Starting phenix.real_space_refine on Fri Mar 22 07:52:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bof_12241/03_2024/7bof_12241_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bof_12241/03_2024/7bof_12241.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bof_12241/03_2024/7bof_12241_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bof_12241/03_2024/7bof_12241_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bof_12241/03_2024/7bof_12241_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bof_12241/03_2024/7bof_12241.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bof_12241/03_2024/7bof_12241.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bof_12241/03_2024/7bof_12241_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bof_12241/03_2024/7bof_12241_updated.pdb" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1070 5.49 5 Mg 129 5.21 5 S 40 5.16 5 C 16302 2.51 5 N 6099 2.21 5 O 9174 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32814 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 22995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 22995 Classifications: {'RNA': 1070} Modifications used: {'rna2p_pur': 82, 'rna2p_pyr': 56, 'rna3p': 5, 'rna3p_pur': 534, 'rna3p_pyr': 393} Link IDs: {'rna2p': 137, 'rna3p': 932} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1156 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "F" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Unusual residues: {' MG': 129} Classifications: {'undetermined': 129} Link IDs: {None: 128} Time building chain proxies: 17.81, per 1000 atoms: 0.54 Number of scatterers: 32814 At special positions: 0 Unit cell: (183.75, 150.15, 177.45, 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 40 16.00 P 1070 15.00 Mg 129 11.99 O 9174 8.00 N 6099 7.00 C 16302 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.77 Conformation dependent library (CDL) restraints added in 2.4 seconds 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 11 sheets defined 36.0% alpha, 18.7% beta 363 base pairs and 611 stacking pairs defined. Time for finding SS restraints: 19.91 Creating SS restraints... Processing helix chain 'D' and resid 9 through 15 Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 50 through 65 Processing helix chain 'D' and resid 69 through 81 Processing helix chain 'D' and resid 86 through 96 Processing helix chain 'D' and resid 98 through 105 Processing helix chain 'D' and resid 111 through 119 Processing helix chain 'D' and resid 147 through 150 No H-bonds generated for 'chain 'D' and resid 147 through 150' Processing helix chain 'D' and resid 153 through 164 removed outlier: 3.676A pdb=" N LEU D 159 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 205 Processing helix chain 'E' and resid 56 through 68 Processing helix chain 'E' and resid 109 through 118 removed outlier: 3.575A pdb=" N ALA E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 145 Processing helix chain 'E' and resid 150 through 156 Processing helix chain 'E' and resid 161 through 165 Processing helix chain 'F' and resid 12 through 31 removed outlier: 4.657A pdb=" N GLU F 16 " --> pdb=" O ASP F 13 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL F 18 " --> pdb=" O SER F 15 " (cutoff:3.500A) Proline residue: F 19 - end of helix removed outlier: 4.891A pdb=" N ILE F 22 " --> pdb=" O PRO F 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR F 26 " --> pdb=" O GLU F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 80 Processing helix chain 'H' and resid 6 through 19 Processing helix chain 'H' and resid 31 through 42 Processing helix chain 'H' and resid 113 through 118 Processing helix chain 'K' and resid 47 through 49 No H-bonds generated for 'chain 'K' and resid 47 through 49' Processing helix chain 'K' and resid 54 through 58 Processing helix chain 'K' and resid 60 through 74 removed outlier: 3.589A pdb=" N ALA K 73 " --> pdb=" O ARG K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 102 Processing helix chain 'L' and resid 4 through 9 Processing helix chain 'L' and resid 22 through 24 No H-bonds generated for 'chain 'L' and resid 22 through 24' Processing helix chain 'L' and resid 114 through 116 No H-bonds generated for 'chain 'L' and resid 114 through 116' Processing helix chain 'O' and resid 5 through 15 Processing helix chain 'O' and resid 25 through 45 removed outlier: 4.117A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU O 45 " --> pdb=" O GLY O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 73 removed outlier: 4.082A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 85 Processing helix chain 'P' and resid 54 through 63 Processing helix chain 'P' and resid 69 through 80 Processing helix chain 'Q' and resid 49 through 51 No H-bonds generated for 'chain 'Q' and resid 49 through 51' Processing helix chain 'R' and resid 12 through 16 Processing helix chain 'R' and resid 26 through 28 No H-bonds generated for 'chain 'R' and resid 26 through 28' Processing helix chain 'R' and resid 30 through 32 No H-bonds generated for 'chain 'R' and resid 30 through 32' Processing helix chain 'R' and resid 42 through 45 No H-bonds generated for 'chain 'R' and resid 42 through 45' Processing helix chain 'R' and resid 49 through 64 Processing helix chain 'T' and resid 5 through 41 Processing helix chain 'T' and resid 44 through 63 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 69 through 84 Processing sheet with id= A, first strand: chain 'D' and resid 123 through 125 Processing sheet with id= B, first strand: chain 'E' and resid 71 through 73 removed outlier: 6.662A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 85 through 89 Processing sheet with id= D, first strand: chain 'F' and resid 38 through 41 removed outlier: 4.540A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET F 90 " --> pdb=" O GLU F 5 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 24 through 28 Processing sheet with id= F, first strand: chain 'H' and resid 74 through 77 removed outlier: 6.751A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR H 128 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE H 101 " --> pdb=" O TYR H 128 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'K' and resid 43 through 46 removed outlier: 3.929A pdb=" N GLY K 43 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL K 32 " --> pdb=" O ALA K 45 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN K 81 " --> pdb=" O GLY K 19 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA K 21 " --> pdb=" O ASN K 81 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU K 83 " --> pdb=" O ALA K 21 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE K 23 " --> pdb=" O GLU K 83 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET K 85 " --> pdb=" O ILE K 23 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA K 25 " --> pdb=" O MET K 85 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS K 87 " --> pdb=" O ALA K 25 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG K 106 " --> pdb=" O LEU K 82 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N VAL K 84 " --> pdb=" O ARG K 106 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N THR K 108 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 12.115A pdb=" N VAL K 86 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N ILE K 110 " --> pdb=" O VAL K 86 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 95 through 97 removed outlier: 6.754A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL L 37 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N VAL L 52 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR L 39 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ARG L 50 " --> pdb=" O THR L 39 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'P' and resid 2 through 11 removed outlier: 6.596A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'Q' and resid 73 through 75 removed outlier: 8.172A pdb=" N GLN Q 9 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLU Q 26 " --> pdb=" O GLN Q 9 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL Q 22 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'Q' and resid 58 through 60 removed outlier: 6.637A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL Q 78 " --> pdb=" O GLU Q 60 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1134 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 900 hydrogen bonds 1388 hydrogen bond angles 0 basepair planarities 363 basepair parallelities 611 stacking parallelities Total time for adding SS restraints: 27.09 Time building geometry restraints manager: 19.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5701 1.33 - 1.45: 14616 1.45 - 1.57: 13055 1.57 - 1.70: 2136 1.70 - 1.82: 69 Bond restraints: 35577 Sorted by residual: bond pdb=" C2 G7M A 527 " pdb=" N3 G7M A 527 " ideal model delta sigma weight residual 1.462 1.310 0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" N3 2MG A1516 " pdb=" C4 2MG A1516 " ideal model delta sigma weight residual 1.496 1.349 0.147 2.00e-02 2.50e+03 5.43e+01 bond pdb=" N3 G7M A 527 " pdb=" C4 G7M A 527 " ideal model delta sigma weight residual 1.492 1.355 0.137 2.00e-02 2.50e+03 4.70e+01 bond pdb=" C2 2MG A1516 " pdb=" N2 2MG A1516 " ideal model delta sigma weight residual 1.475 1.346 0.129 2.00e-02 2.50e+03 4.14e+01 bond pdb=" C5 MA6 A1519 " pdb=" C4 MA6 A1519 " ideal model delta sigma weight residual 1.342 1.469 -0.127 2.00e-02 2.50e+03 4.03e+01 ... (remaining 35572 not shown) Histogram of bond angle deviations from ideal: 95.35 - 103.69: 3144 103.69 - 112.03: 22185 112.03 - 120.37: 16142 120.37 - 128.71: 10574 128.71 - 137.05: 1317 Bond angle restraints: 53362 Sorted by residual: angle pdb=" CA D2T L 89 " pdb=" CB D2T L 89 " pdb=" SB D2T L 89 " ideal model delta sigma weight residual 114.38 95.35 19.03 3.00e+00 1.11e-01 4.03e+01 angle pdb=" N6 MA6 A1518 " pdb=" C6 MA6 A1518 " pdb=" N1 MA6 A1518 " ideal model delta sigma weight residual 104.44 122.57 -18.13 3.00e+00 1.11e-01 3.65e+01 angle pdb=" C1' 2MG A1516 " pdb=" N9 2MG A1516 " pdb=" C8 2MG A1516 " ideal model delta sigma weight residual 110.07 127.75 -17.68 3.00e+00 1.11e-01 3.47e+01 angle pdb=" C1' G7M A 527 " pdb=" N9 G7M A 527 " pdb=" C8 G7M A 527 " ideal model delta sigma weight residual 112.61 130.10 -17.49 3.00e+00 1.11e-01 3.40e+01 angle pdb=" N6 MA6 A1519 " pdb=" C6 MA6 A1519 " pdb=" N1 MA6 A1519 " ideal model delta sigma weight residual 104.44 121.05 -16.61 3.00e+00 1.11e-01 3.06e+01 ... (remaining 53357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.37: 19895 34.37 - 68.74: 2594 68.74 - 103.11: 306 103.11 - 137.48: 5 137.48 - 171.84: 5 Dihedral angle restraints: 22805 sinusoidal: 19258 harmonic: 3547 Sorted by residual: dihedral pdb=" O4' C A 754 " pdb=" C1' C A 754 " pdb=" N1 C A 754 " pdb=" C2 C A 754 " ideal model delta sinusoidal sigma weight residual 200.00 56.77 143.23 1 1.50e+01 4.44e-03 7.68e+01 dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 58.06 141.94 1 1.50e+01 4.44e-03 7.63e+01 dihedral pdb=" O4' C A 328 " pdb=" C1' C A 328 " pdb=" N1 C A 328 " pdb=" C2 C A 328 " ideal model delta sinusoidal sigma weight residual 232.00 60.37 171.63 1 1.70e+01 3.46e-03 6.61e+01 ... (remaining 22802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 6645 0.095 - 0.189: 161 0.189 - 0.284: 10 0.284 - 0.379: 1 0.379 - 0.473: 1 Chirality restraints: 6818 Sorted by residual: chirality pdb=" CB D2T L 89 " pdb=" CA D2T L 89 " pdb=" SB D2T L 89 " pdb=" CG D2T L 89 " both_signs ideal model delta sigma weight residual False -3.02 -3.49 0.47 2.00e-01 2.50e+01 5.60e+00 chirality pdb=" CA D2T L 89 " pdb=" N D2T L 89 " pdb=" C D2T L 89 " pdb=" CB D2T L 89 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C3' G A1473 " pdb=" C4' G A1473 " pdb=" O3' G A1473 " pdb=" C2' G A1473 " both_signs ideal model delta sigma weight residual False -2.48 -2.73 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 6815 not shown) Planarity restraints: 2784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " 0.008 2.00e-02 2.50e+03 4.66e-01 4.88e+03 pdb=" C4' 2MG A1516 " 0.402 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " 0.421 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " -0.554 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " -0.393 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " -0.262 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " 0.770 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " 0.260 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " -0.651 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' 2MG A1516 " 0.077 2.00e-02 2.50e+03 1.43e-01 6.61e+02 pdb=" N9 2MG A1516 " 0.012 2.00e-02 2.50e+03 pdb=" C8 2MG A1516 " -0.071 2.00e-02 2.50e+03 pdb=" N7 2MG A1516 " -0.096 2.00e-02 2.50e+03 pdb=" C5 2MG A1516 " -0.028 2.00e-02 2.50e+03 pdb=" C6 2MG A1516 " -0.011 2.00e-02 2.50e+03 pdb=" O6 2MG A1516 " -0.070 2.00e-02 2.50e+03 pdb=" N1 2MG A1516 " 0.069 2.00e-02 2.50e+03 pdb=" C2 2MG A1516 " 0.140 2.00e-02 2.50e+03 pdb=" N2 2MG A1516 " 0.205 2.00e-02 2.50e+03 pdb=" N3 2MG A1516 " 0.121 2.00e-02 2.50e+03 pdb=" C4 2MG A1516 " 0.045 2.00e-02 2.50e+03 pdb=" CM2 2MG A1516 " -0.393 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 MA6 A1519 " -0.127 2.00e-02 2.50e+03 2.08e-01 4.33e+02 pdb=" N6 MA6 A1519 " 0.360 2.00e-02 2.50e+03 pdb=" C10 MA6 A1519 " -0.118 2.00e-02 2.50e+03 pdb=" C9 MA6 A1519 " -0.115 2.00e-02 2.50e+03 ... (remaining 2781 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 302 2.50 - 3.10: 23009 3.10 - 3.70: 65671 3.70 - 4.30: 94467 4.30 - 4.90: 125105 Nonbonded interactions: 308554 Sorted by model distance: nonbonded pdb=" OP1 G A 450 " pdb="MG MG A1663 " model vdw 1.894 2.170 nonbonded pdb=" OP2 G A 100 " pdb="MG MG A1642 " model vdw 1.915 2.170 nonbonded pdb=" OP2 G A 117 " pdb="MG MG A1701 " model vdw 1.922 2.170 nonbonded pdb=" OP2 A A 608 " pdb="MG MG A1622 " model vdw 1.930 2.170 nonbonded pdb=" OP2 G A 597 " pdb="MG MG A1672 " model vdw 1.931 2.170 ... (remaining 308549 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.010 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: 0.030 Extract box with map and model: 14.500 Check model and map are aligned: 0.560 Set scattering table: 0.350 Process input model: 116.210 Find NCS groups from input model: 0.650 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: 0.000 Load rotamer database and sin/cos tables:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 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 : 0.008 0.152 35577 Z= 0.496 Angle : 0.644 19.034 53362 Z= 0.348 Chirality : 0.038 0.473 6818 Planarity : 0.011 0.466 2784 Dihedral : 23.158 171.844 20517 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % 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 (0.22), residues: 1213 helix: -0.79 (0.21), residues: 460 sheet: -2.31 (0.31), residues: 231 loop : -2.02 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 60 HIS 0.004 0.001 HIS O 51 PHE 0.018 0.002 PHE H 66 TYR 0.012 0.001 TYR R 51 ARG 0.009 0.000 ARG D 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 ARG cc_start: 0.7834 (tmm160) cc_final: 0.7319 (ttp80) REVERT: D 141 ASP cc_start: 0.8203 (m-30) cc_final: 0.7797 (m-30) REVERT: E 12 GLN cc_start: 0.9103 (pt0) cc_final: 0.8879 (pt0) REVERT: E 23 LYS cc_start: 0.7636 (ttpt) cc_final: 0.6572 (mptt) REVERT: E 45 ARG cc_start: 0.8195 (ttt-90) cc_final: 0.7794 (ttp80) REVERT: E 61 GLN cc_start: 0.9005 (tp-100) cc_final: 0.8777 (tp-100) REVERT: E 65 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8483 (tp30) REVERT: E 142 ASP cc_start: 0.8229 (t0) cc_final: 0.7961 (t0) REVERT: F 40 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6942 (mt-10) REVERT: F 52 ASN cc_start: 0.8725 (m110) cc_final: 0.8490 (m110) REVERT: F 75 GLU cc_start: 0.8018 (pp20) cc_final: 0.7730 (pp20) REVERT: F 79 ARG cc_start: 0.8714 (ttm110) cc_final: 0.8124 (ttp-110) REVERT: F 88 MET cc_start: 0.8704 (ttt) cc_final: 0.8457 (ttt) REVERT: F 98 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7784 (tm-30) REVERT: H 52 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7841 (mm-30) REVERT: H 58 GLU cc_start: 0.7414 (mp0) cc_final: 0.7110 (mp0) REVERT: H 60 GLU cc_start: 0.8085 (tt0) cc_final: 0.7620 (tm-30) REVERT: H 96 MET cc_start: 0.9218 (mtp) cc_final: 0.8722 (ttp) REVERT: H 124 GLU cc_start: 0.8478 (tt0) cc_final: 0.8262 (tt0) REVERT: K 44 TRP cc_start: 0.8207 (p-90) cc_final: 0.7888 (p-90) REVERT: K 83 GLU cc_start: 0.7259 (mm-30) cc_final: 0.6995 (mm-30) REVERT: K 106 ARG cc_start: 0.8323 (ttp80) cc_final: 0.8073 (tmm-80) REVERT: L 47 SER cc_start: 0.8436 (t) cc_final: 0.7522 (t) REVERT: L 62 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7506 (mt-10) REVERT: O 18 ASP cc_start: 0.8370 (m-30) cc_final: 0.8165 (m-30) REVERT: O 26 GLU cc_start: 0.8842 (mp0) cc_final: 0.8295 (mp0) REVERT: O 68 ASP cc_start: 0.8032 (m-30) cc_final: 0.7721 (m-30) REVERT: O 71 LYS cc_start: 0.8711 (tmmt) cc_final: 0.8452 (ptmm) REVERT: O 82 ILE cc_start: 0.9066 (pt) cc_final: 0.8450 (pp) REVERT: O 88 ARG cc_start: 0.8102 (mmm160) cc_final: 0.7831 (mmm160) REVERT: P 76 LYS cc_start: 0.8985 (ttmm) cc_final: 0.8716 (ttmt) REVERT: P 80 LYS cc_start: 0.8889 (ttpp) cc_final: 0.8489 (ttmm) REVERT: Q 52 GLU cc_start: 0.8684 (tt0) cc_final: 0.8412 (tt0) REVERT: R 20 GLU cc_start: 0.7496 (tp30) cc_final: 0.7100 (tp30) REVERT: R 25 ASP cc_start: 0.8756 (t0) cc_final: 0.8225 (t0) REVERT: T 24 ARG cc_start: 0.8246 (mmt180) cc_final: 0.7542 (mmm160) outliers start: 0 outliers final: 1 residues processed: 379 average time/residue: 1.7621 time to fit residues: 771.3937 Evaluate side-chains 311 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 310 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 174 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 189 optimal weight: 1.9990 chunk 170 optimal weight: 9.9990 chunk 94 optimal weight: 30.0000 chunk 58 optimal weight: 4.9990 chunk 115 optimal weight: 0.0980 chunk 91 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 204 optimal weight: 1.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN D 126 ASN D 136 GLN D 164 GLN E 73 ASN E 83 HIS E 89 HIS E 135 ASN K 28 ASN L 5 ASN L 6 GLN O 46 HIS Q 51 ASN R 74 HIS T 13 GLN T 61 GLN T 70 ASN T 78 ASN T 84 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 35577 Z= 0.218 Angle : 0.569 13.647 53362 Z= 0.301 Chirality : 0.034 0.382 6818 Planarity : 0.005 0.111 2784 Dihedral : 23.556 176.489 18093 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.04 % Allowed : 18.92 % Favored : 77.04 % 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: -0.97 (0.24), residues: 1213 helix: 0.68 (0.24), residues: 460 sheet: -1.80 (0.31), residues: 232 loop : -1.20 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 60 HIS 0.005 0.001 HIS P 59 PHE 0.019 0.002 PHE K 61 TYR 0.009 0.001 TYR T 36 ARG 0.011 0.001 ARG E 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 349 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 ARG cc_start: 0.7755 (tmm160) cc_final: 0.7218 (ttp80) REVERT: D 141 ASP cc_start: 0.8159 (m-30) cc_final: 0.7751 (m-30) REVERT: D 206 LYS cc_start: 0.8209 (ptmm) cc_final: 0.7957 (ptmt) REVERT: E 12 GLN cc_start: 0.9107 (pt0) cc_final: 0.8858 (pt0) REVERT: E 23 LYS cc_start: 0.8338 (ttpt) cc_final: 0.6662 (mptt) REVERT: E 61 GLN cc_start: 0.9006 (tp-100) cc_final: 0.8761 (tp-100) REVERT: E 65 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8480 (tp30) REVERT: E 142 ASP cc_start: 0.8127 (t0) cc_final: 0.7910 (t0) REVERT: F 40 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6881 (mt-10) REVERT: F 65 GLU cc_start: 0.8479 (tt0) cc_final: 0.8197 (tt0) REVERT: F 73 GLU cc_start: 0.8867 (tp30) cc_final: 0.8495 (tp30) REVERT: F 75 GLU cc_start: 0.7949 (pp20) cc_final: 0.7630 (pp20) REVERT: F 79 ARG cc_start: 0.8649 (ttm110) cc_final: 0.7972 (ttp-110) REVERT: F 90 MET cc_start: 0.7953 (ptm) cc_final: 0.7577 (ptm) REVERT: H 52 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7864 (mm-30) REVERT: H 58 GLU cc_start: 0.7507 (mp0) cc_final: 0.7187 (mp0) REVERT: H 96 MET cc_start: 0.9214 (mtp) cc_final: 0.8690 (ttp) REVERT: H 114 ARG cc_start: 0.7818 (ptm160) cc_final: 0.7523 (ptm160) REVERT: H 124 GLU cc_start: 0.8392 (tt0) cc_final: 0.8168 (tt0) REVERT: K 35 THR cc_start: 0.8463 (t) cc_final: 0.8258 (m) REVERT: K 69 ARG cc_start: 0.7102 (ttp-110) cc_final: 0.6778 (ttp-110) REVERT: K 77 TYR cc_start: 0.8283 (m-80) cc_final: 0.7730 (m-10) REVERT: L 62 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7744 (mt-10) REVERT: O 10 LYS cc_start: 0.9120 (tppp) cc_final: 0.8783 (tptm) REVERT: O 14 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7547 (tm-30) REVERT: O 26 GLU cc_start: 0.8889 (mp0) cc_final: 0.8600 (mp0) REVERT: O 62 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8345 (tp40) REVERT: O 68 ASP cc_start: 0.8076 (m-30) cc_final: 0.7740 (m-30) REVERT: O 71 LYS cc_start: 0.8531 (tmmt) cc_final: 0.8296 (ttmm) REVERT: O 82 ILE cc_start: 0.8920 (pt) cc_final: 0.8319 (pp) REVERT: O 83 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8078 (mm-30) REVERT: O 88 ARG cc_start: 0.8168 (mmm160) cc_final: 0.7866 (mmm160) REVERT: P 76 LYS cc_start: 0.8994 (ttmm) cc_final: 0.8744 (ttmt) REVERT: P 77 GLU cc_start: 0.8457 (pp20) cc_final: 0.8181 (pp20) REVERT: P 80 LYS cc_start: 0.8952 (ttpp) cc_final: 0.8518 (ttmm) REVERT: Q 16 LYS cc_start: 0.8927 (mtpp) cc_final: 0.8725 (mtpp) REVERT: Q 52 GLU cc_start: 0.8716 (tt0) cc_final: 0.8489 (tt0) REVERT: Q 57 ASP cc_start: 0.8689 (m-30) cc_final: 0.8354 (m-30) REVERT: R 25 ASP cc_start: 0.8683 (t0) cc_final: 0.8221 (t0) REVERT: T 24 ARG cc_start: 0.8241 (mmt180) cc_final: 0.7462 (mmm160) outliers start: 41 outliers final: 21 residues processed: 357 average time/residue: 1.6739 time to fit residues: 695.8111 Evaluate side-chains 343 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 320 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain T residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 170 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 204 optimal weight: 7.9990 chunk 221 optimal weight: 5.9990 chunk 182 optimal weight: 6.9990 chunk 202 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN T 13 GLN T 20 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 35577 Z= 0.358 Angle : 0.600 11.998 53362 Z= 0.316 Chirality : 0.037 0.353 6818 Planarity : 0.005 0.114 2784 Dihedral : 23.457 177.004 18091 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 6.11 % Allowed : 21.38 % Favored : 72.51 % 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: -0.59 (0.24), residues: 1213 helix: 0.95 (0.25), residues: 455 sheet: -1.49 (0.31), residues: 238 loop : -0.97 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 44 HIS 0.005 0.001 HIS P 59 PHE 0.010 0.002 PHE T 31 TYR 0.011 0.002 TYR D 204 ARG 0.009 0.001 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 315 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 ARG cc_start: 0.7825 (tmm160) cc_final: 0.7329 (ttp80) REVERT: D 141 ASP cc_start: 0.8163 (m-30) cc_final: 0.7771 (m-30) REVERT: D 206 LYS cc_start: 0.8327 (ptmm) cc_final: 0.8011 (ptmt) REVERT: E 10 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8292 (tm-30) REVERT: E 12 GLN cc_start: 0.9044 (pt0) cc_final: 0.8792 (pt0) REVERT: E 20 ARG cc_start: 0.8357 (ttp-170) cc_final: 0.7806 (ttp-170) REVERT: E 23 LYS cc_start: 0.8501 (ttpt) cc_final: 0.6448 (mptt) REVERT: E 61 GLN cc_start: 0.9011 (tp-100) cc_final: 0.8750 (tp-100) REVERT: E 65 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8501 (tp30) REVERT: E 142 ASP cc_start: 0.8119 (t0) cc_final: 0.7907 (t0) REVERT: F 65 GLU cc_start: 0.8503 (tt0) cc_final: 0.8161 (tt0) REVERT: F 73 GLU cc_start: 0.8912 (tp30) cc_final: 0.8644 (tp30) REVERT: F 75 GLU cc_start: 0.7906 (pp20) cc_final: 0.7642 (pp20) REVERT: F 79 ARG cc_start: 0.8536 (ttm110) cc_final: 0.7937 (ttp-170) REVERT: F 80 PHE cc_start: 0.8010 (m-10) cc_final: 0.7789 (m-10) REVERT: H 52 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7917 (mm-30) REVERT: H 58 GLU cc_start: 0.7457 (mp0) cc_final: 0.7088 (mp0) REVERT: H 96 MET cc_start: 0.9253 (mtp) cc_final: 0.8782 (ttp) REVERT: H 114 ARG cc_start: 0.7788 (ptm160) cc_final: 0.7486 (ptm160) REVERT: H 124 GLU cc_start: 0.8505 (tt0) cc_final: 0.8280 (tt0) REVERT: K 74 VAL cc_start: 0.8250 (OUTLIER) cc_final: 0.7934 (p) REVERT: K 77 TYR cc_start: 0.8269 (m-80) cc_final: 0.8004 (m-80) REVERT: L 15 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8224 (mptp) REVERT: L 62 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7720 (mt-10) REVERT: O 10 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8804 (tptm) REVERT: O 14 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7552 (tm-30) REVERT: O 26 GLU cc_start: 0.8927 (mp0) cc_final: 0.8530 (mp0) REVERT: O 58 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8209 (ttt90) REVERT: O 62 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8520 (tt0) REVERT: O 68 ASP cc_start: 0.8117 (m-30) cc_final: 0.7772 (m-30) REVERT: O 71 LYS cc_start: 0.8514 (tmmt) cc_final: 0.8310 (ttmm) REVERT: O 82 ILE cc_start: 0.8941 (pt) cc_final: 0.8303 (pp) REVERT: O 83 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8102 (mm-30) REVERT: O 88 ARG cc_start: 0.8113 (mmm160) cc_final: 0.7836 (mmm160) REVERT: P 34 GLU cc_start: 0.8420 (tt0) cc_final: 0.8191 (tt0) REVERT: P 77 GLU cc_start: 0.8550 (pp20) cc_final: 0.8250 (pp20) REVERT: P 80 LYS cc_start: 0.8942 (ttpp) cc_final: 0.8535 (ttmm) REVERT: Q 52 GLU cc_start: 0.8642 (tt0) cc_final: 0.8426 (tt0) REVERT: R 25 ASP cc_start: 0.8669 (t0) cc_final: 0.8202 (t0) REVERT: T 24 ARG cc_start: 0.8254 (mmt180) cc_final: 0.7550 (mmm160) outliers start: 62 outliers final: 39 residues processed: 337 average time/residue: 1.6654 time to fit residues: 655.2462 Evaluate side-chains 347 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 302 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 40 GLN Chi-restraints excluded: chain O residue 58 ARG Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 43 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 202 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 chunk 217 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 194 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN O 80 GLN P 9 HIS T 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 35577 Z= 0.221 Angle : 0.550 11.856 53362 Z= 0.292 Chirality : 0.033 0.359 6818 Planarity : 0.005 0.113 2784 Dihedral : 23.444 176.061 18091 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.93 % Allowed : 23.74 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.24), residues: 1213 helix: 0.99 (0.24), residues: 461 sheet: -1.25 (0.32), residues: 238 loop : -0.80 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 60 HIS 0.006 0.001 HIS K 118 PHE 0.022 0.002 PHE F 8 TYR 0.010 0.001 TYR F 59 ARG 0.013 0.001 ARG Q 6 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 325 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 ARG cc_start: 0.7768 (tmm160) cc_final: 0.7276 (ttp80) REVERT: D 141 ASP cc_start: 0.8161 (m-30) cc_final: 0.7784 (m-30) REVERT: D 206 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7959 (ptmt) REVERT: E 12 GLN cc_start: 0.9057 (pt0) cc_final: 0.8768 (pt0) REVERT: E 20 ARG cc_start: 0.8299 (ttp-170) cc_final: 0.7710 (ttp-170) REVERT: E 23 LYS cc_start: 0.8508 (ttpt) cc_final: 0.6479 (mptt) REVERT: E 61 GLN cc_start: 0.9019 (tp-100) cc_final: 0.8747 (tp-100) REVERT: E 65 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8464 (tp30) REVERT: E 142 ASP cc_start: 0.8103 (t0) cc_final: 0.7891 (t0) REVERT: F 65 GLU cc_start: 0.8373 (tt0) cc_final: 0.8073 (tt0) REVERT: F 73 GLU cc_start: 0.8904 (tp30) cc_final: 0.8558 (tp30) REVERT: F 75 GLU cc_start: 0.7944 (pp20) cc_final: 0.7678 (pp20) REVERT: F 79 ARG cc_start: 0.8527 (ttm110) cc_final: 0.7979 (ttp-170) REVERT: F 80 PHE cc_start: 0.7981 (m-10) cc_final: 0.7714 (m-10) REVERT: F 90 MET cc_start: 0.7972 (ptm) cc_final: 0.7493 (ptm) REVERT: H 42 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8074 (mt-10) REVERT: H 52 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7854 (mm-30) REVERT: H 58 GLU cc_start: 0.7512 (mp0) cc_final: 0.7098 (mp0) REVERT: H 96 MET cc_start: 0.9240 (mtp) cc_final: 0.8762 (ttp) REVERT: H 114 ARG cc_start: 0.7778 (ptm160) cc_final: 0.7556 (ptm160) REVERT: K 77 TYR cc_start: 0.8282 (m-80) cc_final: 0.7848 (m-10) REVERT: K 106 ARG cc_start: 0.8106 (tmm160) cc_final: 0.7872 (tmm160) REVERT: L 15 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8314 (mptt) REVERT: L 62 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7756 (mt-10) REVERT: O 10 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8811 (tptm) REVERT: O 14 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7590 (tm-30) REVERT: O 26 GLU cc_start: 0.8904 (mp0) cc_final: 0.8523 (mp0) REVERT: O 62 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8369 (tp40) REVERT: O 68 ASP cc_start: 0.8124 (m-30) cc_final: 0.7793 (m-30) REVERT: O 82 ILE cc_start: 0.8907 (pt) cc_final: 0.8236 (pp) REVERT: O 83 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8028 (mm-30) REVERT: O 88 ARG cc_start: 0.8100 (mmm160) cc_final: 0.7817 (mmm160) REVERT: P 77 GLU cc_start: 0.8594 (pp20) cc_final: 0.8176 (pp20) REVERT: P 80 LYS cc_start: 0.8944 (ttpp) cc_final: 0.8533 (ttmm) REVERT: Q 25 ILE cc_start: 0.9308 (mp) cc_final: 0.9044 (mp) REVERT: R 25 ASP cc_start: 0.8608 (t0) cc_final: 0.8362 (t0) REVERT: T 24 ARG cc_start: 0.8240 (mmt180) cc_final: 0.7556 (mmm160) outliers start: 50 outliers final: 32 residues processed: 339 average time/residue: 1.5894 time to fit residues: 630.9043 Evaluate side-chains 344 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 307 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 40 GLN Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 43 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 181 optimal weight: 0.0980 chunk 123 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 185 optimal weight: 0.7980 chunk 150 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 195 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN T 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35577 Z= 0.266 Angle : 0.556 11.948 53362 Z= 0.295 Chirality : 0.034 0.342 6818 Planarity : 0.004 0.113 2784 Dihedral : 23.374 175.914 18091 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 6.21 % Allowed : 24.24 % Favored : 69.56 % 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: -0.24 (0.24), residues: 1213 helix: 1.04 (0.24), residues: 461 sheet: -1.08 (0.33), residues: 233 loop : -0.70 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Q 73 HIS 0.005 0.001 HIS K 118 PHE 0.016 0.001 PHE F 8 TYR 0.010 0.001 TYR R 51 ARG 0.009 0.000 ARG Q 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 315 time to evaluate : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 ARG cc_start: 0.7783 (tmm160) cc_final: 0.7293 (ttp80) REVERT: D 141 ASP cc_start: 0.8162 (m-30) cc_final: 0.7774 (m-30) REVERT: D 206 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7954 (ptmt) REVERT: E 10 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8226 (tm-30) REVERT: E 12 GLN cc_start: 0.9055 (pt0) cc_final: 0.8809 (pt0) REVERT: E 20 ARG cc_start: 0.8313 (ttp-170) cc_final: 0.7727 (ttp-170) REVERT: E 23 LYS cc_start: 0.8534 (ttpt) cc_final: 0.6573 (mptt) REVERT: E 61 GLN cc_start: 0.9018 (tp-100) cc_final: 0.8747 (tp-100) REVERT: E 142 ASP cc_start: 0.8122 (t0) cc_final: 0.7897 (t0) REVERT: F 2 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7815 (ptp-170) REVERT: F 33 GLU cc_start: 0.8491 (mp0) cc_final: 0.7857 (tm-30) REVERT: F 65 GLU cc_start: 0.8445 (tt0) cc_final: 0.8051 (tt0) REVERT: F 73 GLU cc_start: 0.8919 (tp30) cc_final: 0.8475 (tp30) REVERT: F 75 GLU cc_start: 0.7920 (pp20) cc_final: 0.7662 (pp20) REVERT: F 79 ARG cc_start: 0.8500 (ttm110) cc_final: 0.7991 (ttp-170) REVERT: F 80 PHE cc_start: 0.7988 (m-10) cc_final: 0.7670 (m-10) REVERT: F 90 MET cc_start: 0.8009 (ptm) cc_final: 0.7549 (ptm) REVERT: H 52 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7858 (mm-30) REVERT: H 58 GLU cc_start: 0.7521 (mp0) cc_final: 0.7099 (mp0) REVERT: H 114 ARG cc_start: 0.7762 (ptm160) cc_final: 0.7526 (ptm160) REVERT: L 62 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7721 (mt-10) REVERT: O 10 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8812 (tptm) REVERT: O 14 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7568 (tm-30) REVERT: O 26 GLU cc_start: 0.8799 (mp0) cc_final: 0.8513 (mp0) REVERT: O 58 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8201 (ttt90) REVERT: O 62 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8368 (tp40) REVERT: O 68 ASP cc_start: 0.8135 (m-30) cc_final: 0.7796 (m-30) REVERT: O 82 ILE cc_start: 0.8927 (pt) cc_final: 0.8287 (pp) REVERT: O 83 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8133 (mm-30) REVERT: O 88 ARG cc_start: 0.8119 (mmm160) cc_final: 0.7829 (mmm160) REVERT: P 77 GLU cc_start: 0.8581 (pp20) cc_final: 0.8178 (pp20) REVERT: P 80 LYS cc_start: 0.8915 (ttpp) cc_final: 0.8513 (ttmm) REVERT: Q 16 LYS cc_start: 0.8979 (mtpp) cc_final: 0.8763 (mtpp) REVERT: Q 26 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7666 (mm-30) REVERT: R 24 LYS cc_start: 0.8771 (mtmm) cc_final: 0.8558 (mtmm) REVERT: R 25 ASP cc_start: 0.8600 (t0) cc_final: 0.8398 (t0) REVERT: T 24 ARG cc_start: 0.8228 (mmt180) cc_final: 0.7529 (mmm160) outliers start: 63 outliers final: 39 residues processed: 338 average time/residue: 1.6357 time to fit residues: 645.5672 Evaluate side-chains 352 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 306 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 2 ARG Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 40 GLN Chi-restraints excluded: chain O residue 58 ARG Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 26 GLU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain T residue 80 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 73 optimal weight: 7.9990 chunk 195 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 127 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 217 optimal weight: 0.0470 chunk 180 optimal weight: 0.0970 chunk 100 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 overall best weight: 1.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN ** Q 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35577 Z= 0.173 Angle : 0.537 11.844 53362 Z= 0.286 Chirality : 0.032 0.340 6818 Planarity : 0.005 0.113 2784 Dihedral : 23.390 175.624 18091 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 5.32 % Allowed : 26.01 % Favored : 68.67 % 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: -0.14 (0.24), residues: 1213 helix: 1.05 (0.24), residues: 461 sheet: -0.98 (0.34), residues: 233 loop : -0.59 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 60 HIS 0.005 0.001 HIS K 118 PHE 0.023 0.001 PHE K 61 TYR 0.023 0.001 TYR K 77 ARG 0.014 0.000 ARG Q 6 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 319 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 ARG cc_start: 0.7767 (tmm160) cc_final: 0.7298 (ttp80) REVERT: D 141 ASP cc_start: 0.8149 (m-30) cc_final: 0.7779 (m-30) REVERT: D 206 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7924 (ptmt) REVERT: E 11 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8075 (pp) REVERT: E 12 GLN cc_start: 0.9045 (pt0) cc_final: 0.8774 (pt0) REVERT: E 20 ARG cc_start: 0.8274 (ttp-170) cc_final: 0.7682 (ttp-170) REVERT: E 23 LYS cc_start: 0.8569 (ttpt) cc_final: 0.6610 (mptt) REVERT: E 61 GLN cc_start: 0.9018 (tp-100) cc_final: 0.8737 (tp-100) REVERT: E 142 ASP cc_start: 0.8110 (t0) cc_final: 0.7866 (t0) REVERT: F 2 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7842 (ptp-170) REVERT: F 33 GLU cc_start: 0.8524 (mp0) cc_final: 0.7876 (tm-30) REVERT: F 53 LYS cc_start: 0.8774 (mtpp) cc_final: 0.8444 (mtpp) REVERT: F 65 GLU cc_start: 0.8408 (tt0) cc_final: 0.8093 (tt0) REVERT: F 73 GLU cc_start: 0.8924 (tp30) cc_final: 0.8465 (tp30) REVERT: F 75 GLU cc_start: 0.7973 (pp20) cc_final: 0.7696 (pp20) REVERT: F 79 ARG cc_start: 0.8514 (ttm110) cc_final: 0.8010 (ttp-170) REVERT: F 80 PHE cc_start: 0.7956 (m-10) cc_final: 0.7618 (m-10) REVERT: F 90 MET cc_start: 0.7982 (ptm) cc_final: 0.7510 (ptm) REVERT: F 98 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7448 (tm-30) REVERT: H 52 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7888 (mm-30) REVERT: H 58 GLU cc_start: 0.7511 (mp0) cc_final: 0.7086 (mp0) REVERT: K 18 ASP cc_start: 0.8136 (p0) cc_final: 0.7728 (p0) REVERT: K 77 TYR cc_start: 0.8038 (m-80) cc_final: 0.7829 (m-80) REVERT: K 80 LYS cc_start: 0.8660 (mptt) cc_final: 0.8427 (mmtp) REVERT: L 62 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7729 (mt-10) REVERT: L 82 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8868 (tt) REVERT: O 10 LYS cc_start: 0.9145 (tppp) cc_final: 0.8815 (tptm) REVERT: O 14 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7618 (tm-30) REVERT: O 26 GLU cc_start: 0.8778 (mp0) cc_final: 0.8493 (mp0) REVERT: O 62 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8353 (tp40) REVERT: O 68 ASP cc_start: 0.8125 (m-30) cc_final: 0.7801 (m-30) REVERT: O 71 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8171 (ttmm) REVERT: O 82 ILE cc_start: 0.8923 (pt) cc_final: 0.8286 (pp) REVERT: O 83 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8120 (mm-30) REVERT: P 48 GLU cc_start: 0.7895 (tt0) cc_final: 0.7593 (tt0) REVERT: P 76 LYS cc_start: 0.8996 (ttmm) cc_final: 0.8686 (ttmp) REVERT: P 80 LYS cc_start: 0.8914 (ttpp) cc_final: 0.8519 (ttmm) REVERT: Q 80 GLU cc_start: 0.7246 (pp20) cc_final: 0.7043 (pp20) REVERT: T 24 ARG cc_start: 0.8222 (mmt180) cc_final: 0.7519 (mmm160) outliers start: 54 outliers final: 34 residues processed: 340 average time/residue: 1.5982 time to fit residues: 638.1428 Evaluate side-chains 350 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 309 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 185 LYS Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 2 ARG Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 40 GLN Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain O residue 71 LYS Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 44 SER Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 43 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 209 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 183 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 216 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN ** Q 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 35577 Z= 0.428 Angle : 0.634 12.165 53362 Z= 0.332 Chirality : 0.039 0.342 6818 Planarity : 0.005 0.113 2784 Dihedral : 23.353 176.856 18091 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 6.11 % Allowed : 26.60 % Favored : 67.29 % 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: -0.19 (0.24), residues: 1213 helix: 0.98 (0.24), residues: 455 sheet: -1.02 (0.33), residues: 238 loop : -0.56 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 73 HIS 0.004 0.001 HIS T 68 PHE 0.025 0.002 PHE F 8 TYR 0.021 0.002 TYR K 77 ARG 0.007 0.001 ARG Q 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 306 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 ARG cc_start: 0.7877 (tmm160) cc_final: 0.7411 (ttp80) REVERT: D 141 ASP cc_start: 0.8188 (m-30) cc_final: 0.7766 (m-30) REVERT: D 206 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8017 (ptmt) REVERT: E 10 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8198 (tm-30) REVERT: E 11 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8083 (pp) REVERT: E 12 GLN cc_start: 0.9024 (pt0) cc_final: 0.8776 (pt0) REVERT: E 23 LYS cc_start: 0.8528 (ttpt) cc_final: 0.6496 (mptm) REVERT: E 61 GLN cc_start: 0.9018 (tp-100) cc_final: 0.8749 (tp-100) REVERT: F 53 LYS cc_start: 0.8893 (mtpp) cc_final: 0.8580 (mtpp) REVERT: F 65 GLU cc_start: 0.8354 (tt0) cc_final: 0.8074 (tt0) REVERT: F 73 GLU cc_start: 0.8969 (tp30) cc_final: 0.8655 (tp30) REVERT: F 75 GLU cc_start: 0.7936 (pp20) cc_final: 0.7661 (pp20) REVERT: F 79 ARG cc_start: 0.8459 (ttm110) cc_final: 0.7953 (ttp-170) REVERT: F 80 PHE cc_start: 0.8009 (m-10) cc_final: 0.7692 (m-10) REVERT: H 52 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7881 (mm-30) REVERT: H 58 GLU cc_start: 0.7545 (mp0) cc_final: 0.7132 (mp0) REVERT: K 18 ASP cc_start: 0.8191 (p0) cc_final: 0.7689 (p0) REVERT: K 80 LYS cc_start: 0.8688 (mptt) cc_final: 0.8454 (mmtp) REVERT: L 62 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7651 (mt-10) REVERT: O 10 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8793 (tptm) REVERT: O 14 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7521 (tm-30) REVERT: O 26 GLU cc_start: 0.8816 (mp0) cc_final: 0.8459 (mp0) REVERT: O 58 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8256 (ttt90) REVERT: O 62 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8535 (tt0) REVERT: O 68 ASP cc_start: 0.8119 (m-30) cc_final: 0.7772 (m-30) REVERT: O 82 ILE cc_start: 0.8946 (pt) cc_final: 0.8289 (pp) REVERT: O 83 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8153 (mm-30) REVERT: P 34 GLU cc_start: 0.8423 (tt0) cc_final: 0.8199 (tt0) REVERT: P 77 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8115 (pp20) REVERT: P 80 LYS cc_start: 0.8913 (ttpp) cc_final: 0.8517 (ttmm) REVERT: Q 39 LYS cc_start: 0.8794 (mtpt) cc_final: 0.8586 (mtmm) REVERT: R 25 ASP cc_start: 0.8592 (t0) cc_final: 0.8286 (t70) REVERT: T 24 ARG cc_start: 0.8247 (mmt180) cc_final: 0.7532 (mmm160) outliers start: 62 outliers final: 42 residues processed: 331 average time/residue: 1.6055 time to fit residues: 621.6218 Evaluate side-chains 346 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 297 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 109 ASN Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 40 GLN Chi-restraints excluded: chain O residue 58 ARG Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 80 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 134 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 137 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 170 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN ** Q 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 35577 Z= 0.261 Angle : 0.588 12.029 53362 Z= 0.312 Chirality : 0.034 0.340 6818 Planarity : 0.005 0.113 2784 Dihedral : 23.406 176.659 18091 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 5.71 % Allowed : 27.68 % Favored : 66.60 % 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: -0.16 (0.24), residues: 1213 helix: 0.94 (0.24), residues: 456 sheet: -0.92 (0.34), residues: 233 loop : -0.53 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 73 HIS 0.005 0.001 HIS P 59 PHE 0.028 0.002 PHE K 61 TYR 0.042 0.002 TYR K 77 ARG 0.017 0.001 ARG Q 6 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 307 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 ARG cc_start: 0.7880 (tmm160) cc_final: 0.7400 (ttp80) REVERT: D 141 ASP cc_start: 0.8169 (m-30) cc_final: 0.7760 (m-30) REVERT: D 206 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7977 (ptmt) REVERT: E 10 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8215 (tm-30) REVERT: E 11 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8061 (pp) REVERT: E 12 GLN cc_start: 0.9026 (pt0) cc_final: 0.8741 (pt0) REVERT: E 23 LYS cc_start: 0.8505 (ttpt) cc_final: 0.6511 (mptt) REVERT: E 61 GLN cc_start: 0.9012 (tp-100) cc_final: 0.8749 (tp-100) REVERT: F 53 LYS cc_start: 0.8809 (mtpp) cc_final: 0.8490 (mtpp) REVERT: F 65 GLU cc_start: 0.8371 (tt0) cc_final: 0.8119 (tt0) REVERT: F 73 GLU cc_start: 0.8932 (tp30) cc_final: 0.8618 (tp30) REVERT: F 75 GLU cc_start: 0.7921 (pp20) cc_final: 0.7639 (pp20) REVERT: F 79 ARG cc_start: 0.8467 (ttm110) cc_final: 0.7966 (ttp-170) REVERT: F 80 PHE cc_start: 0.7999 (m-10) cc_final: 0.7686 (m-10) REVERT: H 52 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7861 (mm-30) REVERT: H 58 GLU cc_start: 0.7511 (mp0) cc_final: 0.7115 (mp0) REVERT: L 62 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7677 (mt-10) REVERT: O 10 LYS cc_start: 0.9127 (tppp) cc_final: 0.8782 (tptm) REVERT: O 14 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7532 (tm-30) REVERT: O 26 GLU cc_start: 0.8793 (mp0) cc_final: 0.8444 (mp0) REVERT: O 58 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8234 (ttt90) REVERT: O 62 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8378 (tp40) REVERT: O 68 ASP cc_start: 0.8116 (m-30) cc_final: 0.7781 (m-30) REVERT: O 82 ILE cc_start: 0.8945 (pt) cc_final: 0.8270 (pp) REVERT: O 83 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8083 (mm-30) REVERT: P 34 GLU cc_start: 0.8391 (tt0) cc_final: 0.8142 (tt0) REVERT: P 76 LYS cc_start: 0.9026 (ttmm) cc_final: 0.8726 (ttmp) REVERT: P 77 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8093 (pp20) REVERT: P 80 LYS cc_start: 0.8908 (ttpp) cc_final: 0.8518 (ttmm) REVERT: R 25 ASP cc_start: 0.8546 (t0) cc_final: 0.8244 (t0) REVERT: T 12 ILE cc_start: 0.9107 (mt) cc_final: 0.8905 (mt) REVERT: T 24 ARG cc_start: 0.8232 (mmt180) cc_final: 0.7519 (mmm160) outliers start: 58 outliers final: 43 residues processed: 329 average time/residue: 1.6274 time to fit residues: 628.0426 Evaluate side-chains 350 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 301 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 40 GLN Chi-restraints excluded: chain O residue 58 ARG Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 80 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 207 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 202 optimal weight: 0.8980 chunk 121 optimal weight: 0.0020 chunk 88 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 201 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 overall best weight: 1.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 HIS L 5 ASN O 80 GLN ** Q 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35577 Z= 0.201 Angle : 0.551 11.886 53362 Z= 0.292 Chirality : 0.032 0.331 6818 Planarity : 0.004 0.113 2784 Dihedral : 23.342 175.468 18091 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.43 % Allowed : 28.57 % Favored : 67.00 % 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: 0.03 (0.25), residues: 1213 helix: 1.16 (0.25), residues: 451 sheet: -0.92 (0.34), residues: 238 loop : -0.40 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Q 73 HIS 0.004 0.001 HIS K 118 PHE 0.023 0.001 PHE F 8 TYR 0.029 0.002 TYR K 77 ARG 0.009 0.000 ARG Q 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 308 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 ARG cc_start: 0.7772 (tmm160) cc_final: 0.7353 (ttp80) REVERT: D 141 ASP cc_start: 0.8155 (m-30) cc_final: 0.7780 (m-30) REVERT: D 174 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.7245 (p0) REVERT: D 206 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7933 (ptmt) REVERT: E 11 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8060 (pp) REVERT: E 12 GLN cc_start: 0.9026 (pt0) cc_final: 0.8738 (pt0) REVERT: E 23 LYS cc_start: 0.8507 (ttpt) cc_final: 0.6530 (mptt) REVERT: E 61 GLN cc_start: 0.9011 (tp-100) cc_final: 0.8740 (tp-100) REVERT: F 5 GLU cc_start: 0.8499 (tt0) cc_final: 0.8109 (tt0) REVERT: F 65 GLU cc_start: 0.8419 (tt0) cc_final: 0.8140 (tt0) REVERT: F 73 GLU cc_start: 0.8914 (tp30) cc_final: 0.8484 (tp30) REVERT: F 75 GLU cc_start: 0.7936 (pp20) cc_final: 0.7677 (pp20) REVERT: F 79 ARG cc_start: 0.8488 (ttm110) cc_final: 0.8006 (ttp-170) REVERT: F 80 PHE cc_start: 0.7993 (m-10) cc_final: 0.7709 (m-10) REVERT: F 90 MET cc_start: 0.7956 (ptm) cc_final: 0.7488 (ptm) REVERT: H 52 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7896 (mm-30) REVERT: H 58 GLU cc_start: 0.7560 (mp0) cc_final: 0.7133 (mp0) REVERT: K 18 ASP cc_start: 0.7991 (p0) cc_final: 0.7563 (p0) REVERT: L 62 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7717 (mt-10) REVERT: O 10 LYS cc_start: 0.9143 (tppp) cc_final: 0.8814 (tptm) REVERT: O 14 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7605 (tm-30) REVERT: O 26 GLU cc_start: 0.8810 (mp0) cc_final: 0.8475 (mp0) REVERT: O 58 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8211 (ttt90) REVERT: O 62 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8360 (tp40) REVERT: O 68 ASP cc_start: 0.8079 (m-30) cc_final: 0.7752 (m-30) REVERT: O 82 ILE cc_start: 0.8918 (pt) cc_final: 0.8274 (pp) REVERT: O 83 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8079 (mm-30) REVERT: P 77 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8155 (pp20) REVERT: P 80 LYS cc_start: 0.8908 (ttpp) cc_final: 0.8514 (ttmm) REVERT: Q 39 LYS cc_start: 0.8731 (mtpt) cc_final: 0.8456 (mtmm) REVERT: R 25 ASP cc_start: 0.8483 (t0) cc_final: 0.8143 (t0) REVERT: T 24 ARG cc_start: 0.8215 (mmt180) cc_final: 0.7502 (mmm160) outliers start: 45 outliers final: 32 residues processed: 327 average time/residue: 1.5587 time to fit residues: 598.8007 Evaluate side-chains 339 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 300 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 40 GLN Chi-restraints excluded: chain O residue 58 ARG Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 80 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 213 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 chunk 101 optimal weight: 20.0000 chunk 148 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 chunk 206 optimal weight: 0.8980 chunk 178 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 137 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN O 80 GLN ** P 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35577 Z= 0.206 Angle : 0.553 11.873 53362 Z= 0.293 Chirality : 0.032 0.321 6818 Planarity : 0.005 0.113 2784 Dihedral : 23.312 175.354 18091 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.04 % Allowed : 29.26 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.25), residues: 1213 helix: 1.12 (0.25), residues: 455 sheet: -0.84 (0.34), residues: 234 loop : -0.34 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Q 73 HIS 0.006 0.001 HIS P 59 PHE 0.031 0.002 PHE K 61 TYR 0.010 0.001 TYR Q 34 ARG 0.020 0.001 ARG Q 6 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 309 time to evaluate : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 ARG cc_start: 0.7776 (tmm160) cc_final: 0.7365 (ttp80) REVERT: D 141 ASP cc_start: 0.8161 (m-30) cc_final: 0.7792 (m-30) REVERT: D 174 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7270 (p0) REVERT: D 206 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7932 (ptmt) REVERT: E 11 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8098 (pp) REVERT: E 12 GLN cc_start: 0.9020 (pt0) cc_final: 0.8728 (pt0) REVERT: E 23 LYS cc_start: 0.8508 (ttpt) cc_final: 0.6533 (mptt) REVERT: E 61 GLN cc_start: 0.9008 (tp-100) cc_final: 0.8725 (tp-100) REVERT: E 163 GLU cc_start: 0.8136 (tt0) cc_final: 0.7920 (tm-30) REVERT: F 5 GLU cc_start: 0.8477 (tt0) cc_final: 0.8053 (tt0) REVERT: F 44 ARG cc_start: 0.8249 (mtt180) cc_final: 0.7892 (mtt180) REVERT: F 53 LYS cc_start: 0.8658 (mtpp) cc_final: 0.8269 (mtpp) REVERT: F 65 GLU cc_start: 0.8445 (tt0) cc_final: 0.8175 (tt0) REVERT: F 73 GLU cc_start: 0.8931 (tp30) cc_final: 0.8553 (tp30) REVERT: F 75 GLU cc_start: 0.7913 (pp20) cc_final: 0.7674 (pp20) REVERT: F 79 ARG cc_start: 0.8510 (ttm110) cc_final: 0.8078 (ttp-110) REVERT: F 80 PHE cc_start: 0.8001 (m-10) cc_final: 0.7714 (m-10) REVERT: F 90 MET cc_start: 0.7929 (ptm) cc_final: 0.7507 (ptm) REVERT: H 42 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7856 (mt-10) REVERT: H 52 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7896 (mm-30) REVERT: H 58 GLU cc_start: 0.7553 (mp0) cc_final: 0.7128 (mp0) REVERT: K 18 ASP cc_start: 0.8035 (p0) cc_final: 0.7608 (p0) REVERT: L 62 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7714 (mt-10) REVERT: O 10 LYS cc_start: 0.9146 (tppp) cc_final: 0.8818 (tptm) REVERT: O 14 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7614 (tm-30) REVERT: O 26 GLU cc_start: 0.8811 (mp0) cc_final: 0.8477 (mp0) REVERT: O 58 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8202 (ttt90) REVERT: O 62 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8355 (tp40) REVERT: O 68 ASP cc_start: 0.8080 (m-30) cc_final: 0.7751 (m-30) REVERT: O 82 ILE cc_start: 0.8900 (pt) cc_final: 0.8244 (pp) REVERT: O 83 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8072 (mm-30) REVERT: P 77 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8153 (pp20) REVERT: P 80 LYS cc_start: 0.8915 (ttpp) cc_final: 0.8528 (ttmm) REVERT: Q 39 LYS cc_start: 0.8776 (mtpt) cc_final: 0.8463 (mtmm) REVERT: R 25 ASP cc_start: 0.8434 (t0) cc_final: 0.8095 (t0) REVERT: T 24 ARG cc_start: 0.8215 (mmt180) cc_final: 0.7490 (mmm160) REVERT: T 53 GLU cc_start: 0.8665 (tt0) cc_final: 0.8462 (tp30) outliers start: 41 outliers final: 31 residues processed: 327 average time/residue: 1.6432 time to fit residues: 628.8783 Evaluate side-chains 341 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 303 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 40 GLN Chi-restraints excluded: chain O residue 58 ARG Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 80 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 190 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 164 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 178 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 183 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN O 80 GLN ** P 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.070599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.047418 restraints weight = 86550.818| |-----------------------------------------------------------------------------| r_work (start): 0.2675 rms_B_bonded: 1.11 r_work: 0.2554 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2457 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 35577 Z= 0.325 Angle : 0.596 12.021 53362 Z= 0.313 Chirality : 0.035 0.318 6818 Planarity : 0.005 0.113 2784 Dihedral : 23.295 176.397 18091 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.83 % Allowed : 29.16 % Favored : 66.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.24), residues: 1213 helix: 0.95 (0.24), residues: 461 sheet: -0.88 (0.34), residues: 236 loop : -0.41 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 73 HIS 0.006 0.001 HIS P 59 PHE 0.021 0.002 PHE F 8 TYR 0.023 0.002 TYR F 4 ARG 0.011 0.001 ARG Q 6 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10410.03 seconds wall clock time: 186 minutes 3.73 seconds (11163.73 seconds total)