 (t) REVERT: K 7 GLU cc_start: 0.7821 (mp0) cc_final: 0.7567 (mp0) REVERT: K 70 ASP cc_start: 0.8165 (t70) cc_final: 0.7801 (t0) REVERT: K 86 PHE cc_start: 0.8576 (m-80) cc_final: 0.8234 (m-80) REVERT: K 106 ASN cc_start: 0.9386 (m-40) cc_final: 0.8951 (m110) REVERT: K 123 PHE cc_start: 0.7999 (m-80) cc_final: 0.7728 (m-80) REVERT: K 152 VAL cc_start: 0.9569 (t) cc_final: 0.9175 (m) REVERT: K 170 ARG cc_start: 0.8297 (ptm160) cc_final: 0.8054 (ttp-170) REVERT: K 191 MET cc_start: 0.5984 (mtt) cc_final: 0.5294 (tmm) REVERT: K 197 TYR cc_start: 0.7340 (m-10) cc_final: 0.6999 (m-10) outliers start: 24 outliers final: 16 residues processed: 334 average time/residue: 0.3240 time to fit residues: 143.1600 Evaluate side-chains 296 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 280 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 53 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 112 optimal weight: 30.0000 chunk 92 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN F 64 ASN G 38 ASN H 67 ASN H 82 HIS K 77 HIS K 113 GLN K 118 ASN K 185 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 13936 Z= 0.464 Angle : 0.764 9.169 20016 Z= 0.427 Chirality : 0.043 0.156 2270 Planarity : 0.005 0.058 1559 Dihedral : 31.876 176.547 4054 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 7.78 % Allowed : 17.47 % Favored : 74.74 % 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 (0.27), residues: 905 helix: -0.01 (0.20), residues: 610 sheet: 0.03 (0.81), residues: 38 loop : -2.28 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 28 HIS 0.007 0.001 HIS B 75 PHE 0.023 0.002 PHE A 67 TYR 0.028 0.003 TYR H 83 ARG 0.006 0.001 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 292 time to evaluate : 1.076 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: B 84 MET cc_start: 0.8162 (mmm) cc_final: 0.7775 (mmm) REVERT: B 88 TYR cc_start: 0.8781 (m-10) cc_final: 0.8226 (m-10) REVERT: D 38 SER cc_start: 0.9200 (p) cc_final: 0.8888 (t) REVERT: D 43 LYS cc_start: 0.8777 (ttpt) cc_final: 0.8470 (ttpt) REVERT: F 30 THR cc_start: 0.8386 (p) cc_final: 0.8156 (t) REVERT: F 84 MET cc_start: 0.8075 (tpp) cc_final: 0.7825 (tpp) REVERT: F 88 TYR cc_start: 0.8400 (m-10) cc_final: 0.7726 (m-10) REVERT: G 61 GLU cc_start: 0.8878 (tp30) cc_final: 0.8524 (tm-30) REVERT: G 77 ARG cc_start: 0.8281 (ttm-80) cc_final: 0.7961 (mtp85) REVERT: G 84 GLN cc_start: 0.9237 (tp-100) cc_final: 0.8558 (tp-100) REVERT: K 37 GLN cc_start: 0.8642 (tt0) cc_final: 0.8432 (mm-40) REVERT: K 70 ASP cc_start: 0.8243 (t70) cc_final: 0.7978 (t0) REVERT: K 124 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.6494 (ttp-170) REVERT: K 175 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8815 (tt) REVERT: K 185 HIS cc_start: 0.8476 (m-70) cc_final: 0.7773 (m-70) REVERT: K 191 MET cc_start: 0.5954 (mtt) cc_final: 0.5127 (tmm) outliers start: 61 outliers final: 40 residues processed: 321 average time/residue: 0.3236 time to fit residues: 137.1674 Evaluate side-chains 293 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 251 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 124 ARG Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 175 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 110 optimal weight: 20.0000 chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN H 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13936 Z= 0.225 Angle : 0.620 6.596 20016 Z= 0.360 Chirality : 0.037 0.169 2270 Planarity : 0.004 0.047 1559 Dihedral : 31.535 179.183 4054 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 5.36 % Allowed : 21.17 % Favored : 73.47 % 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: -0.21 (0.28), residues: 905 helix: 0.71 (0.21), residues: 604 sheet: 0.34 (0.79), residues: 38 loop : -2.19 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 28 HIS 0.005 0.001 HIS H 82 PHE 0.008 0.001 PHE K 162 TYR 0.016 0.002 TYR K 160 ARG 0.007 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 283 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.7961 (mmm) cc_final: 0.7619 (mmm) REVERT: B 88 TYR cc_start: 0.8749 (m-10) cc_final: 0.8244 (m-80) REVERT: C 94 ASN cc_start: 0.9268 (t0) cc_final: 0.8981 (t0) REVERT: D 43 LYS cc_start: 0.8802 (ttpt) cc_final: 0.8468 (ttpt) REVERT: G 24 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7574 (mm-40) REVERT: G 61 GLU cc_start: 0.8814 (tp30) cc_final: 0.8601 (tm-30) REVERT: G 84 GLN cc_start: 0.9251 (tp-100) cc_final: 0.8946 (tp40) REVERT: H 101 LEU cc_start: 0.8426 (mm) cc_final: 0.8030 (mt) REVERT: K 3 GLU cc_start: 0.8268 (tp30) cc_final: 0.8060 (tp30) REVERT: K 5 VAL cc_start: 0.8852 (m) cc_final: 0.8524 (t) REVERT: K 70 ASP cc_start: 0.8147 (t70) cc_final: 0.7850 (t0) REVERT: K 124 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7580 (mtp-110) REVERT: K 152 VAL cc_start: 0.9563 (t) cc_final: 0.9354 (p) REVERT: K 170 ARG cc_start: 0.8440 (ptm160) cc_final: 0.7878 (ttm170) REVERT: K 175 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8878 (tt) REVERT: K 185 HIS cc_start: 0.8342 (m-70) cc_final: 0.7646 (m-70) REVERT: K 191 MET cc_start: 0.6097 (mtt) cc_final: 0.5212 (tmm) outliers start: 42 outliers final: 26 residues processed: 303 average time/residue: 0.3295 time to fit residues: 132.0910 Evaluate side-chains 294 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 266 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 124 ARG Chi-restraints excluded: chain K residue 175 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 0 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 ASN H 82 HIS ** K 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13936 Z= 0.272 Angle : 0.632 6.126 20016 Z= 0.365 Chirality : 0.038 0.181 2270 Planarity : 0.005 0.072 1559 Dihedral : 31.464 178.133 4054 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 7.14 % Allowed : 21.56 % Favored : 71.30 % 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: 0.18 (0.29), residues: 905 helix: 0.99 (0.22), residues: 604 sheet: 0.52 (0.83), residues: 38 loop : -1.99 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 28 HIS 0.002 0.001 HIS B 75 PHE 0.012 0.001 PHE A 67 TYR 0.026 0.002 TYR K 160 ARG 0.006 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 269 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8477 (mpp80) cc_final: 0.7946 (mtm-85) REVERT: B 84 MET cc_start: 0.8000 (mmm) cc_final: 0.7660 (mmm) REVERT: B 88 TYR cc_start: 0.8753 (m-10) cc_final: 0.8200 (m-80) REVERT: C 61 GLU cc_start: 0.7966 (tp30) cc_final: 0.7209 (tp30) REVERT: C 94 ASN cc_start: 0.9329 (t0) cc_final: 0.9053 (t0) REVERT: D 43 LYS cc_start: 0.8789 (ttpt) cc_final: 0.8471 (tmmt) REVERT: E 85 ASN cc_start: 0.8661 (m-40) cc_final: 0.8413 (m-40) REVERT: E 127 GLN cc_start: 0.8255 (mm-40) cc_final: 0.8004 (mm-40) REVERT: G 24 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7589 (mm-40) REVERT: G 84 GLN cc_start: 0.9250 (tp-100) cc_final: 0.9006 (tp40) REVERT: H 101 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.7973 (mt) REVERT: K 70 ASP cc_start: 0.8194 (t70) cc_final: 0.7834 (t0) REVERT: K 86 PHE cc_start: 0.8487 (m-80) cc_final: 0.8286 (m-80) REVERT: K 123 PHE cc_start: 0.7874 (m-80) cc_final: 0.7607 (m-80) REVERT: K 170 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7914 (ttm170) REVERT: K 175 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8880 (tt) REVERT: K 191 MET cc_start: 0.6214 (mtt) cc_final: 0.5429 (tmm) REVERT: K 196 ARG cc_start: 0.7504 (ttm-80) cc_final: 0.7030 (ttm170) outliers start: 56 outliers final: 41 residues processed: 295 average time/residue: 0.3061 time to fit residues: 121.1042 Evaluate side-chains 304 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 260 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 114 ARG Chi-restraints excluded: chain K residue 156 SER Chi-restraints excluded: chain K residue 170 ARG Chi-restraints excluded: chain K residue 175 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 51 optimal weight: 0.0980 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 57 optimal weight: 9.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN H 82 HIS ** K 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13936 Z= 0.180 Angle : 0.593 8.238 20016 Z= 0.345 Chirality : 0.036 0.159 2270 Planarity : 0.004 0.058 1559 Dihedral : 31.218 179.648 4054 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.46 % Allowed : 24.36 % Favored : 71.17 % 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: 0.48 (0.29), residues: 905 helix: 1.21 (0.22), residues: 608 sheet: 0.61 (0.85), residues: 38 loop : -1.90 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 137 HIS 0.006 0.001 HIS H 82 PHE 0.017 0.001 PHE K 206 TYR 0.014 0.002 TYR C 50 ARG 0.007 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 283 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8293 (mpp80) cc_final: 0.7922 (mtm-85) REVERT: B 84 MET cc_start: 0.7826 (mmm) cc_final: 0.7504 (mmm) REVERT: B 88 TYR cc_start: 0.8740 (m-10) cc_final: 0.8241 (m-80) REVERT: C 35 ARG cc_start: 0.8440 (ttp-170) cc_final: 0.8229 (ttp-110) REVERT: C 74 LYS cc_start: 0.8763 (mtmt) cc_final: 0.8509 (mtmm) REVERT: C 94 ASN cc_start: 0.9288 (t0) cc_final: 0.9005 (t0) REVERT: D 43 LYS cc_start: 0.8749 (ttpt) cc_final: 0.8354 (ttpt) REVERT: E 85 ASN cc_start: 0.8615 (m-40) cc_final: 0.8301 (m-40) REVERT: G 24 GLN cc_start: 0.7761 (mm-40) cc_final: 0.7553 (mm-40) REVERT: G 39 TYR cc_start: 0.8915 (m-10) cc_final: 0.8303 (m-80) REVERT: G 84 GLN cc_start: 0.9145 (tp-100) cc_final: 0.8909 (tp40) REVERT: H 62 MET cc_start: 0.8880 (tpp) cc_final: 0.8654 (tpp) REVERT: H 86 ARG cc_start: 0.8801 (tpp80) cc_final: 0.8530 (tpp80) REVERT: H 101 LEU cc_start: 0.8339 (mm) cc_final: 0.7989 (mt) REVERT: K 5 VAL cc_start: 0.8626 (m) cc_final: 0.8329 (t) REVERT: K 70 ASP cc_start: 0.8191 (t70) cc_final: 0.7864 (t0) REVERT: K 74 MET cc_start: 0.8382 (tpt) cc_final: 0.8107 (tpt) REVERT: K 88 MET cc_start: 0.3190 (mmm) cc_final: 0.2873 (mmm) REVERT: K 108 PHE cc_start: 0.8826 (t80) cc_final: 0.8620 (t80) REVERT: K 122 SER cc_start: 0.8215 (OUTLIER) cc_final: 0.7939 (p) REVERT: K 152 VAL cc_start: 0.9561 (t) cc_final: 0.9310 (p) REVERT: K 170 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7674 (ttm170) REVERT: K 175 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8698 (tt) REVERT: K 185 HIS cc_start: 0.8541 (m-70) cc_final: 0.7834 (m-70) REVERT: K 191 MET cc_start: 0.5769 (mtt) cc_final: 0.5445 (tmm) outliers start: 35 outliers final: 25 residues processed: 300 average time/residue: 0.2999 time to fit residues: 121.3459 Evaluate side-chains 288 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 260 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 156 SER Chi-restraints excluded: chain K residue 170 ARG Chi-restraints excluded: chain K residue 175 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 20.0000 chunk 12 optimal weight: 0.2980 chunk 62 optimal weight: 7.9990 chunk 80 optimal weight: 20.0000 chunk 92 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 109 optimal weight: 40.0000 chunk 68 optimal weight: 30.0000 chunk 66 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN H 82 HIS ** K 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13936 Z= 0.201 Angle : 0.604 7.534 20016 Z= 0.348 Chirality : 0.036 0.206 2270 Planarity : 0.004 0.052 1559 Dihedral : 31.174 178.467 4054 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.46 % Allowed : 25.38 % Favored : 70.15 % 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: 0.71 (0.29), residues: 905 helix: 1.34 (0.22), residues: 607 sheet: 0.63 (0.85), residues: 38 loop : -1.66 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 28 HIS 0.007 0.001 HIS H 82 PHE 0.010 0.001 PHE K 206 TYR 0.027 0.002 TYR K 160 ARG 0.007 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 267 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8401 (mpp80) cc_final: 0.7986 (mtm-85) REVERT: B 84 MET cc_start: 0.7839 (mmm) cc_final: 0.7584 (mmm) REVERT: B 88 TYR cc_start: 0.8737 (m-10) cc_final: 0.8198 (m-80) REVERT: C 61 GLU cc_start: 0.7796 (tp30) cc_final: 0.7578 (tp30) REVERT: C 94 ASN cc_start: 0.9276 (t0) cc_final: 0.8976 (t0) REVERT: D 43 LYS cc_start: 0.8737 (ttpt) cc_final: 0.8337 (ttpt) REVERT: E 58 THR cc_start: 0.9086 (p) cc_final: 0.8665 (t) REVERT: E 85 ASN cc_start: 0.8588 (m-40) cc_final: 0.8282 (m-40) REVERT: G 39 TYR cc_start: 0.8957 (m-10) cc_final: 0.8372 (m-80) REVERT: G 84 GLN cc_start: 0.9149 (tp-100) cc_final: 0.8925 (tp40) REVERT: H 86 ARG cc_start: 0.8768 (tpp80) cc_final: 0.8488 (tpp80) REVERT: H 101 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8053 (mt) REVERT: K 5 VAL cc_start: 0.8642 (m) cc_final: 0.8366 (t) REVERT: K 70 ASP cc_start: 0.8211 (t70) cc_final: 0.7874 (t0) REVERT: K 74 MET cc_start: 0.8361 (tpt) cc_final: 0.8115 (tpt) REVERT: K 122 SER cc_start: 0.8146 (OUTLIER) cc_final: 0.7918 (p) REVERT: K 123 PHE cc_start: 0.7780 (m-80) cc_final: 0.7476 (m-80) REVERT: K 152 VAL cc_start: 0.9566 (t) cc_final: 0.9252 (m) REVERT: K 170 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7625 (ttm170) REVERT: K 191 MET cc_start: 0.6119 (mtt) cc_final: 0.5862 (ttm) REVERT: K 196 ARG cc_start: 0.7419 (ttm-80) cc_final: 0.6888 (ttm-80) outliers start: 35 outliers final: 27 residues processed: 282 average time/residue: 0.3219 time to fit residues: 121.5415 Evaluate side-chains 293 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 263 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 170 ARG Chi-restraints excluded: chain K residue 175 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 69 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 HIS H 84 ASN ** K 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13936 Z= 0.225 Angle : 0.611 8.761 20016 Z= 0.352 Chirality : 0.036 0.189 2270 Planarity : 0.004 0.053 1559 Dihedral : 31.169 178.035 4054 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.85 % Allowed : 25.26 % Favored : 69.90 % 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: 0.75 (0.29), residues: 905 helix: 1.36 (0.22), residues: 611 sheet: 0.69 (0.84), residues: 38 loop : -1.65 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 28 HIS 0.007 0.001 HIS H 82 PHE 0.013 0.001 PHE K 162 TYR 0.021 0.002 TYR K 160 ARG 0.009 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 262 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8416 (mpp80) cc_final: 0.7987 (mtm-85) REVERT: B 49 LEU cc_start: 0.8032 (mt) cc_final: 0.7670 (mm) REVERT: B 84 MET cc_start: 0.7879 (mmm) cc_final: 0.7636 (mmm) REVERT: B 88 TYR cc_start: 0.8743 (m-10) cc_final: 0.8231 (m-80) REVERT: C 61 GLU cc_start: 0.7800 (tp30) cc_final: 0.7566 (tp30) REVERT: C 94 ASN cc_start: 0.9340 (t0) cc_final: 0.9047 (t0) REVERT: E 58 THR cc_start: 0.9080 (p) cc_final: 0.8671 (t) REVERT: E 85 ASN cc_start: 0.8627 (m-40) cc_final: 0.8300 (m-40) REVERT: G 84 GLN cc_start: 0.9157 (tp-100) cc_final: 0.8907 (tp40) REVERT: H 101 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8057 (mt) REVERT: K 70 ASP cc_start: 0.8221 (t70) cc_final: 0.7904 (t0) REVERT: K 74 MET cc_start: 0.8375 (tpt) cc_final: 0.8137 (tpt) REVERT: K 122 SER cc_start: 0.8152 (OUTLIER) cc_final: 0.7913 (p) REVERT: K 123 PHE cc_start: 0.7689 (m-80) cc_final: 0.7428 (m-80) REVERT: K 170 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7755 (ttm170) REVERT: K 175 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8688 (tt) REVERT: K 185 HIS cc_start: 0.8650 (m-70) cc_final: 0.7980 (m-70) REVERT: K 196 ARG cc_start: 0.7419 (ttm-80) cc_final: 0.6906 (ttm-80) outliers start: 38 outliers final: 29 residues processed: 279 average time/residue: 0.3062 time to fit residues: 114.3489 Evaluate side-chains 289 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 256 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 170 ARG Chi-restraints excluded: chain K residue 175 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 105 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN H 67 ASN H 82 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13936 Z= 0.296 Angle : 0.655 8.738 20016 Z= 0.373 Chirality : 0.038 0.205 2270 Planarity : 0.004 0.049 1559 Dihedral : 31.292 177.324 4054 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 5.10 % Allowed : 26.15 % Favored : 68.75 % 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: 0.63 (0.29), residues: 905 helix: 1.21 (0.22), residues: 612 sheet: 0.89 (0.82), residues: 38 loop : -1.59 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 28 HIS 0.005 0.001 HIS H 82 PHE 0.017 0.001 PHE K 108 TYR 0.018 0.002 TYR K 154 ARG 0.008 0.001 ARG K 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 256 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8432 (mpp80) cc_final: 0.8048 (mtm-85) REVERT: B 84 MET cc_start: 0.7907 (mmm) cc_final: 0.7667 (mmm) REVERT: B 88 TYR cc_start: 0.8784 (m-10) cc_final: 0.8245 (m-80) REVERT: C 61 GLU cc_start: 0.7925 (tp30) cc_final: 0.7694 (tp30) REVERT: C 94 ASN cc_start: 0.9368 (t0) cc_final: 0.9055 (t0) REVERT: E 58 THR cc_start: 0.9105 (p) cc_final: 0.8679 (t) REVERT: E 85 ASN cc_start: 0.8615 (m-40) cc_final: 0.8375 (m-40) REVERT: G 84 GLN cc_start: 0.9188 (tp-100) cc_final: 0.8906 (tp40) REVERT: H 86 ARG cc_start: 0.8822 (tpp80) cc_final: 0.8578 (tpp80) REVERT: H 101 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8090 (mt) REVERT: K 70 ASP cc_start: 0.8211 (t70) cc_final: 0.7871 (t0) REVERT: K 74 MET cc_start: 0.8417 (tpt) cc_final: 0.8152 (tpt) REVERT: K 122 SER cc_start: 0.8120 (OUTLIER) cc_final: 0.7888 (p) REVERT: K 123 PHE cc_start: 0.7721 (m-80) cc_final: 0.7449 (m-80) REVERT: K 170 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7915 (ttm170) REVERT: K 185 HIS cc_start: 0.8639 (m-70) cc_final: 0.7947 (m-70) REVERT: K 196 ARG cc_start: 0.7399 (ttm-80) cc_final: 0.6952 (ttm170) outliers start: 40 outliers final: 30 residues processed: 273 average time/residue: 0.3141 time to fit residues: 114.9616 Evaluate side-chains 283 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 250 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 156 SER Chi-restraints excluded: chain K residue 170 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 113 optimal weight: 20.0000 chunk 104 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 20.0000 chunk 55 optimal weight: 0.4980 chunk 71 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS H 82 HIS H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13936 Z= 0.228 Angle : 0.635 9.260 20016 Z= 0.363 Chirality : 0.037 0.185 2270 Planarity : 0.004 0.057 1559 Dihedral : 31.191 178.306 4054 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.83 % Allowed : 27.17 % Favored : 69.01 % 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: 0.74 (0.29), residues: 905 helix: 1.32 (0.22), residues: 611 sheet: 1.00 (0.83), residues: 38 loop : -1.62 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 28 HIS 0.007 0.001 HIS H 82 PHE 0.014 0.001 PHE K 162 TYR 0.017 0.002 TYR D 40 ARG 0.011 0.001 ARG F 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 257 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8330 (mpp80) cc_final: 0.7938 (mtm-85) REVERT: B 88 TYR cc_start: 0.8766 (m-10) cc_final: 0.8222 (m-80) REVERT: C 61 GLU cc_start: 0.7825 (tp30) cc_final: 0.7594 (tp30) REVERT: C 94 ASN cc_start: 0.9345 (t0) cc_final: 0.9066 (t0) REVERT: E 58 THR cc_start: 0.9026 (p) cc_final: 0.8623 (t) REVERT: E 85 ASN cc_start: 0.8602 (m-40) cc_final: 0.8362 (m-40) REVERT: G 39 TYR cc_start: 0.8829 (m-10) cc_final: 0.8566 (m-80) REVERT: G 84 GLN cc_start: 0.9163 (tp-100) cc_final: 0.8877 (tp40) REVERT: H 86 ARG cc_start: 0.8740 (tpp80) cc_final: 0.8500 (tpp80) REVERT: H 101 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8039 (mt) REVERT: K 7 GLU cc_start: 0.8422 (pm20) cc_final: 0.8198 (pm20) REVERT: K 70 ASP cc_start: 0.8206 (t70) cc_final: 0.7883 (t0) REVERT: K 74 MET cc_start: 0.8372 (tpt) cc_final: 0.8101 (tpt) REVERT: K 122 SER cc_start: 0.8068 (OUTLIER) cc_final: 0.7829 (p) REVERT: K 123 PHE cc_start: 0.7693 (m-80) cc_final: 0.7428 (m-80) REVERT: K 170 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7850 (ttm170) REVERT: K 185 HIS cc_start: 0.8643 (m-70) cc_final: 0.7993 (m-70) outliers start: 30 outliers final: 26 residues processed: 270 average time/residue: 0.3135 time to fit residues: 113.6165 Evaluate side-chains 281 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 252 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 156 SER Chi-restraints excluded: chain K residue 170 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 10.0000 chunk 13 optimal weight: 0.0980 chunk 25 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 HIS H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.129769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.092009 restraints weight = 26283.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.094432 restraints weight = 15294.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.095969 restraints weight = 11099.990| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13936 Z= 0.183 Angle : 0.612 9.352 20016 Z= 0.351 Chirality : 0.035 0.187 2270 Planarity : 0.004 0.048 1559 Dihedral : 30.988 179.176 4054 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.93 % Allowed : 28.06 % Favored : 69.01 % 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 (0.29), residues: 905 helix: 1.49 (0.22), residues: 603 sheet: 1.11 (0.83), residues: 38 loop : -1.29 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 137 HIS 0.009 0.001 HIS H 82 PHE 0.016 0.001 PHE K 162 TYR 0.021 0.002 TYR K 154 ARG 0.009 0.001 ARG F 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2654.63 seconds wall clock time: 48 minutes 32.26 seconds (2912.26 seconds total)