Starting phenix.real_space_refine on Mon Feb 19 09:00:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u46_26330/02_2024/7u46_26330.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u46_26330/02_2024/7u46_26330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u46_26330/02_2024/7u46_26330.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u46_26330/02_2024/7u46_26330.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u46_26330/02_2024/7u46_26330.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u46_26330/02_2024/7u46_26330.pdb" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.030 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 288 5.49 5 S 16 5.16 5 C 7565 2.51 5 N 2453 2.21 5 O 3038 1.98 5 H 11015 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 GLU 73": "OE1" <-> "OE2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E GLU 107": "OE1" <-> "OE2" Residue "E PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "H PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "K ASP 2": "OD1" <-> "OD2" Residue "K ASP 65": "OD1" <-> "OD2" Residue "K PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 134": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24375 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1503 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "B" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1307 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1573 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "D" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1458 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1539 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "F" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1283 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1589 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "H" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1458 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "K" Number of atoms: 3451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 3451 Classifications: {'peptide': 205} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 199} Chain breaks: 1 Chain: "I" Number of atoms: 4607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 4607 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 4607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 4607 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 10.57, per 1000 atoms: 0.43 Number of scatterers: 24375 At special positions: 0 Unit cell: (108.385, 128.092, 119.881, 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 16 16.00 P 288 15.00 O 3038 8.00 N 2453 7.00 C 7565 6.00 H 11015 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: 21.03 Conformation dependent library (CDL) restraints added in 1.4 seconds 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1740 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 11 sheets defined 69.0% alpha, 5.9% beta 139 base pairs and 262 stacking pairs defined. Time for finding SS restraints: 13.43 Creating SS restraints... Processing helix chain 'A' and resid 46 through 57 removed outlier: 3.604A pdb=" N GLU A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.701A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 removed outlier: 3.891A pdb=" N LEU A 91 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A 93 " --> pdb=" O GLN A 89 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 114 " --> pdb=" O TYR A 110 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.550A pdb=" N VAL A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.840A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.686A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.929A pdb=" N ARG C 20 " --> pdb=" O SER C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.704A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.541A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 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 104 through 123 Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'E' and resid 63 through 78 removed outlier: 3.715A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 116 removed outlier: 3.606A pdb=" N LEU E 91 " --> pdb=" O GLN E 87 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU E 112 " --> pdb=" O ASP E 108 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU E 114 " --> pdb=" O TYR E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 134 removed outlier: 3.949A pdb=" N VAL E 126 " --> pdb=" O PHE E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.668A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.630A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.734A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.524A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.576A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 123 Processing helix chain 'K' and resid 2 through 15 removed outlier: 3.673A pdb=" N GLU K 7 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE K 8 " --> pdb=" O THR K 4 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS K 15 " --> pdb=" O ARG K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 29 Processing helix chain 'K' and resid 32 through 39 Processing helix chain 'K' and resid 44 through 59 Processing helix chain 'K' and resid 62 through 77 removed outlier: 3.612A pdb=" N PHE K 76 " --> pdb=" O ILE K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 81 Processing helix chain 'K' and resid 100 through 116 Processing helix chain 'K' and resid 171 through 183 Processing helix chain 'K' and resid 197 through 211 Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.970A pdb=" N ASN A 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.407A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.057A 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 101 through 102 removed outlier: 6.751A pdb=" N THR C 101 " --> 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 85 through 86 removed outlier: 7.070A pdb=" N ASN E 85 " --> 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 120 through 121 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.146A 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 Processing sheet with id=AB2, first strand: chain 'K' and resid 120 through 126 removed outlier: 5.300A pdb=" N TYR K 151 " --> pdb=" O SER K 164 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR K 155 " --> pdb=" O TYR K 160 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N TYR K 160 " --> pdb=" O TYR K 155 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N TRP K 83 " --> pdb=" O LEU K 193 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LEU K 193 " --> pdb=" O TRP K 83 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VAL K 85 " --> pdb=" O MET K 191 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN K 187 " --> pdb=" O SER K 89 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1380 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 335 hydrogen bonds 670 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 262 stacking parallelities Total time for adding SS restraints: 10.38 Time building geometry restraints manager: 21.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 11012 1.03 - 1.22: 125 1.22 - 1.42: 6172 1.42 - 1.61: 7880 1.61 - 1.81: 30 Bond restraints: 25219 Sorted by residual: bond pdb=" CB VAL G 49 " pdb=" CG2 VAL G 49 " ideal model delta sigma weight residual 1.521 1.431 0.090 3.30e-02 9.18e+02 7.45e+00 bond pdb=" CB THR B 73 " pdb=" CG2 THR B 73 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.50e+00 bond pdb=" CB THR A 113 " pdb=" CG2 THR A 113 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.76e+00 bond pdb=" CB VAL F 57 " pdb=" CG1 VAL F 57 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.20e+00 bond pdb=" CG1 ILE D 61 " pdb=" CD1 ILE D 61 " ideal model delta sigma weight residual 1.513 1.427 0.086 3.90e-02 6.57e+02 4.81e+00 ... (remaining 25214 not shown) Histogram of bond angle deviations from ideal: 97.66 - 104.95: 1208 104.95 - 112.23: 27511 112.23 - 119.52: 6721 119.52 - 126.80: 9392 126.80 - 134.09: 873 Bond angle restraints: 45705 Sorted by residual: angle pdb=" N VAL A 119 " pdb=" CA VAL A 119 " pdb=" C VAL A 119 " ideal model delta sigma weight residual 113.53 109.43 4.10 9.80e-01 1.04e+00 1.75e+01 angle pdb=" N ILE F 26 " pdb=" CA ILE F 26 " pdb=" C ILE F 26 " ideal model delta sigma weight residual 113.43 109.09 4.34 1.09e+00 8.42e-01 1.58e+01 angle pdb=" N GLY H 104 " pdb=" CA GLY H 104 " pdb=" C GLY H 104 " ideal model delta sigma weight residual 111.02 118.01 -6.99 1.86e+00 2.89e-01 1.41e+01 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 111.02 117.96 -6.94 1.86e+00 2.89e-01 1.39e+01 angle pdb=" OP1 DC I -24 " pdb=" P DC I -24 " pdb=" OP2 DC I -24 " ideal model delta sigma weight residual 120.00 110.20 9.80 3.00e+00 1.11e-01 1.07e+01 ... (remaining 45700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.26: 8823 32.26 - 64.52: 1843 64.52 - 96.78: 61 96.78 - 129.04: 2 129.04 - 161.30: 3 Dihedral angle restraints: 10732 sinusoidal: 7617 harmonic: 3115 Sorted by residual: dihedral pdb=" CA HIS F 75 " pdb=" C HIS F 75 " pdb=" N ALA F 76 " pdb=" CA ALA F 76 " ideal model delta harmonic sigma weight residual 180.00 157.48 22.52 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA TYR B 98 " pdb=" C TYR B 98 " pdb=" N GLY B 99 " pdb=" CA GLY B 99 " ideal model delta harmonic sigma weight residual -180.00 -160.20 -19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" C4' DT J -22 " pdb=" C3' DT J -22 " pdb=" O3' DT J -22 " pdb=" P DC J -21 " ideal model delta sinusoidal sigma weight residual 220.00 58.70 161.30 1 3.50e+01 8.16e-04 1.53e+01 ... (remaining 10729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1767 0.067 - 0.134: 513 0.134 - 0.200: 32 0.200 - 0.267: 2 0.267 - 0.334: 2 Chirality restraints: 2316 Sorted by residual: chirality pdb=" P DC I -24 " pdb=" OP1 DC I -24 " pdb=" OP2 DC I -24 " pdb=" O5' DC I -24 " both_signs ideal model delta sigma weight residual True 2.35 -2.68 -0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" P DC J -24 " pdb=" OP1 DC J -24 " pdb=" OP2 DC J -24 " pdb=" O5' DC J -24 " both_signs ideal model delta sigma weight residual True 2.35 -2.64 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB VAL F 81 " pdb=" CA VAL F 81 " pdb=" CG1 VAL F 81 " pdb=" CG2 VAL F 81 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 2313 not shown) Planarity restraints: 2666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G 50 " -0.028 2.00e-02 2.50e+03 2.35e-02 1.66e+01 pdb=" CG TYR G 50 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR G 50 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR G 50 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR G 50 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR G 50 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR G 50 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR G 50 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TYR G 50 " 0.008 2.00e-02 2.50e+03 pdb=" HD2 TYR G 50 " 0.004 2.00e-02 2.50e+03 pdb=" HE1 TYR G 50 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 TYR G 50 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 98 " 0.035 2.00e-02 2.50e+03 1.59e-02 7.61e+00 pdb=" CG TYR B 98 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR B 98 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 98 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 98 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 98 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 98 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 98 " 0.010 2.00e-02 2.50e+03 pdb=" HD1 TYR B 98 " -0.003 2.00e-02 2.50e+03 pdb=" HD2 TYR B 98 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 TYR B 98 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR B 98 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE E 122 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.32e+00 pdb=" N PRO E 123 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO E 123 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 123 " 0.032 5.00e-02 4.00e+02 ... (remaining 2663 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 959 2.17 - 2.78: 41187 2.78 - 3.38: 59937 3.38 - 3.99: 87001 3.99 - 4.60: 134856 Nonbonded interactions: 323940 Sorted by model distance: nonbonded pdb=" O4 DT I 23 " pdb=" H62 DA J -23 " model vdw 1.559 1.850 nonbonded pdb=" OD2 ASP K 70 " pdb=" HH TYR K 151 " model vdw 1.594 1.850 nonbonded pdb="HH11 ARG A 80 " pdb=" OE1 GLU K 7 " model vdw 1.627 1.850 nonbonded pdb=" HG SER K 32 " pdb=" OE1 GLN K 35 " model vdw 1.651 1.850 nonbonded pdb=" OE1 GLU E 73 " pdb="HD21 ASN F 25 " model vdw 1.655 1.850 ... (remaining 323935 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 46 through 134) } ncs_group { reference = (chain 'B' and resid 24 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 15 through 112) selection = (chain 'G' and resid 15 through 112) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid -72 through -1 or resid 1 through 72)) selection = (chain 'J' and (resid -72 through -1 or resid 1 through 72)) } 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: 4.180 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: 0.280 Extract box with map and model: 9.840 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 87.690 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.080 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:13.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 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 : 0.011 0.090 14204 Z= 0.680 Angle : 0.791 10.948 20430 Z= 0.471 Chirality : 0.057 0.334 2316 Planarity : 0.005 0.058 1569 Dihedral : 26.919 161.305 6092 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.77 % Allowed : 0.77 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.27), residues: 905 helix: 0.57 (0.21), residues: 620 sheet: -1.15 (0.70), residues: 43 loop : -1.72 (0.32), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 86 HIS 0.007 0.002 HIS K 186 PHE 0.013 0.002 PHE H 70 TYR 0.065 0.003 TYR G 50 ARG 0.022 0.001 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.7783 (ttpt) cc_final: 0.7566 (ttpt) REVERT: K 140 GLN cc_start: 0.8563 (tt0) cc_final: 0.7648 (tp-100) outliers start: 6 outliers final: 0 residues processed: 85 average time/residue: 3.8238 time to fit residues: 345.6889 Evaluate side-chains 60 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 48 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 0.2980 chunk 55 optimal weight: 0.4980 chunk 67 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS C 73 ASN ** K 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14204 Z= 0.203 Angle : 0.613 4.645 20430 Z= 0.380 Chirality : 0.037 0.140 2316 Planarity : 0.004 0.050 1569 Dihedral : 30.245 160.232 4266 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.51 % Allowed : 5.87 % Favored : 93.62 % 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: 1.36 (0.27), residues: 905 helix: 1.75 (0.21), residues: 633 sheet: -0.19 (0.73), residues: 45 loop : -1.32 (0.34), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 28 HIS 0.005 0.001 HIS F 75 PHE 0.009 0.001 PHE K 206 TYR 0.018 0.001 TYR B 98 ARG 0.002 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 1.598 Fit side-chains revert: symmetry clash REVERT: C 64 GLU cc_start: 0.7428 (tt0) cc_final: 0.7153 (tt0) REVERT: C 73 ASN cc_start: 0.6791 (m-40) cc_final: 0.6301 (t0) REVERT: D 59 MET cc_start: 0.7439 (tpp) cc_final: 0.7231 (tpp) REVERT: H 99 ARG cc_start: 0.7256 (mtt-85) cc_final: 0.6998 (mtt180) REVERT: K 54 HIS cc_start: 0.7602 (t-90) cc_final: 0.7116 (t70) REVERT: K 140 GLN cc_start: 0.8590 (tt0) cc_final: 0.7667 (tp-100) outliers start: 4 outliers final: 1 residues processed: 87 average time/residue: 3.7613 time to fit residues: 348.5632 Evaluate side-chains 71 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 117 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14204 Z= 0.308 Angle : 0.644 6.329 20430 Z= 0.394 Chirality : 0.041 0.144 2316 Planarity : 0.005 0.050 1569 Dihedral : 30.169 163.518 4266 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.89 % Allowed : 8.42 % Favored : 90.69 % 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: 1.45 (0.27), residues: 905 helix: 1.80 (0.20), residues: 637 sheet: 0.10 (0.75), residues: 45 loop : -1.31 (0.35), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 86 HIS 0.008 0.001 HIS K 186 PHE 0.008 0.001 PHE K 123 TYR 0.023 0.002 TYR B 98 ARG 0.004 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 1.604 Fit side-chains REVERT: C 64 GLU cc_start: 0.7541 (tt0) cc_final: 0.7280 (tt0) REVERT: C 73 ASN cc_start: 0.6679 (m-40) cc_final: 0.6124 (t0) REVERT: D 85 LYS cc_start: 0.8289 (mttp) cc_final: 0.8003 (mttt) REVERT: H 85 LYS cc_start: 0.8421 (mttp) cc_final: 0.8169 (mttp) REVERT: K 54 HIS cc_start: 0.7640 (t-90) cc_final: 0.7134 (t70) REVERT: K 140 GLN cc_start: 0.8622 (tt0) cc_final: 0.7756 (tp-100) outliers start: 7 outliers final: 3 residues processed: 88 average time/residue: 3.8062 time to fit residues: 357.1117 Evaluate side-chains 83 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain K residue 117 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 30 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: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14204 Z= 0.227 Angle : 0.628 7.625 20430 Z= 0.385 Chirality : 0.038 0.138 2316 Planarity : 0.004 0.045 1569 Dihedral : 30.157 162.533 4266 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.77 % Allowed : 9.18 % Favored : 90.05 % 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: 1.65 (0.28), residues: 905 helix: 1.95 (0.20), residues: 636 sheet: 0.22 (0.76), residues: 45 loop : -1.26 (0.35), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 86 HIS 0.008 0.001 HIS K 186 PHE 0.009 0.001 PHE K 162 TYR 0.013 0.001 TYR B 98 ARG 0.004 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 1.622 Fit side-chains REVERT: C 64 GLU cc_start: 0.7518 (tt0) cc_final: 0.7280 (tt0) REVERT: C 73 ASN cc_start: 0.6631 (m-40) cc_final: 0.6049 (t0) REVERT: H 85 LYS cc_start: 0.8414 (mttp) cc_final: 0.8167 (mttp) REVERT: K 101 MET cc_start: 0.5712 (tpp) cc_final: 0.5492 (tpp) REVERT: K 140 GLN cc_start: 0.8621 (tt0) cc_final: 0.7753 (tp-100) outliers start: 6 outliers final: 6 residues processed: 83 average time/residue: 3.8769 time to fit residues: 342.2595 Evaluate side-chains 84 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain F residue 67 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 117 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 0 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14204 Z= 0.283 Angle : 0.631 5.083 20430 Z= 0.385 Chirality : 0.041 0.142 2316 Planarity : 0.005 0.046 1569 Dihedral : 30.065 161.623 4266 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.28 % Allowed : 10.33 % Favored : 88.39 % 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: 1.65 (0.28), residues: 905 helix: 1.96 (0.20), residues: 638 sheet: 0.26 (0.77), residues: 45 loop : -1.34 (0.36), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 86 HIS 0.003 0.001 HIS F 75 PHE 0.010 0.001 PHE K 162 TYR 0.012 0.001 TYR B 98 ARG 0.004 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.7546 (tt0) cc_final: 0.7315 (tt0) REVERT: C 73 ASN cc_start: 0.6640 (m-40) cc_final: 0.6059 (t0) REVERT: C 74 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7405 (mtmm) REVERT: D 85 LYS cc_start: 0.8263 (mttp) cc_final: 0.7925 (mttt) REVERT: H 85 LYS cc_start: 0.8423 (mttp) cc_final: 0.8158 (mttp) REVERT: K 140 GLN cc_start: 0.8664 (tt0) cc_final: 0.7740 (tp-100) outliers start: 10 outliers final: 7 residues processed: 89 average time/residue: 3.7060 time to fit residues: 351.1664 Evaluate side-chains 86 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 67 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 117 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14204 Z= 0.250 Angle : 0.619 6.981 20430 Z= 0.380 Chirality : 0.039 0.139 2316 Planarity : 0.004 0.046 1569 Dihedral : 30.049 161.321 4266 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.15 % Allowed : 11.10 % Favored : 87.76 % 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: 1.73 (0.28), residues: 905 helix: 2.00 (0.20), residues: 639 sheet: 0.44 (0.78), residues: 45 loop : -1.29 (0.36), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 86 HIS 0.003 0.001 HIS K 51 PHE 0.008 0.001 PHE K 162 TYR 0.010 0.001 TYR K 155 ARG 0.002 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 1.417 Fit side-chains revert: symmetry clash REVERT: C 64 GLU cc_start: 0.7554 (tt0) cc_final: 0.7308 (tt0) REVERT: C 73 ASN cc_start: 0.6603 (m-40) cc_final: 0.6018 (t0) REVERT: C 92 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7833 (mt-10) REVERT: K 140 GLN cc_start: 0.8670 (tt0) cc_final: 0.7781 (tp-100) REVERT: K 191 MET cc_start: 0.7615 (tpp) cc_final: 0.6696 (mpp) outliers start: 9 outliers final: 8 residues processed: 86 average time/residue: 3.8025 time to fit residues: 349.7682 Evaluate side-chains 87 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain F residue 67 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 117 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 0.0270 chunk 94 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14204 Z= 0.195 Angle : 0.608 6.274 20430 Z= 0.376 Chirality : 0.038 0.147 2316 Planarity : 0.004 0.045 1569 Dihedral : 30.043 161.394 4266 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.15 % Allowed : 11.35 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.82 (0.28), residues: 905 helix: 2.06 (0.20), residues: 639 sheet: 0.53 (0.79), residues: 45 loop : -1.25 (0.36), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 86 HIS 0.003 0.001 HIS F 75 PHE 0.007 0.001 PHE K 108 TYR 0.010 0.001 TYR F 51 ARG 0.001 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.7525 (tt0) cc_final: 0.7279 (tt0) REVERT: C 73 ASN cc_start: 0.6570 (m-40) cc_final: 0.5983 (t0) REVERT: E 92 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7488 (mp) REVERT: K 140 GLN cc_start: 0.8674 (tt0) cc_final: 0.7766 (tp-100) REVERT: K 191 MET cc_start: 0.7610 (tpp) cc_final: 0.6695 (mpp) outliers start: 9 outliers final: 8 residues processed: 84 average time/residue: 3.7116 time to fit residues: 332.2767 Evaluate side-chains 86 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 67 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 117 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.0980 chunk 21 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 55 optimal weight: 0.0770 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14204 Z= 0.212 Angle : 0.608 5.597 20430 Z= 0.375 Chirality : 0.038 0.143 2316 Planarity : 0.004 0.045 1569 Dihedral : 30.035 161.444 4266 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.02 % Allowed : 11.48 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.88 (0.28), residues: 905 helix: 2.10 (0.20), residues: 639 sheet: 0.54 (0.78), residues: 45 loop : -1.22 (0.37), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 86 HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE K 108 TYR 0.009 0.001 TYR F 51 ARG 0.004 0.000 ARG E 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.7537 (tt0) cc_final: 0.7290 (tt0) REVERT: C 73 ASN cc_start: 0.6562 (m-40) cc_final: 0.5998 (t0) REVERT: C 92 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7804 (mt-10) REVERT: K 140 GLN cc_start: 0.8674 (tt0) cc_final: 0.7767 (tp-100) REVERT: K 191 MET cc_start: 0.7613 (tpp) cc_final: 0.6692 (mpp) outliers start: 8 outliers final: 6 residues processed: 82 average time/residue: 3.7533 time to fit residues: 327.5862 Evaluate side-chains 84 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain F residue 67 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 117 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 81 optimal weight: 0.0050 chunk 31 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14204 Z= 0.237 Angle : 0.608 5.155 20430 Z= 0.374 Chirality : 0.039 0.139 2316 Planarity : 0.005 0.063 1569 Dihedral : 29.976 160.742 4266 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.40 % Allowed : 11.10 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.95 (0.28), residues: 905 helix: 2.16 (0.20), residues: 639 sheet: 0.74 (0.81), residues: 45 loop : -1.25 (0.37), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 86 HIS 0.003 0.001 HIS F 75 PHE 0.007 0.001 PHE K 123 TYR 0.010 0.001 TYR F 51 ARG 0.009 0.000 ARG E 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 79 time to evaluate : 1.652 Fit side-chains revert: symmetry clash REVERT: C 64 GLU cc_start: 0.7587 (tt0) cc_final: 0.7339 (tt0) REVERT: C 73 ASN cc_start: 0.6558 (m-40) cc_final: 0.6023 (t0) REVERT: C 92 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7832 (mt-10) REVERT: E 92 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7466 (mp) REVERT: K 140 GLN cc_start: 0.8689 (tt0) cc_final: 0.7802 (tp-100) REVERT: K 167 MET cc_start: 0.7737 (ttm) cc_final: 0.7493 (ttm) outliers start: 11 outliers final: 7 residues processed: 87 average time/residue: 3.6548 time to fit residues: 339.3018 Evaluate side-chains 85 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 67 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 117 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.1980 chunk 76 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14204 Z= 0.288 Angle : 0.632 5.648 20430 Z= 0.386 Chirality : 0.041 0.142 2316 Planarity : 0.005 0.047 1569 Dihedral : 29.965 161.633 4266 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.28 % Allowed : 11.10 % Favored : 87.63 % 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: 1.77 (0.28), residues: 905 helix: 2.00 (0.20), residues: 639 sheet: 0.92 (0.81), residues: 45 loop : -1.31 (0.36), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 86 HIS 0.003 0.001 HIS A 115 PHE 0.008 0.001 PHE K 162 TYR 0.010 0.001 TYR F 51 ARG 0.002 0.000 ARG H 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.7575 (tt0) cc_final: 0.7343 (tt0) REVERT: C 73 ASN cc_start: 0.6627 (m-40) cc_final: 0.6037 (t0) REVERT: C 92 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7892 (mt-10) REVERT: E 64 LYS cc_start: 0.7408 (mttt) cc_final: 0.6804 (mtpp) REVERT: E 92 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7429 (mp) REVERT: H 85 LYS cc_start: 0.8415 (mttp) cc_final: 0.8123 (mttp) REVERT: K 140 GLN cc_start: 0.8693 (tt0) cc_final: 0.7787 (tp-100) outliers start: 10 outliers final: 7 residues processed: 86 average time/residue: 3.7831 time to fit residues: 347.9789 Evaluate side-chains 86 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 67 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 117 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 66 optimal weight: 0.0060 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.181218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.112342 restraints weight = 32224.980| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.20 r_work: 0.3176 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14204 Z= 0.204 Angle : 0.610 5.560 20430 Z= 0.377 Chirality : 0.037 0.135 2316 Planarity : 0.004 0.046 1569 Dihedral : 29.955 161.913 4266 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.15 % Allowed : 11.35 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.94 (0.28), residues: 905 helix: 2.12 (0.20), residues: 639 sheet: 1.00 (0.82), residues: 45 loop : -1.22 (0.37), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 86 HIS 0.003 0.001 HIS F 75 PHE 0.007 0.001 PHE K 162 TYR 0.026 0.001 TYR K 209 ARG 0.002 0.000 ARG H 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8693.76 seconds wall clock time: 152 minutes 42.49 seconds (9162.49 seconds total)