Starting phenix.real_space_refine on Sun Aug 4 07:27:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ybk_39120/08_2024/8ybk_39120.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ybk_39120/08_2024/8ybk_39120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ybk_39120/08_2024/8ybk_39120.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ybk_39120/08_2024/8ybk_39120.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ybk_39120/08_2024/8ybk_39120.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ybk_39120/08_2024/8ybk_39120.cif" } resolution = 2.69 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 228 5.49 5 S 14 5.16 5 C 5726 2.51 5 N 1932 2.21 5 O 2361 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 83": "NH1" <-> "NH2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B ARG 36": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 40": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 55": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "C ARG 11": "NH1" <-> "NH2" Residue "C ARG 17": "NH1" <-> "NH2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C ARG 29": "NH1" <-> "NH2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "D ARG 31": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D ARG 79": "NH1" <-> "NH2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "D ARG 99": "NH1" <-> "NH2" Residue "E ARG 63": "NH1" <-> "NH2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E ARG 83": "NH1" <-> "NH2" Residue "E ARG 116": "NH1" <-> "NH2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ARG 35": "NH1" <-> "NH2" Residue "F ARG 36": "NH1" <-> "NH2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F ARG 40": "NH1" <-> "NH2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F ARG 78": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G ARG 17": "NH1" <-> "NH2" Residue "G ARG 20": "NH1" <-> "NH2" Residue "G ARG 29": "NH1" <-> "NH2" Residue "G ARG 32": "NH1" <-> "NH2" Residue "G ARG 35": "NH1" <-> "NH2" Residue "G ARG 42": "NH1" <-> "NH2" Residue "G ARG 71": "NH1" <-> "NH2" Residue "G ARG 77": "NH1" <-> "NH2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G ARG 88": "NH1" <-> "NH2" Residue "G ARG 99": "NH1" <-> "NH2" Residue "H ARG 33": "NH1" <-> "NH2" Residue "H ARG 72": "NH1" <-> "NH2" Residue "H ARG 79": "NH1" <-> "NH2" Residue "H ARG 86": "NH1" <-> "NH2" Residue "H ARG 92": "NH1" <-> "NH2" Residue "H ARG 99": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10261 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 632 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 764 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 773 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 2321 Classifications: {'DNA': 114} Link IDs: {'rna3p': 113} Chain: "J" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 2353 Classifications: {'DNA': 114} Link IDs: {'rna3p': 113} Time building chain proxies: 6.05, per 1000 atoms: 0.59 Number of scatterers: 10261 At special positions: 0 Unit cell: (113.42, 122.96, 109.18, 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 14 16.00 P 228 15.00 O 2361 8.00 N 1932 7.00 C 5726 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: 4.57 Conformation dependent library (CDL) restraints added in 1.1 seconds 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1316 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 73.0% alpha, 3.1% beta 114 base pairs and 211 stacking pairs defined. Time for finding SS restraints: 5.22 Creating SS restraints... Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.505A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.736A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.894A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.375A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 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 Processing helix chain 'D' and resid 103 through 124 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.638A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.887A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.486A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.551A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.580A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.916A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.046A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.939A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.051A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 389 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 296 hydrogen bonds 592 hydrogen bond angles 0 basepair planarities 114 basepair parallelities 211 stacking parallelities Total time for adding SS restraints: 4.01 Time building geometry restraints manager: 4.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1361 1.32 - 1.44: 3911 1.44 - 1.57: 5143 1.57 - 1.69: 456 1.69 - 1.81: 24 Bond restraints: 10895 Sorted by residual: bond pdb=" C ILE B 26 " pdb=" O ILE B 26 " ideal model delta sigma weight residual 1.237 1.197 0.040 1.23e-02 6.61e+03 1.07e+01 bond pdb=" C ASN D 67 " pdb=" O ASN D 67 " ideal model delta sigma weight residual 1.236 1.201 0.035 1.15e-02 7.56e+03 9.51e+00 bond pdb=" CZ ARG G 29 " pdb=" NH2 ARG G 29 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.40e+00 bond pdb=" CA ARG G 81 " pdb=" CB ARG G 81 " ideal model delta sigma weight residual 1.528 1.576 -0.047 1.56e-02 4.11e+03 9.16e+00 bond pdb=" CZ ARG C 29 " pdb=" NH2 ARG C 29 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 9.07e+00 ... (remaining 10890 not shown) Histogram of bond angle deviations from ideal: 98.10 - 105.22: 977 105.22 - 112.34: 5954 112.34 - 119.46: 3476 119.46 - 126.58: 4591 126.58 - 133.70: 677 Bond angle restraints: 15675 Sorted by residual: angle pdb=" CA HIS D 82 " pdb=" CB HIS D 82 " pdb=" CG HIS D 82 " ideal model delta sigma weight residual 113.80 109.84 3.96 1.00e+00 1.00e+00 1.57e+01 angle pdb=" O3' DA I -13 " pdb=" C3' DA I -13 " pdb=" C2' DA I -13 " ideal model delta sigma weight residual 111.50 117.43 -5.93 1.50e+00 4.44e-01 1.56e+01 angle pdb=" C4' DG I -55 " pdb=" C3' DG I -55 " pdb=" O3' DG I -55 " ideal model delta sigma weight residual 110.00 115.89 -5.89 1.50e+00 4.44e-01 1.54e+01 angle pdb=" OE1 GLN E 85 " pdb=" CD GLN E 85 " pdb=" NE2 GLN E 85 " ideal model delta sigma weight residual 122.60 118.69 3.91 1.00e+00 1.00e+00 1.53e+01 angle pdb=" C4' DT I -17 " pdb=" C3' DT I -17 " pdb=" O3' DT I -17 " ideal model delta sigma weight residual 110.00 104.14 5.86 1.50e+00 4.44e-01 1.52e+01 ... (remaining 15670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.78: 4002 19.78 - 39.55: 945 39.55 - 59.33: 953 59.33 - 79.11: 56 79.11 - 98.88: 7 Dihedral angle restraints: 5963 sinusoidal: 3921 harmonic: 2042 Sorted by residual: dihedral pdb=" CA LEU E 61 " pdb=" C LEU E 61 " pdb=" N ILE E 62 " pdb=" CA ILE E 62 " ideal model delta harmonic sigma weight residual 180.00 151.54 28.46 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA LEU A 61 " pdb=" C LEU A 61 " pdb=" N ILE A 62 " pdb=" CA ILE A 62 " ideal model delta harmonic sigma weight residual 180.00 153.36 26.64 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA VAL G 107 " pdb=" C VAL G 107 " pdb=" N LEU G 108 " pdb=" CA LEU G 108 " ideal model delta harmonic sigma weight residual 180.00 -154.21 -25.79 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 5960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1534 0.062 - 0.124: 209 0.124 - 0.186: 35 0.186 - 0.248: 9 0.248 - 0.310: 2 Chirality restraints: 1789 Sorted by residual: chirality pdb=" CA ARG B 40 " pdb=" N ARG B 40 " pdb=" C ARG B 40 " pdb=" CB ARG B 40 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CA LYS C 36 " pdb=" N LYS C 36 " pdb=" C LYS C 36 " pdb=" CB LYS C 36 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA GLU H 71 " pdb=" N GLU H 71 " pdb=" C GLU H 71 " pdb=" CB GLU H 71 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 1786 not shown) Planarity restraints: 1195 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I -7 " -0.099 2.00e-02 2.50e+03 6.11e-02 1.12e+02 pdb=" N9 DG I -7 " -0.020 2.00e-02 2.50e+03 pdb=" C8 DG I -7 " 0.117 2.00e-02 2.50e+03 pdb=" N7 DG I -7 " 0.077 2.00e-02 2.50e+03 pdb=" C5 DG I -7 " -0.024 2.00e-02 2.50e+03 pdb=" C6 DG I -7 " -0.037 2.00e-02 2.50e+03 pdb=" O6 DG I -7 " -0.076 2.00e-02 2.50e+03 pdb=" N1 DG I -7 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DG I -7 " 0.015 2.00e-02 2.50e+03 pdb=" N2 DG I -7 " 0.080 2.00e-02 2.50e+03 pdb=" N3 DG I -7 " -0.008 2.00e-02 2.50e+03 pdb=" C4 DG I -7 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -11 " 0.089 2.00e-02 2.50e+03 5.96e-02 1.07e+02 pdb=" N9 DG I -11 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DG I -11 " -0.105 2.00e-02 2.50e+03 pdb=" N7 DG I -11 " -0.085 2.00e-02 2.50e+03 pdb=" C5 DG I -11 " 0.013 2.00e-02 2.50e+03 pdb=" C6 DG I -11 " 0.040 2.00e-02 2.50e+03 pdb=" O6 DG I -11 " 0.069 2.00e-02 2.50e+03 pdb=" N1 DG I -11 " 0.017 2.00e-02 2.50e+03 pdb=" C2 DG I -11 " -0.020 2.00e-02 2.50e+03 pdb=" N2 DG I -11 " -0.087 2.00e-02 2.50e+03 pdb=" N3 DG I -11 " 0.014 2.00e-02 2.50e+03 pdb=" C4 DG I -11 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -13 " 0.111 2.00e-02 2.50e+03 5.95e-02 9.75e+01 pdb=" N9 DA I -13 " 0.008 2.00e-02 2.50e+03 pdb=" C8 DA I -13 " -0.102 2.00e-02 2.50e+03 pdb=" N7 DA I -13 " -0.050 2.00e-02 2.50e+03 pdb=" C5 DA I -13 " 0.022 2.00e-02 2.50e+03 pdb=" C6 DA I -13 " 0.027 2.00e-02 2.50e+03 pdb=" N6 DA I -13 " 0.087 2.00e-02 2.50e+03 pdb=" N1 DA I -13 " -0.026 2.00e-02 2.50e+03 pdb=" C2 DA I -13 " -0.055 2.00e-02 2.50e+03 pdb=" N3 DA I -13 " -0.032 2.00e-02 2.50e+03 pdb=" C4 DA I -13 " 0.010 2.00e-02 2.50e+03 ... (remaining 1192 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 3137 2.87 - 3.38: 8636 3.38 - 3.89: 20259 3.89 - 4.39: 23298 4.39 - 4.90: 32409 Nonbonded interactions: 87739 Sorted by model distance: nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 68 " model vdw 2.369 3.040 nonbonded pdb=" OD2 ASP E 106 " pdb=" NE ARG E 131 " model vdw 2.423 3.120 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.427 3.040 nonbonded pdb=" NH1 ARG A 72 " pdb=" OP1 DC I -23 " model vdw 2.440 3.120 nonbonded pdb=" O ALA D 124 " pdb=" OXT LYS D 125 " model vdw 2.446 3.040 ... (remaining 87734 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 58 through 135) } ncs_group { reference = (chain 'B' and resid 22 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 10 through 108) } ncs_group { reference = (chain 'D' and resid 32 through 125) 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 34.700 Find NCS groups from input model: 0.260 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:13.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 0.047 10895 Z= 0.409 Angle : 0.994 8.212 15675 Z= 0.636 Chirality : 0.048 0.310 1789 Planarity : 0.014 0.125 1195 Dihedral : 27.854 98.881 4647 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 14.78 % Favored : 85.22 % 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: 1.55 (0.30), residues: 692 helix: 1.85 (0.22), residues: 506 sheet: None (None), residues: 0 loop : -1.32 (0.36), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS D 82 PHE 0.054 0.004 PHE H 70 TYR 0.068 0.005 TYR H 42 ARG 0.017 0.002 ARG E 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.755 Fit side-chains REVERT: C 75 LYS cc_start: 0.8227 (mttp) cc_final: 0.7490 (tptt) REVERT: C 95 LYS cc_start: 0.8838 (tttt) cc_final: 0.8233 (ttpt) REVERT: E 94 GLU cc_start: 0.8407 (tp30) cc_final: 0.8166 (mm-30) REVERT: F 39 ARG cc_start: 0.8046 (mpt180) cc_final: 0.7800 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 1.9057 time to fit residues: 278.4225 Evaluate side-chains 126 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 26 optimal weight: 0.1980 chunk 42 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 104 GLN D 82 HIS D 84 ASN E 76 GLN G 24 GLN H 63 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10895 Z= 0.194 Angle : 0.548 5.246 15675 Z= 0.337 Chirality : 0.034 0.144 1789 Planarity : 0.004 0.039 1195 Dihedral : 29.873 100.565 3267 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 1.89 % Allowed : 16.32 % Favored : 81.79 % 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: 2.72 (0.31), residues: 692 helix: 2.77 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.29 (0.37), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE B 61 TYR 0.009 0.001 TYR F 51 ARG 0.008 0.001 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8142 (tt0) cc_final: 0.7725 (tt0) REVERT: B 25 ASN cc_start: 0.8117 (m-40) cc_final: 0.7914 (m-40) REVERT: B 35 ARG cc_start: 0.8779 (mtp85) cc_final: 0.8517 (mtp180) REVERT: C 75 LYS cc_start: 0.8090 (mttp) cc_final: 0.7377 (tptt) REVERT: E 94 GLU cc_start: 0.8313 (tp30) cc_final: 0.8101 (mm-30) REVERT: H 113 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8288 (mm-30) outliers start: 11 outliers final: 4 residues processed: 133 average time/residue: 1.8474 time to fit residues: 257.2901 Evaluate side-chains 129 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 125 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 82 HIS D 84 ASN E 76 GLN G 104 GLN H 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 10895 Z= 0.396 Angle : 0.622 5.502 15675 Z= 0.372 Chirality : 0.040 0.140 1789 Planarity : 0.005 0.041 1195 Dihedral : 30.349 91.737 3267 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.41 % Allowed : 15.64 % Favored : 81.96 % 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: 2.37 (0.31), residues: 692 helix: 2.55 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.51 (0.36), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 113 PHE 0.009 0.002 PHE B 100 TYR 0.010 0.002 TYR G 50 ARG 0.009 0.001 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8788 (mtp85) cc_final: 0.8586 (mtp180) REVERT: B 93 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8145 (mm-40) REVERT: C 75 LYS cc_start: 0.8196 (mttp) cc_final: 0.7521 (tptt) REVERT: F 93 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8286 (mm-40) REVERT: G 75 LYS cc_start: 0.8204 (mmmt) cc_final: 0.7274 (tptt) outliers start: 14 outliers final: 7 residues processed: 130 average time/residue: 2.0183 time to fit residues: 274.7106 Evaluate side-chains 130 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 121 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 8 optimal weight: 0.0980 chunk 38 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 104 GLN D 82 HIS E 76 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10895 Z= 0.190 Angle : 0.573 8.863 15675 Z= 0.348 Chirality : 0.035 0.132 1789 Planarity : 0.004 0.040 1195 Dihedral : 30.287 94.752 3267 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.06 % Allowed : 17.01 % Favored : 80.93 % 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: 2.72 (0.31), residues: 692 helix: 2.80 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.43 (0.37), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE B 61 TYR 0.008 0.001 TYR G 50 ARG 0.007 0.001 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 0.779 Fit side-chains REVERT: A 73 GLU cc_start: 0.8237 (tt0) cc_final: 0.7824 (tt0) REVERT: B 25 ASN cc_start: 0.8315 (m-40) cc_final: 0.8104 (m-40) REVERT: B 35 ARG cc_start: 0.8771 (mtp85) cc_final: 0.8564 (mtp180) REVERT: B 93 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8143 (mm-40) REVERT: C 75 LYS cc_start: 0.8185 (mttp) cc_final: 0.7534 (tptt) REVERT: E 133 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8529 (mt-10) REVERT: F 24 ASP cc_start: 0.7154 (t0) cc_final: 0.6910 (t70) REVERT: G 75 LYS cc_start: 0.8154 (mmmt) cc_final: 0.7388 (tmtt) REVERT: H 71 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7888 (mt-10) outliers start: 12 outliers final: 4 residues processed: 134 average time/residue: 1.8931 time to fit residues: 265.4796 Evaluate side-chains 128 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 121 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 82 HIS E 76 GLN G 104 GLN H 63 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 10895 Z= 0.348 Angle : 0.606 6.565 15675 Z= 0.363 Chirality : 0.038 0.137 1789 Planarity : 0.005 0.040 1195 Dihedral : 30.254 94.035 3267 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.75 % Allowed : 16.84 % Favored : 80.41 % 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: 2.45 (0.31), residues: 692 helix: 2.60 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.52 (0.36), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 113 PHE 0.008 0.002 PHE B 61 TYR 0.010 0.002 TYR H 121 ARG 0.007 0.001 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 0.752 Fit side-chains REVERT: B 29 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7645 (mm) REVERT: B 35 ARG cc_start: 0.8837 (mtp85) cc_final: 0.8620 (mtp180) REVERT: B 93 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8224 (mm-40) REVERT: C 75 LYS cc_start: 0.8174 (mttp) cc_final: 0.7452 (tptt) REVERT: E 133 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8552 (mt-10) REVERT: F 24 ASP cc_start: 0.7238 (t0) cc_final: 0.6950 (t70) REVERT: G 75 LYS cc_start: 0.8072 (mmmt) cc_final: 0.7347 (tptt) outliers start: 16 outliers final: 7 residues processed: 133 average time/residue: 1.9209 time to fit residues: 267.2422 Evaluate side-chains 128 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 0.0770 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 104 GLN D 82 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN G 104 GLN H 47 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10895 Z= 0.226 Angle : 0.577 7.552 15675 Z= 0.351 Chirality : 0.035 0.135 1789 Planarity : 0.004 0.039 1195 Dihedral : 30.245 94.807 3267 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.89 % Allowed : 17.87 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.66 (0.31), residues: 692 helix: 2.76 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.46 (0.36), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE B 61 TYR 0.009 0.001 TYR F 51 ARG 0.007 0.000 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 0.755 Fit side-chains REVERT: B 29 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7630 (mm) REVERT: B 35 ARG cc_start: 0.8768 (mtp85) cc_final: 0.8563 (mtp180) REVERT: B 93 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8156 (mm-40) REVERT: C 75 LYS cc_start: 0.8163 (mttp) cc_final: 0.7451 (tptt) REVERT: F 24 ASP cc_start: 0.7198 (t0) cc_final: 0.6927 (t70) REVERT: G 75 LYS cc_start: 0.8070 (mmmt) cc_final: 0.7319 (tptt) outliers start: 11 outliers final: 6 residues processed: 127 average time/residue: 1.9516 time to fit residues: 259.1759 Evaluate side-chains 127 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 119 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 74 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.6980 chunk 48 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 104 GLN D 82 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN G 104 GLN H 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10895 Z= 0.217 Angle : 0.576 9.352 15675 Z= 0.348 Chirality : 0.035 0.132 1789 Planarity : 0.004 0.039 1195 Dihedral : 30.208 95.792 3267 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.55 % Allowed : 17.70 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.73 (0.31), residues: 692 helix: 2.81 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.43 (0.36), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE B 61 TYR 0.009 0.001 TYR B 51 ARG 0.002 0.000 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 0.871 Fit side-chains REVERT: B 29 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7617 (mm) REVERT: B 35 ARG cc_start: 0.8766 (mtp85) cc_final: 0.8551 (mtp180) REVERT: B 93 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8137 (mm-40) REVERT: C 75 LYS cc_start: 0.8167 (mttp) cc_final: 0.7456 (tptt) REVERT: F 24 ASP cc_start: 0.7195 (t0) cc_final: 0.6931 (t70) REVERT: G 75 LYS cc_start: 0.8051 (mmmt) cc_final: 0.7291 (tptt) REVERT: H 71 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7818 (mt-10) outliers start: 9 outliers final: 5 residues processed: 127 average time/residue: 1.9360 time to fit residues: 257.0919 Evaluate side-chains 128 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 58 optimal weight: 0.0870 chunk 42 optimal weight: 0.7980 chunk 7 optimal weight: 0.0670 chunk 67 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 104 GLN D 82 HIS E 76 GLN G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10895 Z= 0.200 Angle : 0.569 6.231 15675 Z= 0.344 Chirality : 0.034 0.131 1789 Planarity : 0.004 0.039 1195 Dihedral : 30.170 96.450 3267 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.72 % Allowed : 18.04 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.79 (0.31), residues: 692 helix: 2.85 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.39 (0.37), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE D 65 TYR 0.009 0.001 TYR B 51 ARG 0.006 0.000 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 0.801 Fit side-chains REVERT: A 73 GLU cc_start: 0.8186 (tt0) cc_final: 0.7837 (tt0) REVERT: B 25 ASN cc_start: 0.8342 (m110) cc_final: 0.8021 (m-40) REVERT: B 29 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7630 (mm) REVERT: B 35 ARG cc_start: 0.8759 (mtp85) cc_final: 0.8552 (mtp180) REVERT: B 93 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8127 (mm-40) REVERT: C 75 LYS cc_start: 0.8164 (mttp) cc_final: 0.7452 (tptt) REVERT: E 120 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8106 (mtt) REVERT: F 24 ASP cc_start: 0.7187 (t0) cc_final: 0.6921 (t70) REVERT: G 75 LYS cc_start: 0.8034 (mmmt) cc_final: 0.7283 (tptt) REVERT: H 71 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7820 (mt-10) outliers start: 10 outliers final: 5 residues processed: 126 average time/residue: 2.0094 time to fit residues: 264.8769 Evaluate side-chains 126 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.3980 chunk 62 optimal weight: 0.6980 chunk 24 optimal weight: 0.2980 chunk 72 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 82 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 47 GLN H 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10895 Z= 0.196 Angle : 0.568 10.992 15675 Z= 0.342 Chirality : 0.034 0.130 1789 Planarity : 0.004 0.039 1195 Dihedral : 30.142 96.947 3267 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.55 % Allowed : 18.38 % Favored : 80.07 % 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: 2.84 (0.31), residues: 692 helix: 2.89 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -1.36 (0.37), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE B 61 TYR 0.009 0.001 TYR B 51 ARG 0.008 0.000 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 0.814 Fit side-chains REVERT: A 73 GLU cc_start: 0.8192 (tt0) cc_final: 0.7836 (tt0) REVERT: B 25 ASN cc_start: 0.8356 (m110) cc_final: 0.8036 (m-40) REVERT: B 29 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7583 (mm) REVERT: B 35 ARG cc_start: 0.8760 (mtp85) cc_final: 0.8551 (mtp180) REVERT: B 93 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8120 (mm-40) REVERT: C 75 LYS cc_start: 0.8166 (mttp) cc_final: 0.7449 (tptt) REVERT: E 120 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8096 (mtt) REVERT: F 24 ASP cc_start: 0.7184 (t0) cc_final: 0.6917 (t70) REVERT: G 75 LYS cc_start: 0.8010 (mmmt) cc_final: 0.7276 (tptt) REVERT: H 71 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7821 (mt-10) outliers start: 9 outliers final: 5 residues processed: 122 average time/residue: 1.9204 time to fit residues: 245.1383 Evaluate side-chains 124 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 21 optimal weight: 0.0070 chunk 65 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 82 HIS E 76 GLN F 25 ASN G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10895 Z= 0.290 Angle : 0.578 5.972 15675 Z= 0.349 Chirality : 0.036 0.135 1789 Planarity : 0.005 0.041 1195 Dihedral : 30.104 95.388 3267 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.37 % Allowed : 18.90 % Favored : 79.73 % 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: 2.70 (0.31), residues: 692 helix: 2.79 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.40 (0.36), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.002 PHE B 61 TYR 0.010 0.002 TYR B 51 ARG 0.009 0.000 ARG E 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 119 time to evaluate : 0.789 Fit side-chains REVERT: A 73 GLU cc_start: 0.8240 (tt0) cc_final: 0.7780 (tt0) REVERT: B 29 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7618 (mm) REVERT: B 35 ARG cc_start: 0.8773 (mtp85) cc_final: 0.8566 (mtp180) REVERT: B 93 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8138 (mm-40) REVERT: C 75 LYS cc_start: 0.8174 (mttp) cc_final: 0.7448 (tptt) REVERT: F 24 ASP cc_start: 0.7223 (t0) cc_final: 0.6938 (t70) REVERT: G 75 LYS cc_start: 0.8042 (mmmt) cc_final: 0.7310 (tptt) REVERT: H 71 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7830 (mt-10) outliers start: 8 outliers final: 5 residues processed: 123 average time/residue: 1.9400 time to fit residues: 249.5953 Evaluate side-chains 124 residues out of total 582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 82 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN G 104 GLN H 47 GLN H 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.144468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.108872 restraints weight = 11449.524| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.27 r_work: 0.3155 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10895 Z= 0.242 Angle : 0.578 8.664 15675 Z= 0.348 Chirality : 0.035 0.134 1789 Planarity : 0.004 0.043 1195 Dihedral : 30.105 95.417 3267 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.72 % Allowed : 18.73 % Favored : 79.55 % 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: 2.73 (0.31), residues: 692 helix: 2.81 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.39 (0.36), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.002 PHE B 61 TYR 0.010 0.001 TYR B 51 ARG 0.011 0.000 ARG D 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4313.19 seconds wall clock time: 75 minutes 29.43 seconds (4529.43 seconds total)