Starting phenix.real_space_refine on Sun Mar 17 14:15:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca7_16520/03_2024/8ca7_16520_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca7_16520/03_2024/8ca7_16520.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca7_16520/03_2024/8ca7_16520_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca7_16520/03_2024/8ca7_16520_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca7_16520/03_2024/8ca7_16520_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca7_16520/03_2024/8ca7_16520.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca7_16520/03_2024/8ca7_16520.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca7_16520/03_2024/8ca7_16520_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca7_16520/03_2024/8ca7_16520_updated.pdb" } resolution = 2.06 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= 0.002 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: 7 Type Number sf(0) Gaussians K 14 8.98 5 P 502 5.49 5 Mg 26 5.21 5 S 18 5.16 5 C 9045 2.51 5 N 3258 2.21 5 O 5230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 28": "OE1" <-> "OE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C GLU 152": "OE1" <-> "OE2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "C ARG 164": "NH1" <-> "NH2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C GLU 206": "OE1" <-> "OE2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G GLU 40": "OE1" <-> "OE2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "G GLU 67": "OE1" <-> "OE2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "G GLU 106": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "I GLU 36": "OE1" <-> "OE2" Residue "I ARG 41": "NH1" <-> "NH2" Residue "I GLU 53": "OE1" <-> "OE2" Residue "I GLU 59": "OE1" <-> "OE2" Residue "I GLU 89": "OE1" <-> "OE2" Residue "I GLU 92": "OE1" <-> "OE2" Residue "I ARG 99": "NH1" <-> "NH2" Residue "I ARG 106": "NH1" <-> "NH2" Residue "I ARG 109": "NH1" <-> "NH2" Residue "I GLU 112": "OE1" <-> "OE2" Residue "I ARG 113": "NH1" <-> "NH2" Residue "I ARG 123": "NH1" <-> "NH2" Residue "J GLU 24": "OE1" <-> "OE2" Residue "J GLU 27": "OE1" <-> "OE2" Residue "J GLU 66": "OE1" <-> "OE2" Residue "M GLU 41": "OE1" <-> "OE2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M GLU 50": "OE1" <-> "OE2" Residue "M GLU 59": "OE1" <-> "OE2" Residue "M GLU 66": "OE1" <-> "OE2" Residue "M GLU 72": "OE1" <-> "OE2" Residue "M TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 87": "NH1" <-> "NH2" Residue "N GLU 10": "OE1" <-> "OE2" Residue "N GLU 26": "OE1" <-> "OE2" Residue "N GLU 39": "OE1" <-> "OE2" Residue "N GLU 86": "OE1" <-> "OE2" Residue "N GLU 92": "OE1" <-> "OE2" Residue "S GLU 20": "OE1" <-> "OE2" Residue "S GLU 24": "OE1" <-> "OE2" Residue "S ARG 36": "NH1" <-> "NH2" Residue "S ASP 64": "OD1" <-> "OD2" Residue "S GLU 65": "OE1" <-> "OE2" Residue "S GLU 73": "OE1" <-> "OE2" Residue "S ARG 81": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18093 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 10741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 10741 Classifications: {'RNA': 502} Modifications used: {'rna2p_pur': 44, 'rna2p_pyr': 35, 'rna3p': 4, 'rna3p_pur': 228, 'rna3p_pyr': 191} Link IDs: {'rna2p': 79, 'rna3p': 422} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "E" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 272 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain breaks: 1 Chain: "G" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 793 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain breaks: 2 Chain: "I" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1001 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "J" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 667 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain breaks: 1 Chain: "M" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 876 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "S" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 668 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 102 Unusual residues: {' K': 14, ' MG': 25, 'SCM': 1, 'U3B': 1} Classifications: {'undetermined': 41} Link IDs: {None: 40} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 449 Classifications: {'water': 449} Link IDs: {None: 448} Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "J" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "M" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "N" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "S" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 9.94, per 1000 atoms: 0.55 Number of scatterers: 18093 At special positions: 0 Unit cell: (117.348, 128.016, 125.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 14 19.00 S 18 16.00 P 502 15.00 Mg 26 11.99 O 5230 8.00 N 3258 7.00 C 9045 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: 10.93 Conformation dependent library (CDL) restraints added in 1.4 seconds 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1570 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 35 helices and 8 sheets defined 42.3% alpha, 15.9% beta 153 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 10.49 Creating SS restraints... Processing helix chain 'C' and resid 7 through 11 removed outlier: 3.824A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 7 through 11' Processing helix chain 'C' and resid 26 through 46 removed outlier: 4.370A pdb=" N ALA C 30 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ASP C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 79 through 95 removed outlier: 6.237A pdb=" N ASP C 83 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL C 84 " --> pdb=" O GLY C 81 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS C 86 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS C 89 " --> pdb=" O LYS C 86 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL C 91 " --> pdb=" O ARG C 88 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA C 95 " --> pdb=" O ALA C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 111 No H-bonds generated for 'chain 'C' and resid 109 through 111' Processing helix chain 'C' and resid 113 through 126 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'E' and resid 56 through 64 Processing helix chain 'G' and resid 21 through 30 Processing helix chain 'G' and resid 36 through 52 Processing helix chain 'G' and resid 58 through 69 removed outlier: 3.536A pdb=" N ASN G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 110 Processing helix chain 'G' and resid 116 through 125 Processing helix chain 'I' and resid 35 through 38 No H-bonds generated for 'chain 'I' and resid 35 through 38' Processing helix chain 'I' and resid 42 through 55 Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 72 through 90 removed outlier: 3.502A pdb=" N GLU I 89 " --> pdb=" O ARG I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 100 Processing helix chain 'J' and resid 15 through 32 removed outlier: 3.503A pdb=" N THR J 32 " --> pdb=" O THR J 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 21 removed outlier: 4.088A pdb=" N THR M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 37 Processing helix chain 'M' and resid 45 through 47 No H-bonds generated for 'chain 'M' and resid 45 through 47' Processing helix chain 'M' and resid 50 through 62 removed outlier: 3.564A pdb=" N ALA M 61 " --> pdb=" O ARG M 57 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 83 Processing helix chain 'M' and resid 86 through 93 Processing helix chain 'M' and resid 107 through 110 No H-bonds generated for 'chain 'M' and resid 107 through 110' Processing helix chain 'N' and resid 4 through 19 Processing helix chain 'N' and resid 21 through 32 Processing helix chain 'N' and resid 38 through 50 removed outlier: 3.584A pdb=" N GLN N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR N 50 " --> pdb=" O LEU N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 55 No H-bonds generated for 'chain 'N' and resid 53 through 55' Processing helix chain 'N' and resid 57 through 59 No H-bonds generated for 'chain 'N' and resid 57 through 59' Processing helix chain 'N' and resid 81 through 89 Processing helix chain 'S' and resid 13 through 25 Processing helix chain 'S' and resid 42 through 44 No H-bonds generated for 'chain 'S' and resid 42 through 44' Processing helix chain 'S' and resid 71 through 74 Processing sheet with id= A, first strand: chain 'C' and resid 99 through 105 removed outlier: 6.527A pdb=" N ILE C 64 " --> pdb=" O GLN C 100 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ASN C 102 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL C 66 " --> pdb=" O ASN C 102 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ALA C 104 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ILE C 68 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 164 through 171 Processing sheet with id= C, first strand: chain 'E' and resid 20 through 25 removed outlier: 3.985A pdb=" N ALA E 35 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY E 51 " --> pdb=" O ALA E 35 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'I' and resid 6 through 12 Processing sheet with id= E, first strand: chain 'J' and resid 96 through 101 removed outlier: 3.515A pdb=" N ARG J 7 " --> pdb=" O SER J 101 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP J 75 " --> pdb=" O ARG J 37 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'J' and resid 40 through 42 removed outlier: 4.551A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 45 through 52 Processing sheet with id= H, first strand: chain 'S' and resid 31 through 33 298 hydrogen bonds defined for protein. 831 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 382 hydrogen bonds 608 hydrogen bond angles 0 basepair planarities 153 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 13.27 Time building geometry restraints manager: 11.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2700 1.34 - 1.46: 8578 1.46 - 1.59: 6572 1.59 - 1.71: 997 1.71 - 1.83: 34 Bond restraints: 18881 Sorted by residual: bond pdb=" C6 SCM A1603 " pdb=" O1 SCM A1603 " ideal model delta sigma weight residual 0.917 1.416 -0.499 2.00e-02 2.50e+03 6.22e+02 bond pdb=" C3 SCM A1603 " pdb=" C4 SCM A1603 " ideal model delta sigma weight residual 1.054 1.509 -0.455 2.00e-02 2.50e+03 5.18e+02 bond pdb=" C7 SCM A1603 " pdb=" O1B SCM A1603 " ideal model delta sigma weight residual 1.166 1.429 -0.263 2.00e-02 2.50e+03 1.73e+02 bond pdb=" C6 SCM A1603 " pdb=" O2B SCM A1603 " ideal model delta sigma weight residual 1.165 1.417 -0.252 2.00e-02 2.50e+03 1.59e+02 bond pdb=" C20 U3B A1602 " pdb=" C21 U3B A1602 " ideal model delta sigma weight residual 1.605 1.390 0.215 2.00e-02 2.50e+03 1.15e+02 ... (remaining 18876 not shown) Histogram of bond angle deviations from ideal: 81.86 - 92.53: 2 92.53 - 103.20: 1498 103.20 - 113.87: 12714 113.87 - 124.54: 11518 124.54 - 135.21: 2207 Bond angle restraints: 27939 Sorted by residual: angle pdb=" O3' U A 981 " pdb=" P U A 982 " pdb=" OP2 U A 982 " ideal model delta sigma weight residual 108.00 81.86 26.14 3.00e+00 1.11e-01 7.59e+01 angle pdb=" O3' C A1369 " pdb=" P G A1370 " pdb=" O5' G A1370 " ideal model delta sigma weight residual 104.00 92.15 11.85 1.50e+00 4.44e-01 6.24e+01 angle pdb=" O3' G A1347 " pdb=" P U A1348 " pdb=" O5' U A1348 " ideal model delta sigma weight residual 104.00 92.56 11.44 1.50e+00 4.44e-01 5.82e+01 angle pdb=" O3' U A 981 " pdb=" P U A 982 " pdb=" OP1 U A 982 " ideal model delta sigma weight residual 108.00 129.92 -21.92 3.00e+00 1.11e-01 5.34e+01 angle pdb=" C1' 2MG A1207 " pdb=" N9 2MG A1207 " pdb=" C8 2MG A1207 " ideal model delta sigma weight residual 110.07 129.03 -18.96 3.00e+00 1.11e-01 3.99e+01 ... (remaining 27934 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.67: 10790 33.67 - 67.35: 1099 67.35 - 101.02: 155 101.02 - 134.69: 0 134.69 - 168.37: 5 Dihedral angle restraints: 12049 sinusoidal: 9627 harmonic: 2422 Sorted by residual: dihedral pdb=" O4' C A1158 " pdb=" C1' C A1158 " pdb=" N1 C A1158 " pdb=" C2 C A1158 " ideal model delta sinusoidal sigma weight residual 200.00 61.99 138.01 1 1.50e+01 4.44e-03 7.44e+01 dihedral pdb=" O4' U A 960 " pdb=" C1' U A 960 " pdb=" N1 U A 960 " pdb=" C2 U A 960 " ideal model delta sinusoidal sigma weight residual 232.00 67.20 164.80 1 1.70e+01 3.46e-03 6.53e+01 dihedral pdb=" C5' A A1319 " pdb=" C4' A A1319 " pdb=" C3' A A1319 " pdb=" O3' A A1319 " ideal model delta sinusoidal sigma weight residual 147.00 105.50 41.50 1 8.00e+00 1.56e-02 3.77e+01 ... (remaining 12046 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.983: 3525 0.983 - 1.965: 0 1.965 - 2.948: 0 2.948 - 3.930: 1 3.930 - 4.913: 1 Chirality restraints: 3527 Sorted by residual: chirality pdb=" C5 SCM A1603 " pdb=" C4 SCM A1603 " pdb=" C6 SCM A1603 " pdb=" O1B SCM A1603 " both_signs ideal model delta sigma weight residual False 2.40 -2.52 4.91 2.00e-01 2.50e+01 6.03e+02 chirality pdb=" C6 SCM A1603 " pdb=" C5 SCM A1603 " pdb=" O1 SCM A1603 " pdb=" O2B SCM A1603 " both_signs ideal model delta sigma weight residual False 1.09 -2.31 3.40 2.00e-01 2.50e+01 2.89e+02 chirality pdb=" P A A 919 " pdb=" OP1 A A 919 " pdb=" OP2 A A 919 " pdb=" O5' A A 919 " both_signs ideal model delta sigma weight residual True 2.41 -3.00 -0.59 2.00e-01 2.50e+01 8.72e+00 ... (remaining 3524 not shown) Planarity restraints: 1681 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1207 " 0.063 2.00e-02 2.50e+03 5.91e-01 7.86e+03 pdb=" C4' 2MG A1207 " 0.423 2.00e-02 2.50e+03 pdb=" O4' 2MG A1207 " 0.642 2.00e-02 2.50e+03 pdb=" C3' 2MG A1207 " -0.628 2.00e-02 2.50e+03 pdb=" O3' 2MG A1207 " -0.610 2.00e-02 2.50e+03 pdb=" C2' 2MG A1207 " -0.156 2.00e-02 2.50e+03 pdb=" O2' 2MG A1207 " 0.950 2.00e-02 2.50e+03 pdb=" C1' 2MG A1207 " 0.217 2.00e-02 2.50e+03 pdb=" N9 2MG A1207 " -0.900 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A 966 " 0.039 2.00e-02 2.50e+03 5.68e-01 7.25e+03 pdb=" C4' 2MG A 966 " 0.431 2.00e-02 2.50e+03 pdb=" O4' 2MG A 966 " 0.673 2.00e-02 2.50e+03 pdb=" C3' 2MG A 966 " -0.612 2.00e-02 2.50e+03 pdb=" O3' 2MG A 966 " -0.542 2.00e-02 2.50e+03 pdb=" C2' 2MG A 966 " -0.207 2.00e-02 2.50e+03 pdb=" O2' 2MG A 966 " 0.874 2.00e-02 2.50e+03 pdb=" C1' 2MG A 966 " 0.206 2.00e-02 2.50e+03 pdb=" N9 2MG A 966 " -0.862 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A 967 " 0.039 2.00e-02 2.50e+03 5.51e-01 6.84e+03 pdb=" C4' 5MC A 967 " 0.415 2.00e-02 2.50e+03 pdb=" O4' 5MC A 967 " 0.631 2.00e-02 2.50e+03 pdb=" C3' 5MC A 967 " -0.627 2.00e-02 2.50e+03 pdb=" O3' 5MC A 967 " -0.514 2.00e-02 2.50e+03 pdb=" C2' 5MC A 967 " -0.219 2.00e-02 2.50e+03 pdb=" O2' 5MC A 967 " 0.857 2.00e-02 2.50e+03 pdb=" C1' 5MC A 967 " 0.236 2.00e-02 2.50e+03 pdb=" N1 5MC A 967 " -0.818 2.00e-02 2.50e+03 ... (remaining 1678 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.41: 126 2.41 - 3.09: 12460 3.09 - 3.77: 42338 3.77 - 4.46: 64588 4.46 - 5.14: 87703 Nonbonded interactions: 207215 Sorted by model distance: nonbonded pdb=" OP1 C A 980 " pdb="MG MG A1618 " model vdw 1.726 2.170 nonbonded pdb=" OP1 U A1224 " pdb="MG MG A1624 " model vdw 1.831 2.170 nonbonded pdb=" O6 G A1370 " pdb="MG MG A1607 " model vdw 1.848 2.170 nonbonded pdb="MG MG A1609 " pdb=" O HOH A1722 " model vdw 1.856 2.170 nonbonded pdb=" OP1 C A1303 " pdb="MG MG A1625 " model vdw 1.877 2.170 ... (remaining 207210 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: 10.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 27.370 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 66.740 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 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 : 0.012 0.499 18881 Z= 0.749 Angle : 1.534 26.143 27939 Z= 0.950 Chirality : 0.144 4.913 3527 Planarity : 0.031 0.591 1681 Dihedral : 21.905 168.365 10479 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.03 % Favored : 96.84 % Rotamer: Outliers : 0.71 % Allowed : 4.13 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.24), residues: 824 helix: -1.01 (0.22), residues: 352 sheet: -0.44 (0.39), residues: 147 loop : -0.95 (0.30), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.005 TRP C 201 HIS 0.007 0.002 HIS J 56 PHE 0.039 0.004 PHE S 10 TYR 0.032 0.004 TYR I 7 ARG 0.052 0.004 ARG I 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 198 time to evaluate : 1.042 Fit side-chains REVERT: C 19 ASN cc_start: 0.8135 (m-40) cc_final: 0.7734 (m-40) REVERT: C 72 ARG cc_start: 0.6763 (mtt180) cc_final: 0.5807 (mmm160) REVERT: C 86 LYS cc_start: 0.6284 (ptpt) cc_final: 0.5610 (tppp) REVERT: C 89 LYS cc_start: 0.6275 (mttt) cc_final: 0.5952 (mptm) REVERT: C 107 ARG cc_start: 0.6753 (mtp85) cc_final: 0.6435 (mtt-85) REVERT: C 110 GLU cc_start: 0.6741 (mp0) cc_final: 0.6415 (mp0) REVERT: C 170 GLU cc_start: 0.7468 (tt0) cc_final: 0.7125 (mm-30) REVERT: C 201 TRP cc_start: 0.8875 (OUTLIER) cc_final: 0.8041 (m-90) REVERT: G 21 GLU cc_start: 0.4798 (mt-10) cc_final: 0.4302 (pt0) REVERT: G 23 LEU cc_start: 0.5924 (tp) cc_final: 0.5638 (tm) REVERT: G 25 LYS cc_start: 0.6847 (mttt) cc_final: 0.6453 (tppt) REVERT: G 36 LYS cc_start: 0.7049 (tttm) cc_final: 0.6684 (ttmt) REVERT: G 40 GLU cc_start: 0.6570 (mt-10) cc_final: 0.6222 (mm-30) REVERT: G 101 MET cc_start: 0.7371 (mtm) cc_final: 0.7131 (mtm) REVERT: G 106 GLU cc_start: 0.6165 (mt-10) cc_final: 0.5779 (mp0) REVERT: I 41 ARG cc_start: 0.5803 (mtp180) cc_final: 0.5466 (mtm180) REVERT: I 50 GLN cc_start: 0.6344 (mt0) cc_final: 0.5998 (mt0) REVERT: I 99 ARG cc_start: 0.5849 (ttt90) cc_final: 0.5480 (ttm170) REVERT: I 107 ASP cc_start: 0.7211 (t0) cc_final: 0.6974 (t0) REVERT: I 119 ARG cc_start: 0.6944 (mmt90) cc_final: 0.6705 (mmm-85) REVERT: M 41 GLU cc_start: 0.5925 (mt-10) cc_final: 0.5698 (mt-10) REVERT: M 79 ARG cc_start: 0.6544 (ttp80) cc_final: 0.6198 (ttt-90) REVERT: M 81 MET cc_start: 0.7105 (mtm) cc_final: 0.6735 (mtm) REVERT: M 93 ARG cc_start: 0.6978 (mtt180) cc_final: 0.6457 (mmp80) REVERT: N 12 LYS cc_start: 0.7423 (tttt) cc_final: 0.7138 (tttm) REVERT: S 5 LEU cc_start: 0.5565 (mt) cc_final: 0.5357 (mp) REVERT: S 17 LYS cc_start: 0.6482 (mtpt) cc_final: 0.6229 (mmtt) REVERT: S 18 LYS cc_start: 0.6580 (mttt) cc_final: 0.6009 (mttm) REVERT: S 21 LYS cc_start: 0.6220 (tttt) cc_final: 0.5844 (mttp) REVERT: S 31 LEU cc_start: 0.6908 (mt) cc_final: 0.6634 (mm) outliers start: 5 outliers final: 1 residues processed: 200 average time/residue: 1.9415 time to fit residues: 422.3319 Evaluate side-chains 152 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 150 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 201 TRP Chi-restraints excluded: chain G residue 2 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 103 optimal weight: 0.0970 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 77 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 69 HIS C 102 ASN C 139 GLN C 190 HIS I 75 GLN I 81 HIS I 126 GLN J 56 HIS J 58 ASN J 64 GLN N 60 GLN ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 83 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18881 Z= 0.163 Angle : 0.719 22.194 27939 Z= 0.393 Chirality : 0.050 1.949 3527 Planarity : 0.007 0.127 1681 Dihedral : 22.726 162.868 8775 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.82 % Favored : 98.06 % Rotamer: Outliers : 1.56 % Allowed : 9.82 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.28), residues: 824 helix: 1.14 (0.27), residues: 362 sheet: 0.11 (0.38), residues: 150 loop : -0.02 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 201 HIS 0.006 0.002 HIS S 14 PHE 0.019 0.002 PHE S 10 TYR 0.016 0.002 TYR C 42 ARG 0.006 0.001 ARG C 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 167 time to evaluate : 1.158 Fit side-chains REVERT: C 19 ASN cc_start: 0.8077 (m-40) cc_final: 0.7556 (m-40) REVERT: C 72 ARG cc_start: 0.6678 (mtt180) cc_final: 0.6371 (mtp85) REVERT: C 86 LYS cc_start: 0.6282 (ptpt) cc_final: 0.5600 (tppp) REVERT: C 88 ARG cc_start: 0.6004 (ttp80) cc_final: 0.5684 (ttp80) REVERT: C 100 GLN cc_start: 0.6629 (mt0) cc_final: 0.6225 (tt0) REVERT: C 107 ARG cc_start: 0.6819 (mtp85) cc_final: 0.6354 (mmm-85) REVERT: C 110 GLU cc_start: 0.6757 (mp0) cc_final: 0.6554 (mp0) REVERT: C 170 GLU cc_start: 0.7386 (tt0) cc_final: 0.7082 (mm-30) REVERT: E 30 ILE cc_start: 0.6889 (mt) cc_final: 0.6469 (mm) REVERT: G 21 GLU cc_start: 0.4766 (mt-10) cc_final: 0.4249 (pt0) REVERT: G 25 LYS cc_start: 0.6705 (mttt) cc_final: 0.6415 (tptt) REVERT: G 40 GLU cc_start: 0.6504 (mt-10) cc_final: 0.6089 (mm-30) REVERT: G 101 MET cc_start: 0.7348 (mtm) cc_final: 0.7048 (mtm) REVERT: G 106 GLU cc_start: 0.6007 (mt-10) cc_final: 0.5677 (tt0) REVERT: G 111 ARG cc_start: 0.5712 (mtp85) cc_final: 0.5478 (mtt-85) REVERT: G 119 ARG cc_start: 0.6349 (mpp80) cc_final: 0.6007 (mpp80) REVERT: I 41 ARG cc_start: 0.5728 (mtp180) cc_final: 0.5357 (mtm180) REVERT: I 46 MET cc_start: 0.6608 (tmm) cc_final: 0.6267 (tmt) REVERT: I 50 GLN cc_start: 0.6224 (mt0) cc_final: 0.5914 (mt0) REVERT: I 53 GLU cc_start: 0.5414 (mt-10) cc_final: 0.5189 (mt-10) REVERT: J 66 GLU cc_start: 0.6948 (pt0) cc_final: 0.6581 (pt0) REVERT: M 31 LYS cc_start: 0.6839 (mttm) cc_final: 0.6482 (mtpp) REVERT: M 59 GLU cc_start: 0.5828 (mm-30) cc_final: 0.5546 (mm-30) REVERT: M 81 MET cc_start: 0.7153 (mtm) cc_final: 0.6671 (mtm) REVERT: M 92 ARG cc_start: 0.6710 (mtm180) cc_final: 0.6196 (mtm180) REVERT: M 93 ARG cc_start: 0.6746 (mtt180) cc_final: 0.6298 (mmp80) REVERT: S 13 LEU cc_start: 0.6639 (tt) cc_final: 0.6296 (mt) REVERT: S 17 LYS cc_start: 0.6505 (mtpt) cc_final: 0.6243 (mmtt) REVERT: S 18 LYS cc_start: 0.6322 (mttt) cc_final: 0.5897 (mttm) REVERT: S 21 LYS cc_start: 0.6166 (tttt) cc_final: 0.5726 (mttp) REVERT: S 31 LEU cc_start: 0.6860 (mt) cc_final: 0.6594 (mm) outliers start: 11 outliers final: 4 residues processed: 175 average time/residue: 1.8621 time to fit residues: 353.5958 Evaluate side-chains 142 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 138 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain S residue 44 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 120 optimal weight: 0.2980 chunk 129 optimal weight: 1.9990 chunk 106 optimal weight: 0.2980 chunk 119 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 96 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 102 ASN C 139 GLN G 97 ASN I 75 GLN ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18881 Z= 0.186 Angle : 0.733 23.014 27939 Z= 0.394 Chirality : 0.051 2.000 3527 Planarity : 0.007 0.131 1681 Dihedral : 22.769 162.476 8770 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.82 % Favored : 98.06 % Rotamer: Outliers : 1.28 % Allowed : 12.38 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.28), residues: 824 helix: 1.56 (0.27), residues: 356 sheet: 0.60 (0.39), residues: 146 loop : 0.12 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 201 HIS 0.007 0.002 HIS M 12 PHE 0.019 0.002 PHE S 10 TYR 0.023 0.002 TYR C 42 ARG 0.006 0.001 ARG I 119 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 144 time to evaluate : 1.114 Fit side-chains REVERT: C 19 ASN cc_start: 0.8038 (m-40) cc_final: 0.7671 (m-40) REVERT: C 72 ARG cc_start: 0.6659 (mtt180) cc_final: 0.6311 (mtp85) REVERT: C 88 ARG cc_start: 0.5981 (ttp80) cc_final: 0.5683 (ttp80) REVERT: C 100 GLN cc_start: 0.6660 (mt0) cc_final: 0.6343 (tt0) REVERT: C 107 ARG cc_start: 0.6843 (mtp85) cc_final: 0.6361 (mmt-90) REVERT: C 110 GLU cc_start: 0.6808 (mp0) cc_final: 0.6606 (mp0) REVERT: C 170 GLU cc_start: 0.7401 (tt0) cc_final: 0.7103 (mm-30) REVERT: E 30 ILE cc_start: 0.6880 (mt) cc_final: 0.6465 (mm) REVERT: G 21 GLU cc_start: 0.5042 (mt-10) cc_final: 0.4437 (pt0) REVERT: G 25 LYS cc_start: 0.6734 (mttt) cc_final: 0.6390 (tppt) REVERT: G 40 GLU cc_start: 0.6555 (mt-10) cc_final: 0.6123 (mm-30) REVERT: G 101 MET cc_start: 0.7377 (mtm) cc_final: 0.7104 (mtm) REVERT: G 106 GLU cc_start: 0.5992 (mt-10) cc_final: 0.5724 (pt0) REVERT: G 119 ARG cc_start: 0.6398 (mpp80) cc_final: 0.5986 (mpp80) REVERT: I 41 ARG cc_start: 0.5762 (mtp180) cc_final: 0.5370 (mtm180) REVERT: I 46 MET cc_start: 0.6589 (tmm) cc_final: 0.6251 (tmt) REVERT: I 119 ARG cc_start: 0.7128 (mmt90) cc_final: 0.6675 (mmm-85) REVERT: J 66 GLU cc_start: 0.6948 (pt0) cc_final: 0.6668 (pt0) REVERT: M 59 GLU cc_start: 0.5858 (mm-30) cc_final: 0.5551 (mm-30) REVERT: M 71 ARG cc_start: 0.6019 (mtm110) cc_final: 0.5756 (ttm-80) REVERT: M 81 MET cc_start: 0.7199 (mtm) cc_final: 0.6735 (mtm) REVERT: M 92 ARG cc_start: 0.6781 (mtm180) cc_final: 0.6510 (mtm180) REVERT: M 93 ARG cc_start: 0.6803 (mtt180) cc_final: 0.6285 (mmp80) REVERT: S 17 LYS cc_start: 0.6501 (mtpt) cc_final: 0.6219 (mmtt) REVERT: S 18 LYS cc_start: 0.6357 (mttt) cc_final: 0.5946 (mttm) REVERT: S 21 LYS cc_start: 0.6160 (tttt) cc_final: 0.5573 (mptm) REVERT: S 31 LEU cc_start: 0.6924 (mt) cc_final: 0.6658 (mm) outliers start: 9 outliers final: 6 residues processed: 151 average time/residue: 1.9021 time to fit residues: 311.3131 Evaluate side-chains 143 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 137 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain S residue 44 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 120 optimal weight: 0.0070 chunk 127 optimal weight: 0.5980 chunk 114 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 106 optimal weight: 0.0970 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 102 ASN C 139 GLN G 97 ASN I 75 GLN ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18881 Z= 0.139 Angle : 0.686 23.357 27939 Z= 0.374 Chirality : 0.049 1.952 3527 Planarity : 0.007 0.129 1681 Dihedral : 22.751 163.265 8770 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.70 % Favored : 98.18 % Rotamer: Outliers : 1.56 % Allowed : 13.37 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.29), residues: 824 helix: 1.82 (0.27), residues: 356 sheet: 0.77 (0.39), residues: 146 loop : 0.22 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 201 HIS 0.005 0.001 HIS S 14 PHE 0.015 0.002 PHE S 10 TYR 0.030 0.002 TYR C 42 ARG 0.006 0.001 ARG C 164 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 140 time to evaluate : 1.131 Fit side-chains REVERT: C 19 ASN cc_start: 0.8016 (m-40) cc_final: 0.7570 (m-40) REVERT: C 72 ARG cc_start: 0.6626 (mtt180) cc_final: 0.6287 (mtp85) REVERT: C 88 ARG cc_start: 0.5933 (ttp80) cc_final: 0.5604 (ttp80) REVERT: C 100 GLN cc_start: 0.6666 (mt0) cc_final: 0.6322 (tt0) REVERT: C 107 ARG cc_start: 0.6826 (mtp85) cc_final: 0.6354 (mmt-90) REVERT: C 110 GLU cc_start: 0.6808 (mp0) cc_final: 0.6595 (mp0) REVERT: C 170 GLU cc_start: 0.7380 (tt0) cc_final: 0.7093 (mm-30) REVERT: E 30 ILE cc_start: 0.6870 (mt) cc_final: 0.6445 (mm) REVERT: E 64 MET cc_start: 0.1317 (mmm) cc_final: 0.1098 (mmm) REVERT: G 21 GLU cc_start: 0.5046 (mt-10) cc_final: 0.4435 (pt0) REVERT: G 25 LYS cc_start: 0.6707 (mttt) cc_final: 0.6365 (tppt) REVERT: G 101 MET cc_start: 0.7344 (mtm) cc_final: 0.7066 (mtm) REVERT: G 106 GLU cc_start: 0.5993 (mt-10) cc_final: 0.5718 (pt0) REVERT: G 119 ARG cc_start: 0.6340 (OUTLIER) cc_final: 0.5878 (mpp80) REVERT: I 41 ARG cc_start: 0.5760 (mtp180) cc_final: 0.5365 (mtm180) REVERT: I 46 MET cc_start: 0.6575 (tmm) cc_final: 0.6145 (tmt) REVERT: I 104 VAL cc_start: 0.6923 (t) cc_final: 0.6570 (m) REVERT: J 66 GLU cc_start: 0.6940 (pt0) cc_final: 0.6661 (pt0) REVERT: M 59 GLU cc_start: 0.5865 (mm-30) cc_final: 0.5534 (mm-30) REVERT: M 81 MET cc_start: 0.7215 (mtm) cc_final: 0.6707 (mtm) REVERT: M 92 ARG cc_start: 0.6710 (mtm180) cc_final: 0.6434 (mtm180) REVERT: M 93 ARG cc_start: 0.6764 (mtt180) cc_final: 0.6256 (mmp80) REVERT: N 19 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6631 (tttm) REVERT: S 17 LYS cc_start: 0.6503 (mtpt) cc_final: 0.6206 (mmtt) REVERT: S 18 LYS cc_start: 0.6287 (mttt) cc_final: 0.5826 (mttm) REVERT: S 21 LYS cc_start: 0.6171 (tttt) cc_final: 0.5584 (mptm) REVERT: S 31 LEU cc_start: 0.6935 (mt) cc_final: 0.6672 (mm) REVERT: S 32 ARG cc_start: 0.7222 (ttp80) cc_final: 0.6775 (ttt-90) outliers start: 11 outliers final: 6 residues processed: 149 average time/residue: 1.8427 time to fit residues: 299.1260 Evaluate side-chains 142 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 134 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 119 ARG Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain N residue 19 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.0770 chunk 1 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 102 ASN C 139 GLN G 97 ASN I 75 GLN M 14 HIS ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18881 Z= 0.329 Angle : 0.924 22.297 27939 Z= 0.474 Chirality : 0.058 2.112 3527 Planarity : 0.009 0.139 1681 Dihedral : 22.948 161.495 8770 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.82 % Favored : 98.06 % Rotamer: Outliers : 1.71 % Allowed : 14.22 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.28), residues: 824 helix: 1.15 (0.27), residues: 356 sheet: 0.68 (0.38), residues: 150 loop : 0.11 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C 201 HIS 0.009 0.003 HIS M 12 PHE 0.022 0.003 PHE S 74 TYR 0.031 0.003 TYR C 42 ARG 0.008 0.001 ARG I 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 133 time to evaluate : 1.176 Fit side-chains REVERT: C 42 TYR cc_start: 0.7817 (t80) cc_final: 0.7598 (t80) REVERT: C 44 THR cc_start: 0.7225 (m) cc_final: 0.6613 (p) REVERT: C 72 ARG cc_start: 0.6667 (mtt180) cc_final: 0.6215 (mtp85) REVERT: C 88 ARG cc_start: 0.6069 (ttp80) cc_final: 0.5700 (ttp80) REVERT: C 100 GLN cc_start: 0.6704 (mt0) cc_final: 0.6317 (tt0) REVERT: C 107 ARG cc_start: 0.6818 (mtp85) cc_final: 0.6313 (mmt-90) REVERT: C 170 GLU cc_start: 0.7463 (tt0) cc_final: 0.7176 (mm-30) REVERT: E 64 MET cc_start: 0.1336 (mmm) cc_final: 0.1018 (mmm) REVERT: G 25 LYS cc_start: 0.6822 (mttt) cc_final: 0.6414 (tppt) REVERT: G 106 GLU cc_start: 0.6026 (mt-10) cc_final: 0.5681 (pt0) REVERT: I 46 MET cc_start: 0.6593 (tmm) cc_final: 0.6230 (tmt) REVERT: J 66 GLU cc_start: 0.6864 (pt0) cc_final: 0.6614 (pt0) REVERT: J 97 ASP cc_start: 0.5588 (t70) cc_final: 0.5204 (t70) REVERT: M 31 LYS cc_start: 0.6719 (mttm) cc_final: 0.6385 (mtpp) REVERT: M 81 MET cc_start: 0.7219 (mtm) cc_final: 0.6854 (mtm) REVERT: M 92 ARG cc_start: 0.6779 (mtt180) cc_final: 0.6280 (mtm180) REVERT: M 93 ARG cc_start: 0.6727 (mtt180) cc_final: 0.6187 (mmp80) REVERT: N 19 LYS cc_start: 0.6901 (OUTLIER) cc_final: 0.6566 (tttm) REVERT: S 17 LYS cc_start: 0.6466 (mtpt) cc_final: 0.6201 (mmtt) REVERT: S 18 LYS cc_start: 0.6439 (mttt) cc_final: 0.5832 (mttm) REVERT: S 21 LYS cc_start: 0.6093 (tttt) cc_final: 0.5668 (mttp) REVERT: S 31 LEU cc_start: 0.6920 (mt) cc_final: 0.6681 (mm) outliers start: 12 outliers final: 9 residues processed: 143 average time/residue: 1.8265 time to fit residues: 284.2058 Evaluate side-chains 141 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 131 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain N residue 19 LYS Chi-restraints excluded: chain S residue 5 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 67 optimal weight: 0.4980 chunk 123 optimal weight: 0.2980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 102 ASN C 139 GLN G 97 ASN I 75 GLN ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18881 Z= 0.205 Angle : 0.762 22.990 27939 Z= 0.406 Chirality : 0.052 2.008 3527 Planarity : 0.007 0.132 1681 Dihedral : 22.831 162.137 8770 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.82 % Favored : 98.06 % Rotamer: Outliers : 1.56 % Allowed : 14.37 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.28), residues: 824 helix: 1.42 (0.27), residues: 358 sheet: 0.70 (0.38), residues: 151 loop : 0.28 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 201 HIS 0.006 0.002 HIS J 15 PHE 0.019 0.002 PHE S 10 TYR 0.021 0.002 TYR C 42 ARG 0.006 0.001 ARG C 164 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 1.169 Fit side-chains REVERT: C 42 TYR cc_start: 0.7857 (t80) cc_final: 0.7646 (t80) REVERT: C 72 ARG cc_start: 0.6653 (mtt180) cc_final: 0.6225 (mtp85) REVERT: C 88 ARG cc_start: 0.5930 (ttp80) cc_final: 0.5559 (ttp80) REVERT: C 100 GLN cc_start: 0.6701 (mt0) cc_final: 0.6300 (tt0) REVERT: C 107 ARG cc_start: 0.6811 (mtp85) cc_final: 0.6336 (mmt-90) REVERT: C 170 GLU cc_start: 0.7431 (tt0) cc_final: 0.7143 (mm-30) REVERT: E 64 MET cc_start: 0.1326 (mmm) cc_final: 0.1019 (mmm) REVERT: G 25 LYS cc_start: 0.6742 (mttt) cc_final: 0.6381 (tppt) REVERT: G 106 GLU cc_start: 0.6083 (mt-10) cc_final: 0.5730 (pt0) REVERT: I 41 ARG cc_start: 0.5728 (mtp180) cc_final: 0.5314 (mtm180) REVERT: I 46 MET cc_start: 0.6570 (tmm) cc_final: 0.6173 (tmt) REVERT: J 66 GLU cc_start: 0.6858 (pt0) cc_final: 0.6587 (pt0) REVERT: M 31 LYS cc_start: 0.6723 (mttm) cc_final: 0.6404 (mttm) REVERT: M 59 GLU cc_start: 0.5913 (mm-30) cc_final: 0.5668 (mm-30) REVERT: M 81 MET cc_start: 0.7162 (mtm) cc_final: 0.6750 (mtm) REVERT: M 92 ARG cc_start: 0.6768 (mtt180) cc_final: 0.6393 (mtm180) REVERT: M 93 ARG cc_start: 0.6681 (mtt180) cc_final: 0.6186 (mmp80) REVERT: N 19 LYS cc_start: 0.6926 (OUTLIER) cc_final: 0.6664 (tttm) REVERT: S 13 LEU cc_start: 0.6698 (tt) cc_final: 0.6360 (mt) REVERT: S 17 LYS cc_start: 0.6471 (mtpt) cc_final: 0.6179 (mmtt) REVERT: S 18 LYS cc_start: 0.6372 (mttt) cc_final: 0.5925 (mttm) REVERT: S 21 LYS cc_start: 0.6112 (tttt) cc_final: 0.5541 (mptm) REVERT: S 31 LEU cc_start: 0.6900 (mt) cc_final: 0.6655 (mm) outliers start: 11 outliers final: 7 residues processed: 139 average time/residue: 1.8351 time to fit residues: 276.7301 Evaluate side-chains 139 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain N residue 19 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 79 optimal weight: 0.0370 chunk 77 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 ASN C 102 ASN C 139 GLN G 97 ASN ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18881 Z= 0.187 Angle : 0.735 23.119 27939 Z= 0.396 Chirality : 0.051 1.999 3527 Planarity : 0.007 0.132 1681 Dihedral : 22.825 162.376 8770 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.06 % Favored : 97.82 % Rotamer: Outliers : 1.28 % Allowed : 14.22 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.28), residues: 824 helix: 1.48 (0.27), residues: 358 sheet: 0.73 (0.38), residues: 151 loop : 0.32 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 201 HIS 0.005 0.002 HIS J 15 PHE 0.017 0.002 PHE S 10 TYR 0.019 0.002 TYR C 42 ARG 0.005 0.001 ARG C 164 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 130 time to evaluate : 1.090 Fit side-chains REVERT: C 72 ARG cc_start: 0.6651 (mtt180) cc_final: 0.6227 (mtp85) REVERT: C 88 ARG cc_start: 0.5928 (ttp80) cc_final: 0.5549 (ttp80) REVERT: C 100 GLN cc_start: 0.6680 (mt0) cc_final: 0.6338 (tt0) REVERT: C 107 ARG cc_start: 0.6801 (mtp85) cc_final: 0.6326 (mmt-90) REVERT: C 129 MET cc_start: 0.6583 (tpt) cc_final: 0.5910 (tpt) REVERT: C 170 GLU cc_start: 0.7427 (tt0) cc_final: 0.7139 (mm-30) REVERT: E 30 ILE cc_start: 0.6913 (mt) cc_final: 0.6491 (mm) REVERT: E 64 MET cc_start: 0.1270 (mmm) cc_final: 0.0928 (mmm) REVERT: G 25 LYS cc_start: 0.6741 (mttt) cc_final: 0.6382 (tppt) REVERT: G 106 GLU cc_start: 0.6079 (mt-10) cc_final: 0.5735 (pt0) REVERT: I 41 ARG cc_start: 0.5737 (mtp180) cc_final: 0.5325 (mtm180) REVERT: I 46 MET cc_start: 0.6592 (tmm) cc_final: 0.6196 (tmt) REVERT: J 66 GLU cc_start: 0.6855 (pt0) cc_final: 0.6586 (pt0) REVERT: M 31 LYS cc_start: 0.6723 (mttm) cc_final: 0.6412 (mttm) REVERT: M 59 GLU cc_start: 0.5934 (mm-30) cc_final: 0.5675 (mm-30) REVERT: M 81 MET cc_start: 0.7174 (mtm) cc_final: 0.6713 (mtm) REVERT: M 92 ARG cc_start: 0.6766 (mtt180) cc_final: 0.6366 (mtm180) REVERT: M 93 ARG cc_start: 0.6677 (mtt180) cc_final: 0.6188 (mmp80) REVERT: N 19 LYS cc_start: 0.6941 (OUTLIER) cc_final: 0.6680 (tttm) REVERT: S 13 LEU cc_start: 0.6704 (tt) cc_final: 0.6361 (mt) REVERT: S 17 LYS cc_start: 0.6512 (mtpt) cc_final: 0.6219 (mmtt) REVERT: S 18 LYS cc_start: 0.6357 (mttt) cc_final: 0.5909 (mttm) REVERT: S 21 LYS cc_start: 0.6116 (tttt) cc_final: 0.5545 (mptm) REVERT: S 31 LEU cc_start: 0.6895 (mt) cc_final: 0.6651 (mm) outliers start: 9 outliers final: 8 residues processed: 138 average time/residue: 1.8111 time to fit residues: 272.5917 Evaluate side-chains 137 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 128 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain N residue 19 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 ASN C 102 ASN C 139 GLN G 97 ASN ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18881 Z= 0.267 Angle : 0.833 22.493 27939 Z= 0.437 Chirality : 0.055 2.077 3527 Planarity : 0.008 0.136 1681 Dihedral : 22.888 161.543 8770 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.18 % Favored : 97.69 % Rotamer: Outliers : 1.56 % Allowed : 13.66 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.28), residues: 824 helix: 1.24 (0.27), residues: 359 sheet: 0.83 (0.38), residues: 148 loop : 0.21 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C 201 HIS 0.007 0.002 HIS J 15 PHE 0.019 0.003 PHE S 10 TYR 0.019 0.003 TYR C 42 ARG 0.006 0.001 ARG C 164 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 1.272 Fit side-chains REVERT: C 72 ARG cc_start: 0.6680 (mtt180) cc_final: 0.6225 (mtp85) REVERT: C 88 ARG cc_start: 0.5995 (ttp80) cc_final: 0.5618 (ttp80) REVERT: C 100 GLN cc_start: 0.6683 (mt0) cc_final: 0.6297 (tt0) REVERT: C 107 ARG cc_start: 0.6818 (mtp85) cc_final: 0.6317 (mmt-90) REVERT: C 170 GLU cc_start: 0.7443 (tt0) cc_final: 0.7161 (mm-30) REVERT: E 30 ILE cc_start: 0.6876 (mt) cc_final: 0.6468 (mm) REVERT: E 64 MET cc_start: 0.1319 (mmm) cc_final: 0.1061 (mmm) REVERT: G 25 LYS cc_start: 0.6746 (mttt) cc_final: 0.6382 (tppt) REVERT: G 106 GLU cc_start: 0.6095 (mt-10) cc_final: 0.5773 (pt0) REVERT: I 41 ARG cc_start: 0.5696 (mtp180) cc_final: 0.5299 (mtm180) REVERT: I 46 MET cc_start: 0.6582 (tmm) cc_final: 0.6199 (tmt) REVERT: J 66 GLU cc_start: 0.6867 (pt0) cc_final: 0.6619 (pt0) REVERT: M 31 LYS cc_start: 0.6756 (mttm) cc_final: 0.6415 (mttm) REVERT: M 59 GLU cc_start: 0.5848 (mm-30) cc_final: 0.5588 (mm-30) REVERT: M 81 MET cc_start: 0.7161 (mtm) cc_final: 0.6752 (mtm) REVERT: M 93 ARG cc_start: 0.6671 (mtt180) cc_final: 0.6158 (mmp80) REVERT: S 17 LYS cc_start: 0.6491 (mtpt) cc_final: 0.6207 (mmtt) REVERT: S 18 LYS cc_start: 0.6438 (mttt) cc_final: 0.5979 (mttm) REVERT: S 21 LYS cc_start: 0.6111 (tttt) cc_final: 0.5537 (mptm) REVERT: S 31 LEU cc_start: 0.6901 (mt) cc_final: 0.6662 (mm) outliers start: 11 outliers final: 9 residues processed: 139 average time/residue: 1.8472 time to fit residues: 279.6343 Evaluate side-chains 138 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 129 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain S residue 5 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 112 optimal weight: 0.3980 chunk 77 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 ASN C 102 ASN C 139 GLN G 97 ASN ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18881 Z= 0.187 Angle : 0.735 23.051 27939 Z= 0.396 Chirality : 0.051 2.008 3527 Planarity : 0.007 0.132 1681 Dihedral : 22.824 162.330 8770 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.18 % Favored : 97.69 % Rotamer: Outliers : 1.56 % Allowed : 14.22 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.28), residues: 824 helix: 1.46 (0.27), residues: 359 sheet: 0.89 (0.38), residues: 148 loop : 0.31 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 201 HIS 0.005 0.002 HIS J 15 PHE 0.018 0.002 PHE S 10 TYR 0.016 0.002 TYR C 42 ARG 0.005 0.001 ARG M 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 131 time to evaluate : 1.170 Fit side-chains REVERT: C 88 ARG cc_start: 0.5929 (ttp80) cc_final: 0.5555 (ttp80) REVERT: C 100 GLN cc_start: 0.6668 (mt0) cc_final: 0.6311 (tt0) REVERT: C 107 ARG cc_start: 0.6834 (mtp85) cc_final: 0.6332 (mmt-90) REVERT: C 170 GLU cc_start: 0.7424 (tt0) cc_final: 0.7144 (mm-30) REVERT: E 30 ILE cc_start: 0.6859 (mt) cc_final: 0.6435 (mm) REVERT: E 64 MET cc_start: 0.1243 (mmm) cc_final: 0.0993 (mmm) REVERT: G 25 LYS cc_start: 0.6732 (mttt) cc_final: 0.6378 (tppt) REVERT: G 106 GLU cc_start: 0.6086 (mt-10) cc_final: 0.5761 (pt0) REVERT: I 41 ARG cc_start: 0.5731 (mtp180) cc_final: 0.5329 (mtm180) REVERT: I 46 MET cc_start: 0.6548 (tmm) cc_final: 0.6152 (tmt) REVERT: J 66 GLU cc_start: 0.6852 (pt0) cc_final: 0.6578 (pt0) REVERT: M 31 LYS cc_start: 0.6740 (mttm) cc_final: 0.6415 (mttm) REVERT: M 59 GLU cc_start: 0.5888 (mm-30) cc_final: 0.5611 (mm-30) REVERT: M 81 MET cc_start: 0.7146 (mtm) cc_final: 0.6699 (mtm) REVERT: M 93 ARG cc_start: 0.6669 (mtt180) cc_final: 0.6164 (mmp80) REVERT: S 13 LEU cc_start: 0.6764 (tt) cc_final: 0.6477 (mt) REVERT: S 17 LYS cc_start: 0.6512 (mtpt) cc_final: 0.6218 (mmtt) REVERT: S 18 LYS cc_start: 0.6385 (mttt) cc_final: 0.5933 (mttm) REVERT: S 21 LYS cc_start: 0.6122 (tttt) cc_final: 0.5548 (mptm) REVERT: S 31 LEU cc_start: 0.6892 (mt) cc_final: 0.6649 (mm) outliers start: 11 outliers final: 10 residues processed: 140 average time/residue: 1.8252 time to fit residues: 278.4387 Evaluate side-chains 137 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 127 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain S residue 5 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 131 optimal weight: 0.0270 chunk 121 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 80 optimal weight: 0.1980 chunk 64 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 ASN C 102 ASN C 139 GLN G 97 ASN I 75 GLN ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18881 Z= 0.166 Angle : 0.714 23.253 27939 Z= 0.387 Chirality : 0.050 1.982 3527 Planarity : 0.007 0.131 1681 Dihedral : 22.815 162.767 8770 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.18 % Favored : 97.69 % Rotamer: Outliers : 1.28 % Allowed : 15.08 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.29), residues: 824 helix: 1.53 (0.28), residues: 359 sheet: 0.91 (0.38), residues: 148 loop : 0.33 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 201 HIS 0.005 0.001 HIS S 14 PHE 0.016 0.002 PHE S 10 TYR 0.014 0.002 TYR J 65 ARG 0.005 0.001 ARG I 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 126 time to evaluate : 1.223 Fit side-chains REVERT: C 19 ASN cc_start: 0.7982 (m-40) cc_final: 0.7620 (m-40) REVERT: C 88 ARG cc_start: 0.5923 (ttp80) cc_final: 0.5549 (ttp80) REVERT: C 100 GLN cc_start: 0.6664 (mt0) cc_final: 0.6329 (tt0) REVERT: C 107 ARG cc_start: 0.6819 (mtp85) cc_final: 0.6323 (mmt-90) REVERT: C 170 GLU cc_start: 0.7419 (tt0) cc_final: 0.7139 (mm-30) REVERT: E 30 ILE cc_start: 0.6886 (mt) cc_final: 0.6433 (mm) REVERT: E 64 MET cc_start: 0.1270 (mmm) cc_final: 0.1019 (mmm) REVERT: G 25 LYS cc_start: 0.6734 (mttt) cc_final: 0.6379 (tppt) REVERT: G 106 GLU cc_start: 0.6088 (mt-10) cc_final: 0.5763 (pt0) REVERT: I 41 ARG cc_start: 0.5732 (mtp180) cc_final: 0.5329 (mtm180) REVERT: I 46 MET cc_start: 0.6546 (tmm) cc_final: 0.5972 (tmt) REVERT: J 66 GLU cc_start: 0.6849 (pt0) cc_final: 0.6595 (pt0) REVERT: M 31 LYS cc_start: 0.6729 (mttm) cc_final: 0.6266 (mtpt) REVERT: M 59 GLU cc_start: 0.5892 (mm-30) cc_final: 0.5611 (mm-30) REVERT: M 81 MET cc_start: 0.7143 (mtm) cc_final: 0.6705 (mtm) REVERT: M 93 ARG cc_start: 0.6662 (mtt180) cc_final: 0.6168 (mmp80) REVERT: S 13 LEU cc_start: 0.6756 (tt) cc_final: 0.6464 (mt) REVERT: S 17 LYS cc_start: 0.6482 (mtpt) cc_final: 0.6186 (mmtt) REVERT: S 18 LYS cc_start: 0.6354 (mttt) cc_final: 0.5900 (mttm) REVERT: S 21 LYS cc_start: 0.6125 (tttt) cc_final: 0.5550 (mptm) REVERT: S 31 LEU cc_start: 0.6888 (mt) cc_final: 0.6643 (mm) outliers start: 9 outliers final: 9 residues processed: 133 average time/residue: 1.8551 time to fit residues: 269.5107 Evaluate side-chains 135 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 126 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain S residue 5 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 102 ASN C 139 GLN G 97 ASN ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.163618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.131111 restraints weight = 16343.980| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 0.56 r_work: 0.3433 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18881 Z= 0.264 Angle : 0.825 22.547 27939 Z= 0.434 Chirality : 0.055 2.076 3527 Planarity : 0.008 0.136 1681 Dihedral : 22.881 161.621 8770 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.31 % Favored : 97.57 % Rotamer: Outliers : 1.42 % Allowed : 15.22 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.28), residues: 824 helix: 1.30 (0.27), residues: 358 sheet: 0.86 (0.38), residues: 148 loop : 0.27 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 201 HIS 0.006 0.002 HIS J 15 PHE 0.019 0.002 PHE S 10 TYR 0.020 0.003 TYR J 65 ARG 0.010 0.001 ARG M 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6217.44 seconds wall clock time: 111 minutes 22.09 seconds (6682.09 seconds total)