Starting phenix.real_space_refine on Sun Feb 18 17:59:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssa_25406/02_2024/7ssa_25406.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssa_25406/02_2024/7ssa_25406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssa_25406/02_2024/7ssa_25406.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssa_25406/02_2024/7ssa_25406.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssa_25406/02_2024/7ssa_25406.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssa_25406/02_2024/7ssa_25406.pdb" } resolution = 3.2 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= 0.006 sd= 0.026 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: 6 Type Number sf(0) Gaussians P 273 5.49 5 S 12 5.16 5 C 6974 2.51 5 N 2329 2.21 5 O 2892 1.98 5 H 10277 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 123": "OD1" <-> "OD2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C GLU 93": "OE1" <-> "OE2" Residue "D TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "F TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "G TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "H TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 275": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22757 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1605 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1280 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1518 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "D" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1461 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1519 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "F" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1351 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1652 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1461 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "K" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1110 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 1, 'TRANS': 65} Chain: "L" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1111 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 1, 'TRANS': 65} Chain: "I" Number of atoms: 4325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 4325 Classifications: {'DNA': 137} Link IDs: {'rna3p': 136} Chain: "J" Number of atoms: 4364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 4364 Classifications: {'DNA': 137} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 136} Time building chain proxies: 10.20, per 1000 atoms: 0.45 Number of scatterers: 22757 At special positions: 0 Unit cell: (115.92, 121.072, 130.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 12 16.00 P 273 15.00 O 2892 8.00 N 2329 7.00 C 6974 6.00 H 10277 1.00 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: 20.53 Conformation dependent library (CDL) restraints added in 1.5 seconds 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1638 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 10 sheets defined 77.7% alpha, 2.8% beta 137 base pairs and 225 stacking pairs defined. Time for finding SS restraints: 12.79 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.591A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.566A pdb=" N VAL C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 removed outlier: 3.652A pdb=" N ASP C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'D' and resid 40 through 52 removed outlier: 3.943A pdb=" N THR D 51 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 87 Processing helix chain 'D' and resid 93 through 105 Processing helix chain 'D' and resid 106 through 126 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.825A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.907A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.509A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.522A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 27 through 38 Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.317A pdb=" N VAL G 50 " --> pdb=" O SER G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 removed outlier: 3.563A pdb=" N ASP G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 removed outlier: 3.871A pdb=" N LYS G 96 " --> pdb=" O ASP G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 40 through 50 Processing helix chain 'H' and resid 58 through 87 Processing helix chain 'H' and resid 93 through 105 Processing helix chain 'H' and resid 106 through 127 Processing helix chain 'K' and resid 223 through 249 Processing helix chain 'K' and resid 255 through 288 Processing helix chain 'L' and resid 223 through 249 removed outlier: 3.659A pdb=" N HIS L 227 " --> pdb=" O ARG L 223 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 288 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.918A 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 removed outlier: 3.561A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.510A pdb=" N THR B 96 " --> pdb=" O THR G 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.205A pdb=" N ARG C 43 " --> pdb=" O ILE D 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 103 removed outlier: 6.507A pdb=" N THR C 102 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.135A 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 43 through 44 removed outlier: 7.240A pdb=" N ARG G 43 " --> pdb=" O ILE H 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 505 hydrogen bonds defined for protein. 1497 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 350 hydrogen bonds 700 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 225 stacking parallelities Total time for adding SS restraints: 9.53 Time building geometry restraints manager: 20.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10273 1.03 - 1.23: 128 1.23 - 1.42: 5870 1.42 - 1.62: 7231 1.62 - 1.81: 20 Bond restraints: 23522 Sorted by residual: bond pdb=" N ALA C 14 " pdb=" CA ALA C 14 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N GLN K 222 " pdb=" CA GLN K 222 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N GLN G 16 " pdb=" CA GLN G 16 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N ARG D 36 " pdb=" CA ARG D 36 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N ARG H 36 " pdb=" CA ARG H 36 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.77e+00 ... (remaining 23517 not shown) Histogram of bond angle deviations from ideal: 98.64 - 105.69: 1390 105.69 - 112.75: 26051 112.75 - 119.80: 6421 119.80 - 126.85: 8042 126.85 - 133.91: 733 Bond angle restraints: 42637 Sorted by residual: angle pdb=" N GLU K 229 " pdb=" CA GLU K 229 " pdb=" CB GLU K 229 " ideal model delta sigma weight residual 110.28 115.72 -5.44 1.55e+00 4.16e-01 1.23e+01 angle pdb=" C LEU C 35 " pdb=" N ARG C 36 " pdb=" CA ARG C 36 " ideal model delta sigma weight residual 120.44 116.51 3.93 1.36e+00 5.41e-01 8.37e+00 angle pdb=" CA GLU K 229 " pdb=" CB GLU K 229 " pdb=" CG GLU K 229 " ideal model delta sigma weight residual 114.10 119.60 -5.50 2.00e+00 2.50e-01 7.56e+00 angle pdb=" C3' DA I 23 " pdb=" C2' DA I 23 " pdb=" C1' DA I 23 " ideal model delta sigma weight residual 101.60 105.50 -3.90 1.50e+00 4.44e-01 6.78e+00 angle pdb=" C2' DT I -26 " pdb=" C1' DT I -26 " pdb=" N1 DT I -26 " ideal model delta sigma weight residual 113.50 117.30 -3.80 1.50e+00 4.44e-01 6.42e+00 ... (remaining 42632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 7180 17.85 - 35.70: 1296 35.70 - 53.55: 1012 53.55 - 71.39: 375 71.39 - 89.24: 17 Dihedral angle restraints: 9880 sinusoidal: 7079 harmonic: 2801 Sorted by residual: dihedral pdb=" CA ILE B 29 " pdb=" C ILE B 29 " pdb=" N THR B 30 " pdb=" CA THR B 30 " ideal model delta harmonic sigma weight residual -180.00 -163.61 -16.39 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CG ARG A 128 " pdb=" CD ARG A 128 " pdb=" NE ARG A 128 " pdb=" CZ ARG A 128 " ideal model delta sinusoidal sigma weight residual -90.00 -133.92 43.92 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CG ARG L 233 " pdb=" CD ARG L 233 " pdb=" NE ARG L 233 " pdb=" CZ ARG L 233 " ideal model delta sinusoidal sigma weight residual -90.00 -133.59 43.59 2 1.50e+01 4.44e-03 1.01e+01 ... (remaining 9877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1182 0.028 - 0.056: 589 0.056 - 0.083: 271 0.083 - 0.111: 115 0.111 - 0.139: 24 Chirality restraints: 2181 Sorted by residual: chirality pdb=" CA VAL F 21 " pdb=" N VAL F 21 " pdb=" C VAL F 21 " pdb=" CB VAL F 21 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" C3' DA J -15 " pdb=" C4' DA J -15 " pdb=" O3' DA J -15 " pdb=" C2' DA J -15 " both_signs ideal model delta sigma weight residual False -2.66 -2.53 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" C3' DA I 23 " pdb=" C4' DA I 23 " pdb=" O3' DA I 23 " pdb=" C2' DA I 23 " both_signs ideal model delta sigma weight residual False -2.66 -2.53 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 2178 not shown) Planarity restraints: 2511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I -26 " -0.035 2.00e-02 2.50e+03 1.52e-02 6.90e+00 pdb=" N1 DT I -26 " 0.036 2.00e-02 2.50e+03 pdb=" C2 DT I -26 " 0.004 2.00e-02 2.50e+03 pdb=" O2 DT I -26 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DT I -26 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT I -26 " -0.004 2.00e-02 2.50e+03 pdb=" O4 DT I -26 " -0.012 2.00e-02 2.50e+03 pdb=" C5 DT I -26 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT I -26 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DT I -26 " 0.002 2.00e-02 2.50e+03 pdb=" H3 DT I -26 " -0.002 2.00e-02 2.50e+03 pdb=" H6 DT I -26 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 36 " -0.190 9.50e-02 1.11e+02 6.35e-02 4.41e+00 pdb=" NE ARG C 36 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG C 36 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG C 36 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 36 " -0.002 2.00e-02 2.50e+03 pdb="HH11 ARG C 36 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG C 36 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG C 36 " -0.004 2.00e-02 2.50e+03 pdb="HH22 ARG C 36 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -13 " 0.028 2.00e-02 2.50e+03 1.17e-02 4.41e+00 pdb=" N9 DA I -13 " -0.030 2.00e-02 2.50e+03 pdb=" C8 DA I -13 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DA I -13 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I -13 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I -13 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA I -13 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA I -13 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -13 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA I -13 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA I -13 " -0.001 2.00e-02 2.50e+03 pdb=" H8 DA I -13 " -0.002 2.00e-02 2.50e+03 pdb=" H2 DA I -13 " -0.001 2.00e-02 2.50e+03 ... (remaining 2508 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1446 2.21 - 2.81: 41979 2.81 - 3.40: 59662 3.40 - 4.00: 83895 4.00 - 4.60: 125022 Nonbonded interactions: 312004 Sorted by model distance: nonbonded pdb=" OE1 GLU H 116 " pdb="HH22 ARG H 119 " model vdw 1.610 1.850 nonbonded pdb=" H LYS F 79 " pdb=" OP1 DG I 28 " model vdw 1.615 1.850 nonbonded pdb=" HZ3 LYS L 228 " pdb=" OP2 DT I -59 " model vdw 1.623 1.850 nonbonded pdb=" HG1 THR A 45 " pdb=" OP1 DC I 70 " model vdw 1.628 1.850 nonbonded pdb=" OD1 ASP L 225 " pdb=" H SER L 226 " model vdw 1.653 1.850 ... (remaining 311999 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' and resid 43 through 133) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 102) } ncs_group { reference = (chain 'C' and resid 16 through 110) selection = (chain 'G' and resid 16 through 110) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = (chain 'L' and (resid 222 through 226 or (resid 227 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ e HE2)) or resid 228 through 288)) } 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 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: 1.420 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: 0.240 Extract box with map and model: 5.020 Check model and map are aligned: 0.280 Set scattering table: 0.200 Process input model: 83.760 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.090 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 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 : 0.005 0.040 13245 Z= 0.297 Angle : 0.651 7.158 19057 Z= 0.405 Chirality : 0.042 0.139 2181 Planarity : 0.006 0.083 1465 Dihedral : 26.333 89.242 5672 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.86 (0.28), residues: 845 helix: 1.95 (0.20), residues: 641 sheet: None (None), residues: 0 loop : -1.13 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 281 HIS 0.010 0.002 HIS H 52 PHE 0.009 0.002 PHE A 84 TYR 0.034 0.002 TYR F 88 ARG 0.013 0.001 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 ASN cc_start: 0.8156 (m-40) cc_final: 0.7948 (m-40) REVERT: C 92 ASP cc_start: 0.8081 (t0) cc_final: 0.7762 (t0) REVERT: C 100 ASN cc_start: 0.8292 (p0) cc_final: 0.7968 (p0) REVERT: D 91 THR cc_start: 0.8465 (p) cc_final: 0.8233 (p) REVERT: E 50 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7322 (mt-10) REVERT: E 87 SER cc_start: 0.9207 (p) cc_final: 0.8932 (p) REVERT: F 64 ASN cc_start: 0.8738 (m-40) cc_final: 0.8439 (m-40) REVERT: G 79 ILE cc_start: 0.8897 (mm) cc_final: 0.8631 (mt) REVERT: K 253 GLU cc_start: 0.5889 (tt0) cc_final: 0.5623 (tt0) REVERT: L 231 GLU cc_start: 0.7918 (tp30) cc_final: 0.7494 (tm-30) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.9039 time to fit residues: 303.0347 Evaluate side-chains 204 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 13245 Z= 0.335 Angle : 0.642 4.878 19057 Z= 0.396 Chirality : 0.045 0.143 2181 Planarity : 0.005 0.048 1465 Dihedral : 29.671 84.576 3952 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.92 % Allowed : 10.55 % Favored : 87.53 % 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 (0.29), residues: 845 helix: 2.33 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -1.03 (0.43), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 281 HIS 0.007 0.002 HIS K 227 PHE 0.008 0.001 PHE E 67 TYR 0.012 0.002 TYR C 51 ARG 0.009 0.001 ARG C 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 195 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8414 (mtp) cc_final: 0.8085 (mtp) REVERT: C 100 ASN cc_start: 0.8492 (p0) cc_final: 0.8176 (p0) REVERT: E 50 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7576 (mt-10) REVERT: E 68 GLN cc_start: 0.8530 (tt0) cc_final: 0.8218 (tt0) REVERT: E 87 SER cc_start: 0.9139 (p) cc_final: 0.8937 (p) REVERT: F 64 ASN cc_start: 0.8888 (m-40) cc_final: 0.8515 (m-40) REVERT: G 79 ILE cc_start: 0.8989 (mm) cc_final: 0.8757 (mt) REVERT: K 270 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7346 (mt) REVERT: L 231 GLU cc_start: 0.7871 (tp30) cc_final: 0.7353 (tm-30) outliers start: 14 outliers final: 12 residues processed: 205 average time/residue: 0.8775 time to fit residues: 225.8754 Evaluate side-chains 202 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 189 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain K residue 273 THR Chi-restraints excluded: chain L residue 282 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN D 66 ASN ** K 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 13245 Z= 0.329 Angle : 0.632 4.694 19057 Z= 0.389 Chirality : 0.044 0.139 2181 Planarity : 0.005 0.044 1465 Dihedral : 29.770 83.379 3952 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.47 % Allowed : 11.23 % Favored : 86.30 % 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: 2.57 (0.29), residues: 845 helix: 2.41 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.03 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 281 HIS 0.006 0.002 HIS B 75 PHE 0.008 0.001 PHE B 61 TYR 0.010 0.002 TYR D 43 ARG 0.006 0.001 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 188 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8458 (mtp) cc_final: 0.8090 (mtp) REVERT: B 92 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8259 (ttp80) REVERT: C 100 ASN cc_start: 0.8594 (p0) cc_final: 0.8293 (p0) REVERT: E 50 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7478 (mt-10) REVERT: E 52 ARG cc_start: 0.8088 (ptp90) cc_final: 0.7812 (mtm-85) REVERT: E 55 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.8957 (tt0) REVERT: E 68 GLN cc_start: 0.8569 (tt0) cc_final: 0.8322 (tt0) REVERT: E 87 SER cc_start: 0.9200 (p) cc_final: 0.8975 (p) REVERT: G 79 ILE cc_start: 0.8941 (mm) cc_final: 0.8688 (mt) REVERT: K 232 ARG cc_start: 0.6655 (mmt90) cc_final: 0.6209 (mmp-170) REVERT: K 235 ARG cc_start: 0.7231 (tpt170) cc_final: 0.6917 (tpt170) REVERT: K 270 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7465 (mt) REVERT: L 231 GLU cc_start: 0.7862 (tp30) cc_final: 0.7191 (tm-30) outliers start: 18 outliers final: 13 residues processed: 200 average time/residue: 0.8917 time to fit residues: 223.4016 Evaluate side-chains 197 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 181 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 282 THR Chi-restraints excluded: chain L residue 283 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 16 GLN ** K 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 13245 Z= 0.276 Angle : 0.615 5.788 19057 Z= 0.379 Chirality : 0.042 0.137 2181 Planarity : 0.004 0.040 1465 Dihedral : 29.754 84.751 3952 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.74 % Allowed : 11.51 % Favored : 85.75 % 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: 2.77 (0.29), residues: 845 helix: 2.55 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.95 (0.44), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 281 HIS 0.009 0.001 HIS C 32 PHE 0.008 0.001 PHE E 67 TYR 0.011 0.001 TYR F 88 ARG 0.004 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 185 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8393 (mtp) cc_final: 0.8038 (mtp) REVERT: B 92 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8230 (ttp80) REVERT: C 100 ASN cc_start: 0.8605 (p0) cc_final: 0.8321 (p0) REVERT: E 50 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7512 (mt-10) REVERT: E 52 ARG cc_start: 0.8038 (ptp-170) cc_final: 0.7827 (mtm-85) REVERT: E 55 GLN cc_start: 0.9197 (tt0) cc_final: 0.8980 (tt0) REVERT: E 68 GLN cc_start: 0.8568 (tt0) cc_final: 0.8319 (tt0) REVERT: E 87 SER cc_start: 0.9120 (p) cc_final: 0.8880 (p) REVERT: G 79 ILE cc_start: 0.8950 (mm) cc_final: 0.8708 (mt) REVERT: K 232 ARG cc_start: 0.6666 (mmt90) cc_final: 0.6148 (mmp-170) REVERT: K 270 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7388 (mt) REVERT: L 231 GLU cc_start: 0.7872 (tp30) cc_final: 0.7191 (tm-30) outliers start: 20 outliers final: 14 residues processed: 200 average time/residue: 0.8679 time to fit residues: 217.4917 Evaluate side-chains 198 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 182 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain K residue 273 THR Chi-restraints excluded: chain L residue 237 ASN Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 282 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 13245 Z= 0.328 Angle : 0.630 6.149 19057 Z= 0.388 Chirality : 0.044 0.168 2181 Planarity : 0.004 0.040 1465 Dihedral : 29.852 87.919 3952 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.15 % Allowed : 11.92 % Favored : 84.93 % 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: 2.63 (0.29), residues: 845 helix: 2.45 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.01 (0.44), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 281 HIS 0.008 0.002 HIS C 32 PHE 0.007 0.001 PHE B 61 TYR 0.012 0.001 TYR F 88 ARG 0.006 0.000 ARG C 36 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 185 time to evaluate : 1.359 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 120 MET cc_start: 0.8447 (mtp) cc_final: 0.8124 (mtp) REVERT: C 100 ASN cc_start: 0.8652 (p0) cc_final: 0.8359 (p0) REVERT: E 50 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7476 (mt-10) REVERT: E 55 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.9025 (tt0) REVERT: E 68 GLN cc_start: 0.8600 (tt0) cc_final: 0.8356 (tt0) REVERT: E 87 SER cc_start: 0.9198 (p) cc_final: 0.8953 (p) REVERT: G 79 ILE cc_start: 0.8973 (mm) cc_final: 0.8733 (mt) REVERT: K 259 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.7498 (tp) REVERT: K 266 TYR cc_start: 0.7202 (t80) cc_final: 0.6963 (t80) REVERT: K 270 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7499 (mt) REVERT: L 231 GLU cc_start: 0.7905 (tp30) cc_final: 0.7197 (tm-30) outliers start: 23 outliers final: 16 residues processed: 200 average time/residue: 0.8474 time to fit residues: 212.9922 Evaluate side-chains 201 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 182 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 259 ILE Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain K residue 273 THR Chi-restraints excluded: chain L residue 237 ASN Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 282 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 13245 Z= 0.279 Angle : 0.616 5.651 19057 Z= 0.379 Chirality : 0.042 0.147 2181 Planarity : 0.004 0.042 1465 Dihedral : 29.859 88.120 3952 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.01 % Allowed : 13.42 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.29), residues: 845 helix: 2.58 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.99 (0.44), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 281 HIS 0.005 0.001 HIS C 32 PHE 0.007 0.001 PHE A 67 TYR 0.011 0.001 TYR F 88 ARG 0.006 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 184 time to evaluate : 1.455 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 120 MET cc_start: 0.8433 (mtp) cc_final: 0.8097 (mtp) REVERT: B 92 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8252 (ttp80) REVERT: C 100 ASN cc_start: 0.8651 (p0) cc_final: 0.8362 (p0) REVERT: E 50 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7539 (mt-10) REVERT: E 68 GLN cc_start: 0.8609 (tt0) cc_final: 0.8350 (tt0) REVERT: E 87 SER cc_start: 0.9137 (p) cc_final: 0.8886 (p) REVERT: G 79 ILE cc_start: 0.8986 (mm) cc_final: 0.8761 (mt) REVERT: K 259 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.7467 (tp) REVERT: K 270 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7463 (mt) REVERT: L 231 GLU cc_start: 0.7800 (tp30) cc_final: 0.7044 (tm-30) outliers start: 22 outliers final: 15 residues processed: 198 average time/residue: 0.8694 time to fit residues: 215.4919 Evaluate side-chains 199 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 181 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 259 ILE Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain K residue 273 THR Chi-restraints excluded: chain L residue 237 ASN Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 282 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 13245 Z= 0.300 Angle : 0.625 7.078 19057 Z= 0.384 Chirality : 0.043 0.159 2181 Planarity : 0.005 0.059 1465 Dihedral : 29.918 90.241 3952 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.15 % Allowed : 13.15 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.29), residues: 845 helix: 2.53 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.06 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 281 HIS 0.005 0.001 HIS B 75 PHE 0.007 0.001 PHE B 61 TYR 0.012 0.001 TYR F 88 ARG 0.006 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 184 time to evaluate : 1.589 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 120 MET cc_start: 0.8428 (mtp) cc_final: 0.8108 (mtp) REVERT: B 92 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8262 (ttp80) REVERT: C 100 ASN cc_start: 0.8664 (p0) cc_final: 0.8394 (p0) REVERT: E 50 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7502 (mt-10) REVERT: E 68 GLN cc_start: 0.8623 (tt0) cc_final: 0.8356 (tt0) REVERT: E 87 SER cc_start: 0.9156 (p) cc_final: 0.8879 (p) REVERT: G 79 ILE cc_start: 0.8969 (mm) cc_final: 0.8741 (mt) REVERT: K 259 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.7470 (tp) REVERT: L 231 GLU cc_start: 0.7833 (tp30) cc_final: 0.7034 (tm-30) outliers start: 23 outliers final: 18 residues processed: 198 average time/residue: 0.8227 time to fit residues: 205.6218 Evaluate side-chains 200 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 180 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 236 GLU Chi-restraints excluded: chain K residue 259 ILE Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain K residue 273 THR Chi-restraints excluded: chain L residue 237 ASN Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 282 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 13245 Z= 0.276 Angle : 0.619 6.659 19057 Z= 0.380 Chirality : 0.042 0.154 2181 Planarity : 0.004 0.061 1465 Dihedral : 29.922 89.551 3952 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.88 % Allowed : 13.84 % Favored : 83.29 % 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: 2.83 (0.29), residues: 845 helix: 2.63 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.07 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 281 HIS 0.004 0.001 HIS B 75 PHE 0.007 0.001 PHE A 67 TYR 0.021 0.002 TYR L 266 ARG 0.007 0.000 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 186 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8429 (mtp) cc_final: 0.8103 (mtp) REVERT: B 92 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8257 (ttp80) REVERT: C 100 ASN cc_start: 0.8664 (p0) cc_final: 0.8392 (p0) REVERT: E 68 GLN cc_start: 0.8615 (tt0) cc_final: 0.8353 (tt0) REVERT: E 87 SER cc_start: 0.9134 (p) cc_final: 0.8858 (p) REVERT: G 79 ILE cc_start: 0.8952 (mm) cc_final: 0.8747 (mt) REVERT: K 259 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.7450 (tp) outliers start: 21 outliers final: 16 residues processed: 200 average time/residue: 0.8231 time to fit residues: 208.5906 Evaluate side-chains 201 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 183 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 259 ILE Chi-restraints excluded: chain K residue 273 THR Chi-restraints excluded: chain L residue 237 ASN Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 282 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 13245 Z= 0.358 Angle : 0.643 5.697 19057 Z= 0.394 Chirality : 0.045 0.150 2181 Planarity : 0.005 0.062 1465 Dihedral : 30.059 90.446 3952 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.74 % Allowed : 14.11 % Favored : 83.15 % 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: 2.50 (0.29), residues: 845 helix: 2.40 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.24 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 281 HIS 0.006 0.001 HIS B 75 PHE 0.007 0.001 PHE B 61 TYR 0.014 0.002 TYR K 266 ARG 0.005 0.001 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 188 time to evaluate : 1.607 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 120 MET cc_start: 0.8451 (mtp) cc_final: 0.8151 (mtp) REVERT: B 92 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8269 (ttp80) REVERT: C 100 ASN cc_start: 0.8682 (p0) cc_final: 0.8423 (p0) REVERT: C 105 GLN cc_start: 0.8439 (mm-40) cc_final: 0.8222 (mm-40) REVERT: E 68 GLN cc_start: 0.8601 (tt0) cc_final: 0.8358 (tt0) REVERT: E 87 SER cc_start: 0.9240 (p) cc_final: 0.8952 (p) REVERT: G 79 ILE cc_start: 0.8980 (mm) cc_final: 0.8776 (mt) REVERT: K 259 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.7448 (tp) outliers start: 20 outliers final: 17 residues processed: 200 average time/residue: 0.8450 time to fit residues: 214.5820 Evaluate side-chains 202 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 183 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 236 GLU Chi-restraints excluded: chain K residue 259 ILE Chi-restraints excluded: chain K residue 273 THR Chi-restraints excluded: chain L residue 237 ASN Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 282 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 68 optimal weight: 0.4980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13245 Z= 0.247 Angle : 0.615 7.650 19057 Z= 0.378 Chirality : 0.040 0.129 2181 Planarity : 0.004 0.063 1465 Dihedral : 29.963 88.630 3952 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.05 % Allowed : 15.21 % Favored : 82.74 % 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: 2.85 (0.29), residues: 845 helix: 2.67 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.18 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 281 HIS 0.004 0.001 HIS C 32 PHE 0.008 0.001 PHE A 67 TYR 0.014 0.001 TYR L 266 ARG 0.005 0.000 ARG H 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 187 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8393 (mtp) cc_final: 0.8085 (mtp) REVERT: B 92 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8244 (ttp80) REVERT: C 100 ASN cc_start: 0.8691 (p0) cc_final: 0.8438 (p0) REVERT: E 68 GLN cc_start: 0.8603 (tt0) cc_final: 0.8340 (tt0) REVERT: E 87 SER cc_start: 0.9112 (p) cc_final: 0.8858 (p) REVERT: G 79 ILE cc_start: 0.8952 (mm) cc_final: 0.8747 (mt) REVERT: K 232 ARG cc_start: 0.7028 (mmt90) cc_final: 0.6398 (mmp-170) REVERT: K 259 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.7343 (tp) outliers start: 15 outliers final: 13 residues processed: 197 average time/residue: 0.8223 time to fit residues: 204.4701 Evaluate side-chains 198 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 183 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain K residue 229 GLU Chi-restraints excluded: chain K residue 236 GLU Chi-restraints excluded: chain K residue 259 ILE Chi-restraints excluded: chain L residue 237 ASN Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 262 CYS Chi-restraints excluded: chain L residue 282 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 3.9990 chunk 26 optimal weight: 0.2980 chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.070982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.055745 restraints weight = 98979.072| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.65 r_work: 0.2863 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13245 Z= 0.247 Angle : 0.613 7.708 19057 Z= 0.376 Chirality : 0.040 0.142 2181 Planarity : 0.004 0.063 1465 Dihedral : 29.935 89.465 3952 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.92 % Allowed : 15.62 % Favored : 82.47 % 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: 2.89 (0.29), residues: 845 helix: 2.70 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.19 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 281 HIS 0.004 0.001 HIS B 75 PHE 0.007 0.001 PHE E 67 TYR 0.016 0.001 TYR L 266 ARG 0.004 0.000 ARG H 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6882.07 seconds wall clock time: 121 minutes 40.13 seconds (7300.13 seconds total)