Starting phenix.real_space_refine on Sat Mar 23 00:50:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/03_2024/8cgu_16651_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/03_2024/8cgu_16651.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/03_2024/8cgu_16651_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/03_2024/8cgu_16651_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/03_2024/8cgu_16651_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/03_2024/8cgu_16651.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/03_2024/8cgu_16651.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/03_2024/8cgu_16651_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgu_16651/03_2024/8cgu_16651_updated.pdb" } resolution = 1.89 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 24 8.98 5 P 1078 5.49 5 Mg 58 5.21 5 S 40 5.16 5 C 16620 2.51 5 N 6215 2.21 5 O 11161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 14": "NH1" <-> "NH2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D ARG 128": "NH1" <-> "NH2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "E PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "F ARG 2": "NH1" <-> "NH2" Residue "F PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 16": "OE1" <-> "OE2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "H GLU 91": "OE1" <-> "OE2" Residue "H GLU 124": "OE1" <-> "OE2" Residue "K TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "O GLU 6": "OE1" <-> "OE2" Residue "Q GLU 18": "OE1" <-> "OE2" Residue "Q GLU 26": "OE1" <-> "OE2" Residue "T GLU 40": "OE1" <-> "OE2" Residue "U GLU 31": "OE1" <-> "OE2" Residue "U ARG 55": "NH1" <-> "NH2" 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: 35196 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 22517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1047, 22517 Classifications: {'RNA': 1047} Modifications used: {'rna2p': 1, 'rna2p_pur': 79, 'rna2p_pyr': 51, 'rna3p': 7, 'rna3p_pur': 529, 'rna3p_pyr': 380} Link IDs: {'rna2p': 131, 'rna3p': 915} Chain breaks: 4 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 4 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: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 831 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} 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: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 827 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'IAS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 111} Chain breaks: 1 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: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "Q" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 624 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "R" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} 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: "U" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 386 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain breaks: 1 Chain: "a" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 664 Classifications: {'RNA': 31} Modifications used: {'rna2p_pur': 4, 'rna3p': 2, 'rna3p_pur': 13, 'rna3p_pyr': 11} Link IDs: {'rna2p': 4, 'rna3p': 26} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 204 Unusual residues: {' K': 22, ' MG': 58, 'LLL': 4} Classifications: {'undetermined': 84} Link IDs: {None: 83} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1631, 1631 Classifications: {'water': 1631} Link IDs: {None: 1630} Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "K" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "O" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "P" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "Q" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "T" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "U" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 19.91, per 1000 atoms: 0.57 Number of scatterers: 35196 At special positions: 0 Unit cell: (158.213, 201.362, 123.391, 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 24 19.00 S 40 16.00 P 1078 15.00 Mg 58 11.99 O 11161 8.00 N 6215 7.00 C 16620 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.06 Conformation dependent library (CDL) restraints added in 2.2 seconds 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2346 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 12 sheets defined 37.8% alpha, 19.6% beta 374 base pairs and 615 stacking pairs defined. Time for finding SS restraints: 21.81 Creating SS restraints... Processing helix chain 'D' and resid 9 through 15 Processing helix chain 'D' and resid 28 through 31 No H-bonds generated for 'chain 'D' and resid 28 through 31' 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 95 Processing helix chain 'D' and resid 98 through 105 Processing helix chain 'D' and resid 111 through 119 Processing helix chain 'D' and resid 153 through 164 removed outlier: 3.849A pdb=" N GLN D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 190 No H-bonds generated for 'chain 'D' and resid 188 through 190' Processing helix chain 'D' and resid 197 through 203 Processing helix chain 'E' and resid 56 through 69 removed outlier: 3.524A pdb=" N ARG E 69 " --> pdb=" O GLU E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 118 removed outlier: 3.550A pdb=" N ARG E 112 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL E 114 " --> pdb=" O MET E 111 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL E 117 " --> pdb=" O VAL E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 145 Processing helix chain 'E' and resid 150 through 157 Processing helix chain 'E' and resid 161 through 164 No H-bonds generated for 'chain 'E' and resid 161 through 164' Processing helix chain 'F' and resid 12 through 14 No H-bonds generated for 'chain 'F' and resid 12 through 14' Processing helix chain 'F' and resid 18 through 31 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 89 through 91 No H-bonds generated for 'chain 'H' and resid 89 through 91' Processing helix chain 'H' and resid 95 through 98 Processing helix chain 'H' and resid 113 through 119 Processing helix chain 'K' and resid 48 through 50 No H-bonds generated for 'chain 'K' and resid 48 through 50' Processing helix chain 'K' and resid 60 through 73 Processing helix chain 'K' and resid 91 through 103 removed outlier: 4.416A pdb=" N GLU K 94 " --> pdb=" O PRO K 91 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N SER K 95 " --> pdb=" O GLY K 92 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR K 96 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG K 98 " --> pdb=" O SER K 95 " (cutoff:3.500A) 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: 4.437A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 73 removed outlier: 3.790A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG O 72 " --> pdb=" O ASP O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 85 Processing helix chain 'P' and resid 54 through 62 Processing helix chain 'P' and resid 69 through 78 Processing helix chain 'R' and resid 12 through 16 Processing helix chain 'R' and resid 26 through 32 removed outlier: 3.898A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR R 32 " --> pdb=" O THR R 28 " (cutoff:3.500A) 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 removed outlier: 3.570A pdb=" N VAL T 35 " --> pdb=" O PHE T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 64 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 69 through 86 removed outlier: 3.717A pdb=" N LEU T 86 " --> pdb=" O GLN T 82 " (cutoff:3.500A) Processing helix chain 'U' and resid 15 through 26 Processing helix chain 'U' and resid 28 through 34 Processing helix chain 'U' and resid 41 through 55 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 46 through 53 removed outlier: 6.716A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.266A 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 43 through 46 removed outlier: 3.568A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG F 86 " --> pdb=" O MET F 9 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N HIS F 11 " --> pdb=" O VAL F 84 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL F 84 " --> pdb=" O HIS F 11 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'F' and resid 35 through 41 removed outlier: 6.479A pdb=" N ASN F 63 " --> pdb=" O HIS F 37 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU F 39 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU F 61 " --> pdb=" O LEU F 39 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 24 through 28 removed outlier: 3.625A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 75 through 77 removed outlier: 6.660A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TYR H 128 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE H 101 " --> pdb=" O TYR H 128 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'K' and resid 106 through 112 removed outlier: 6.983A pdb=" N VAL K 84 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE K 110 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL K 86 " --> pdb=" O ILE K 110 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASP K 112 " --> pdb=" O VAL K 86 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'L' and resid 29 through 33 removed outlier: 9.380A pdb=" N ARG L 94 " --> pdb=" O GLU L 62 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N THR L 64 " --> pdb=" O ARG L 94 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N HIS L 96 " --> pdb=" O THR L 64 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N TYR L 66 " --> pdb=" O HIS L 96 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ARG L 56 " --> pdb=" O CYS L 34 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N CYS L 34 " --> pdb=" O ARG L 56 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'P' and resid 2 through 11 removed outlier: 3.559A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'Q' and resid 8 through 11 removed outlier: 9.364A pdb=" N SER Q 72 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N HIS Q 45 " --> pdb=" O SER Q 72 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N THR Q 74 " --> pdb=" O HIS Q 45 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N HIS Q 47 " --> pdb=" O THR Q 74 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ALA Q 24 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL Q 12 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N GLU Q 26 " --> pdb=" O GLY Q 10 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N GLY Q 10 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'Q' and resid 58 through 60 removed outlier: 6.118A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL Q 78 " --> pdb=" O GLU Q 60 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 934 hydrogen bonds 1448 hydrogen bond angles 0 basepair planarities 374 basepair parallelities 615 stacking parallelities Total time for adding SS restraints: 71.66 Time building geometry restraints manager: 21.99 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: 4957 1.34 - 1.46: 16857 1.46 - 1.58: 12137 1.58 - 1.70: 2149 1.70 - 1.83: 68 Bond restraints: 36168 Sorted by residual: bond pdb=" O4' 3TD a1915 " pdb=" C1' 3TD a1915 " ideal model delta sigma weight residual 1.652 1.437 0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C2' 3TD a1915 " pdb=" C1' 3TD a1915 " ideal model delta sigma weight residual 1.329 1.535 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C5 4OC A1402 " pdb=" C6 4OC A1402 " ideal model delta sigma weight residual 1.512 1.342 0.170 2.00e-02 2.50e+03 7.19e+01 bond pdb=" C5 UR3 A1498 " pdb=" C6 UR3 A1498 " ideal model delta sigma weight residual 1.505 1.342 0.163 2.00e-02 2.50e+03 6.62e+01 bond pdb=" C2 4OC A1402 " pdb=" N3 4OC A1402 " ideal model delta sigma weight residual 1.507 1.357 0.150 2.00e-02 2.50e+03 5.62e+01 ... (remaining 36163 not shown) Histogram of bond angle deviations from ideal: 87.08 - 96.57: 44 96.57 - 106.06: 6832 106.06 - 115.55: 23588 115.55 - 125.04: 19197 125.04 - 134.53: 4544 Bond angle restraints: 54205 Sorted by residual: angle pdb=" O3' G A1529 " pdb=" P G A1530 " pdb=" O5' G A1530 " ideal model delta sigma weight residual 104.00 87.08 16.92 1.50e+00 4.44e-01 1.27e+02 angle pdb=" O3' C a1905 " pdb=" P G a1906 " pdb=" O5' G a1906 " ideal model delta sigma weight residual 104.00 89.32 14.68 1.50e+00 4.44e-01 9.57e+01 angle pdb=" O3' A A 746 " pdb=" P A A 747 " pdb=" O5' A A 747 " ideal model delta sigma weight residual 104.00 90.72 13.28 1.50e+00 4.44e-01 7.84e+01 angle pdb=" O3' C A 176 " pdb=" P G A 177 " pdb=" O5' G A 177 " ideal model delta sigma weight residual 104.00 91.08 12.92 1.50e+00 4.44e-01 7.41e+01 angle pdb=" O3' A A 411 " pdb=" C3' A A 411 " pdb=" C2' A A 411 " ideal model delta sigma weight residual 109.50 121.60 -12.10 1.50e+00 4.44e-01 6.51e+01 ... (remaining 54200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 20895 35.74 - 71.49: 2179 71.49 - 107.23: 227 107.23 - 142.97: 6 142.97 - 178.71: 4 Dihedral angle restraints: 23311 sinusoidal: 19680 harmonic: 3631 Sorted by residual: 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 56.16 143.84 1 1.50e+01 4.44e-03 7.71e+01 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 62.68 137.32 1 1.50e+01 4.44e-03 7.40e+01 dihedral pdb=" O4' U A 421 " pdb=" C1' U A 421 " pdb=" N1 U A 421 " pdb=" C2 U A 421 " ideal model delta sinusoidal sigma weight residual 232.00 53.34 178.66 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 23308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 5032 0.126 - 0.253: 1848 0.253 - 0.379: 42 0.379 - 0.506: 3 0.506 - 0.632: 6 Chirality restraints: 6931 Sorted by residual: chirality pdb=" P U A1390 " pdb=" OP1 U A1390 " pdb=" OP2 U A1390 " pdb=" O5' U A1390 " both_signs ideal model delta sigma weight residual True 2.41 -3.04 -0.63 2.00e-01 2.50e+01 9.99e+00 chirality pdb=" P C a1905 " pdb=" OP1 C a1905 " pdb=" OP2 C a1905 " pdb=" O5' C a1905 " both_signs ideal model delta sigma weight residual True 2.41 -3.03 -0.62 2.00e-01 2.50e+01 9.59e+00 chirality pdb=" P U A 92 " pdb=" OP1 U A 92 " pdb=" OP2 U A 92 " pdb=" O5' U A 92 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.16e+00 ... (remaining 6928 not shown) Planarity restraints: 2832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A1407 " 0.091 2.00e-02 2.50e+03 6.15e-01 8.52e+03 pdb=" C4' 5MC A1407 " 0.443 2.00e-02 2.50e+03 pdb=" O4' 5MC A1407 " 0.634 2.00e-02 2.50e+03 pdb=" C3' 5MC A1407 " -0.641 2.00e-02 2.50e+03 pdb=" O3' 5MC A1407 " -0.688 2.00e-02 2.50e+03 pdb=" C2' 5MC A1407 " -0.138 2.00e-02 2.50e+03 pdb=" O2' 5MC A1407 " 0.997 2.00e-02 2.50e+03 pdb=" C1' 5MC A1407 " 0.227 2.00e-02 2.50e+03 pdb=" N1 5MC A1407 " -0.923 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " 0.101 2.00e-02 2.50e+03 6.03e-01 8.19e+03 pdb=" C4' 2MG A1516 " 0.429 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " 0.592 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " -0.642 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " -0.672 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " -0.122 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " 0.991 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " 0.227 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " -0.904 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 587 " -0.130 2.00e-02 2.50e+03 5.19e-02 8.07e+01 pdb=" N9 G A 587 " 0.097 2.00e-02 2.50e+03 pdb=" C8 G A 587 " 0.015 2.00e-02 2.50e+03 pdb=" N7 G A 587 " 0.010 2.00e-02 2.50e+03 pdb=" C5 G A 587 " 0.015 2.00e-02 2.50e+03 pdb=" C6 G A 587 " -0.034 2.00e-02 2.50e+03 pdb=" O6 G A 587 " -0.031 2.00e-02 2.50e+03 pdb=" N1 G A 587 " -0.024 2.00e-02 2.50e+03 pdb=" C2 G A 587 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G A 587 " 0.011 2.00e-02 2.50e+03 pdb=" N3 G A 587 " 0.034 2.00e-02 2.50e+03 pdb=" C4 G A 587 " 0.036 2.00e-02 2.50e+03 ... (remaining 2829 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.54: 434 2.54 - 3.19: 31996 3.19 - 3.84: 91886 3.84 - 4.49: 127134 4.49 - 5.14: 164482 Nonbonded interactions: 415932 Sorted by model distance: nonbonded pdb=" OP2 A A 509 " pdb="MG MG A1624 " model vdw 1.895 2.170 nonbonded pdb=" OP1 G A 21 " pdb="MG MG A1634 " model vdw 1.910 2.170 nonbonded pdb="MG MG A1645 " pdb=" O HOH A2051 " model vdw 1.915 2.170 nonbonded pdb="MG MG A1610 " pdb=" O HOH A2083 " model vdw 1.919 2.170 nonbonded pdb=" OP1 C A 578 " pdb="MG MG A1607 " model vdw 1.925 2.170 ... (remaining 415927 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: 9.370 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: 0.000 Extract box with map and model: 22.740 Check model and map are aligned: 0.490 Set scattering table: 0.310 Process input model: 168.070 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.110 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:13.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 215.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 : 0.009 0.215 36168 Z= 0.535 Angle : 1.584 19.737 54205 Z= 0.962 Chirality : 0.107 0.632 6931 Planarity : 0.024 0.615 2832 Dihedral : 22.073 178.715 20965 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 0.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.38 % Allowed : 3.27 % Favored : 96.34 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.33 % 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: -0.61 (0.21), residues: 1233 helix: -0.14 (0.20), residues: 502 sheet: -0.27 (0.32), residues: 227 loop : -0.55 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP P 60 HIS 0.012 0.003 HIS P 9 PHE 0.030 0.005 PHE O 43 TYR 0.041 0.006 TYR D 76 ARG 0.034 0.004 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 315 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 8 LYS cc_start: 0.7177 (mmtt) cc_final: 0.6861 (mmtp) REVERT: D 25 VAL cc_start: 0.6902 (p) cc_final: 0.6575 (m) REVERT: D 30 THR cc_start: 0.7135 (m) cc_final: 0.6844 (p) REVERT: D 50 ASP cc_start: 0.7325 (m-30) cc_final: 0.6740 (t70) REVERT: D 88 GLU cc_start: 0.7278 (mt-10) cc_final: 0.7051 (mt-10) REVERT: D 151 LYS cc_start: 0.5910 (pttp) cc_final: 0.5427 (pttp) REVERT: D 156 LYS cc_start: 0.6600 (tmtp) cc_final: 0.6136 (mtmt) REVERT: D 160 GLU cc_start: 0.5808 (mt-10) cc_final: 0.5457 (mm-30) REVERT: D 167 LYS cc_start: 0.5785 (mmtm) cc_final: 0.5336 (mtmt) REVERT: D 177 LYS cc_start: 0.5389 (mttm) cc_final: 0.5167 (mtpt) REVERT: D 185 LYS cc_start: 0.6302 (mmtt) cc_final: 0.6043 (mtpt) REVERT: D 187 GLU cc_start: 0.6454 (mm-30) cc_final: 0.6141 (mm-30) REVERT: E 12 GLN cc_start: 0.7108 (mt0) cc_final: 0.6221 (tt0) REVERT: E 14 LYS cc_start: 0.7712 (mtpp) cc_final: 0.7258 (mttm) REVERT: E 26 LYS cc_start: 0.7046 (tttm) cc_final: 0.6163 (tptt) REVERT: E 55 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6280 (pt0) REVERT: E 57 PRO cc_start: 0.7023 (Cg_exo) cc_final: 0.6684 (Cg_endo) REVERT: E 61 GLN cc_start: 0.7111 (tt0) cc_final: 0.6800 (tp40) REVERT: E 65 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7113 (mt-10) REVERT: E 70 ASN cc_start: 0.6792 (m-40) cc_final: 0.6404 (m-40) REVERT: E 78 ASN cc_start: 0.6315 (t0) cc_final: 0.6010 (t0) REVERT: E 134 ILE cc_start: 0.7823 (mt) cc_final: 0.7460 (pt) REVERT: E 146 ASN cc_start: 0.6023 (m-40) cc_final: 0.5416 (p0) REVERT: E 147 MET cc_start: 0.7701 (ttp) cc_final: 0.7416 (ttp) REVERT: E 151 GLU cc_start: 0.6858 (mp0) cc_final: 0.6373 (mm-30) REVERT: E 156 LYS cc_start: 0.7441 (ptpp) cc_final: 0.7086 (pttt) REVERT: F 44 ARG cc_start: 0.6116 (mtm180) cc_final: 0.5760 (mtm-85) REVERT: F 58 HIS cc_start: 0.8085 (t70) cc_final: 0.7822 (t70) REVERT: F 64 VAL cc_start: 0.7748 (t) cc_final: 0.7501 (m) REVERT: F 91 ARG cc_start: 0.7827 (mmm-85) cc_final: 0.7625 (mmm-85) REVERT: H 21 ASN cc_start: 0.7864 (m-40) cc_final: 0.7542 (m110) REVERT: H 22 LYS cc_start: 0.7328 (mmmm) cc_final: 0.7038 (mmmt) REVERT: H 31 LYS cc_start: 0.7562 (mmmm) cc_final: 0.7129 (mtpt) REVERT: H 38 ASN cc_start: 0.7803 (m-40) cc_final: 0.7335 (t0) REVERT: H 58 GLU cc_start: 0.7464 (mm-30) cc_final: 0.6899 (tp30) REVERT: H 60 GLU cc_start: 0.7675 (tt0) cc_final: 0.7334 (tt0) REVERT: H 88 ARG cc_start: 0.7516 (mtm-85) cc_final: 0.7197 (mtp180) REVERT: H 90 ASP cc_start: 0.7214 (p0) cc_final: 0.6933 (p0) REVERT: H 117 ARG cc_start: 0.7662 (mtm-85) cc_final: 0.7413 (mtt90) REVERT: K 31 ILE cc_start: 0.8044 (mt) cc_final: 0.7659 (mm) REVERT: K 40 ASN cc_start: 0.7006 (m-40) cc_final: 0.6748 (m-40) REVERT: K 56 ARG cc_start: 0.6056 (ttm-80) cc_final: 0.5826 (mtm110) REVERT: K 68 GLU cc_start: 0.6561 (mt-10) cc_final: 0.6286 (mt-10) REVERT: K 126 LYS cc_start: 0.7866 (tttt) cc_final: 0.7294 (ttmm) REVERT: L 10 LYS cc_start: 0.7324 (tttt) cc_final: 0.7066 (ttpp) REVERT: L 25 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6724 (mt-10) REVERT: L 43 LYS cc_start: 0.7258 (ttpt) cc_final: 0.6841 (ttmm) REVERT: L 54 ARG cc_start: 0.7313 (ttm-80) cc_final: 0.6929 (ttm-80) REVERT: L 62 GLU cc_start: 0.6888 (tt0) cc_final: 0.6569 (tp30) REVERT: L 75 GLN cc_start: 0.6190 (mt0) cc_final: 0.5931 (pt0) REVERT: L 105 SER cc_start: 0.7501 (m) cc_final: 0.7284 (p) REVERT: L 108 LYS cc_start: 0.6483 (mptt) cc_final: 0.6114 (tttm) REVERT: O 14 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6449 (tt0) REVERT: O 21 ASP cc_start: 0.7925 (t0) cc_final: 0.7633 (t70) REVERT: O 48 LYS cc_start: 0.7664 (mmtt) cc_final: 0.7414 (mmtm) REVERT: O 79 THR cc_start: 0.7235 (m) cc_final: 0.7028 (m) REVERT: P 51 ARG cc_start: 0.7785 (ttm170) cc_final: 0.7545 (ttp-110) REVERT: P 53 ASP cc_start: 0.7589 (t0) cc_final: 0.7339 (t70) REVERT: P 76 LYS cc_start: 0.6305 (mtpp) cc_final: 0.5970 (pttt) REVERT: Q 9 GLN cc_start: 0.7163 (mt0) cc_final: 0.6946 (mt0) REVERT: Q 11 ARG cc_start: 0.6752 (mmt180) cc_final: 0.6353 (mtt-85) REVERT: Q 38 ILE cc_start: 0.7803 (mm) cc_final: 0.7602 (pt) REVERT: Q 39 LYS cc_start: 0.7563 (mttt) cc_final: 0.7165 (mttp) REVERT: Q 40 ARG cc_start: 0.7156 (mmp-170) cc_final: 0.6830 (mmp-170) REVERT: Q 60 GLU cc_start: 0.6983 (tt0) cc_final: 0.6775 (tt0) REVERT: Q 77 ARG cc_start: 0.5814 (ptt90) cc_final: 0.5323 (ptt180) REVERT: R 22 ASP cc_start: 0.7010 (t0) cc_final: 0.6704 (t0) REVERT: R 24 LYS cc_start: 0.6886 (mtmm) cc_final: 0.6538 (mtpt) REVERT: R 25 ASP cc_start: 0.7379 (t0) cc_final: 0.7107 (t0) REVERT: R 30 LYS cc_start: 0.7494 (mttp) cc_final: 0.7198 (mtmt) REVERT: R 42 SER cc_start: 0.8171 (p) cc_final: 0.7885 (p) REVERT: R 43 ARG cc_start: 0.6768 (ptm160) cc_final: 0.6544 (ptt90) REVERT: R 48 ARG cc_start: 0.6718 (mmt-90) cc_final: 0.6041 (mtm110) REVERT: T 3 ASN cc_start: 0.8152 (m110) cc_final: 0.7946 (m110) REVERT: T 48 GLN cc_start: 0.7496 (tp-100) cc_final: 0.7148 (tp-100) REVERT: T 64 LYS cc_start: 0.7918 (mmtm) cc_final: 0.7567 (mttp) REVERT: U 33 ARG cc_start: 0.6671 (mtt90) cc_final: 0.6222 (mtt-85) REVERT: U 44 GLU cc_start: 0.6654 (tm-30) cc_final: 0.6196 (mt-10) REVERT: U 46 LYS cc_start: 0.7116 (ttpt) cc_final: 0.6903 (ttpt) outliers start: 4 outliers final: 2 residues processed: 318 average time/residue: 2.0194 time to fit residues: 737.8748 Evaluate side-chains 274 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 272 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 2 PRO Chi-restraints excluded: chain U residue 4 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 191 optimal weight: 0.9980 chunk 172 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 116 optimal weight: 0.4980 chunk 91 optimal weight: 0.7980 chunk 177 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 GLN D 40 GLN E 121 HIS F 11 HIS H 18 GLN K 81 ASN L 20 ASN O 35 GLN R 19 GLN R 31 ASN T 3 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 36168 Z= 0.139 Angle : 0.584 12.990 54205 Z= 0.322 Chirality : 0.035 0.335 6931 Planarity : 0.005 0.121 2832 Dihedral : 22.646 178.578 18479 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.38 % Allowed : 6.64 % Favored : 92.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.14 (0.23), residues: 1233 helix: 1.88 (0.22), residues: 500 sheet: 0.10 (0.33), residues: 232 loop : 0.03 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 60 HIS 0.004 0.001 HIS D 41 PHE 0.018 0.002 PHE O 43 TYR 0.016 0.002 TYR D 51 ARG 0.003 0.001 ARG D 188 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 268 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 8 LYS cc_start: 0.7004 (mmtt) cc_final: 0.6680 (mmtp) REVERT: D 25 VAL cc_start: 0.6669 (p) cc_final: 0.6419 (m) REVERT: D 30 THR cc_start: 0.7020 (m) cc_final: 0.6717 (p) REVERT: D 151 LYS cc_start: 0.5893 (pttp) cc_final: 0.5289 (pttp) REVERT: D 156 LYS cc_start: 0.6312 (tmtp) cc_final: 0.5980 (mtmt) REVERT: D 160 GLU cc_start: 0.5759 (mt-10) cc_final: 0.5355 (mm-30) REVERT: D 163 GLU cc_start: 0.5854 (mt-10) cc_final: 0.5562 (mm-30) REVERT: D 167 LYS cc_start: 0.6004 (mmtm) cc_final: 0.5595 (mtmt) REVERT: D 185 LYS cc_start: 0.6501 (mmtt) cc_final: 0.6118 (mttm) REVERT: D 187 GLU cc_start: 0.6419 (mm-30) cc_final: 0.6078 (mm-30) REVERT: E 12 GLN cc_start: 0.7015 (mt0) cc_final: 0.6217 (tt0) REVERT: E 14 LYS cc_start: 0.7667 (mtpp) cc_final: 0.7254 (mttm) REVERT: E 26 LYS cc_start: 0.6979 (tttm) cc_final: 0.6453 (ptmt) REVERT: E 54 ARG cc_start: 0.7369 (mmt90) cc_final: 0.7128 (tpp80) REVERT: E 55 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6616 (mp0) REVERT: E 61 GLN cc_start: 0.7054 (tt0) cc_final: 0.6711 (tp40) REVERT: E 65 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7114 (mt-10) REVERT: E 70 ASN cc_start: 0.6610 (m-40) cc_final: 0.6190 (m-40) REVERT: E 134 ILE cc_start: 0.7732 (mt) cc_final: 0.7273 (pt) REVERT: E 146 ASN cc_start: 0.5968 (m-40) cc_final: 0.5494 (p0) REVERT: E 151 GLU cc_start: 0.6641 (mp0) cc_final: 0.6303 (mm-30) REVERT: E 159 LYS cc_start: 0.6988 (mmtp) cc_final: 0.6689 (mmtt) REVERT: F 21 MET cc_start: 0.6430 (mtt) cc_final: 0.6151 (mtp) REVERT: H 21 ASN cc_start: 0.7741 (m-40) cc_final: 0.7519 (m110) REVERT: H 22 LYS cc_start: 0.7202 (mmmm) cc_final: 0.6879 (mmmt) REVERT: H 31 LYS cc_start: 0.7363 (mmmm) cc_final: 0.6941 (mtmt) REVERT: H 38 ASN cc_start: 0.7775 (m-40) cc_final: 0.7422 (t0) REVERT: H 58 GLU cc_start: 0.7433 (mm-30) cc_final: 0.6979 (tp30) REVERT: H 60 GLU cc_start: 0.7745 (tt0) cc_final: 0.7450 (tt0) REVERT: H 88 ARG cc_start: 0.7509 (mtm-85) cc_final: 0.7169 (mtp180) REVERT: H 90 ASP cc_start: 0.7217 (p0) cc_final: 0.6930 (p0) REVERT: H 114 ARG cc_start: 0.6983 (ttp80) cc_final: 0.6283 (ttm-80) REVERT: K 31 ILE cc_start: 0.7966 (mt) cc_final: 0.7531 (mm) REVERT: K 40 ASN cc_start: 0.6878 (m-40) cc_final: 0.6635 (m-40) REVERT: K 68 GLU cc_start: 0.6425 (mt-10) cc_final: 0.6158 (mt-10) REVERT: K 126 LYS cc_start: 0.7885 (tttt) cc_final: 0.7273 (ttmm) REVERT: L 10 LYS cc_start: 0.7131 (tttt) cc_final: 0.6821 (ttpp) REVERT: L 43 LYS cc_start: 0.7161 (ttpt) cc_final: 0.6803 (ttmm) REVERT: L 47 SER cc_start: 0.8214 (m) cc_final: 0.7908 (t) REVERT: L 54 ARG cc_start: 0.6869 (ttm-80) cc_final: 0.6433 (ttm-80) REVERT: L 56 ARG cc_start: 0.6590 (ttm-80) cc_final: 0.6107 (ttm110) REVERT: L 62 GLU cc_start: 0.6805 (tt0) cc_final: 0.6549 (tp30) REVERT: L 75 GLN cc_start: 0.6162 (mt0) cc_final: 0.5936 (pt0) REVERT: L 108 LYS cc_start: 0.6455 (mptt) cc_final: 0.6078 (tttm) REVERT: O 21 ASP cc_start: 0.7981 (t0) cc_final: 0.7600 (t70) REVERT: O 77 ARG cc_start: 0.7020 (mtp180) cc_final: 0.6810 (mtm110) REVERT: P 51 ARG cc_start: 0.7744 (ttm170) cc_final: 0.7535 (ttp-110) REVERT: P 53 ASP cc_start: 0.7661 (t0) cc_final: 0.7431 (t70) REVERT: P 76 LYS cc_start: 0.6328 (mtpp) cc_final: 0.5928 (pttt) REVERT: Q 9 GLN cc_start: 0.7326 (mt0) cc_final: 0.7121 (mt0) REVERT: Q 39 LYS cc_start: 0.7448 (mttt) cc_final: 0.7064 (mttm) REVERT: Q 40 ARG cc_start: 0.7058 (mmp-170) cc_final: 0.6588 (mmp-170) REVERT: R 30 LYS cc_start: 0.7374 (mttp) cc_final: 0.7084 (mtmt) REVERT: R 43 ARG cc_start: 0.6755 (ptm160) cc_final: 0.6512 (ptt90) REVERT: R 48 ARG cc_start: 0.6464 (mmt-90) cc_final: 0.5802 (mtp-110) REVERT: T 48 GLN cc_start: 0.7372 (tp-100) cc_final: 0.6998 (tp-100) REVERT: U 33 ARG cc_start: 0.6532 (mtt90) cc_final: 0.6153 (mtt-85) REVERT: U 44 GLU cc_start: 0.6444 (tm-30) cc_final: 0.6124 (mt-10) outliers start: 4 outliers final: 1 residues processed: 268 average time/residue: 2.1006 time to fit residues: 646.0768 Evaluate side-chains 251 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 250 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 59 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 114 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 171 optimal weight: 0.7980 chunk 140 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 206 optimal weight: 5.9990 chunk 223 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 chunk 204 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 165 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 GLN E 73 ASN E 78 ASN E 121 HIS F 11 HIS L 20 ASN O 35 GLN O 40 GLN T 48 GLN T 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 36168 Z= 0.339 Angle : 0.854 13.178 54205 Z= 0.433 Chirality : 0.045 0.331 6931 Planarity : 0.008 0.139 2832 Dihedral : 22.773 175.292 18474 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.77 % Allowed : 7.89 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.89 (0.23), residues: 1233 helix: 1.49 (0.22), residues: 501 sheet: 0.20 (0.33), residues: 230 loop : -0.02 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP P 60 HIS 0.010 0.002 HIS P 9 PHE 0.024 0.003 PHE O 43 TYR 0.020 0.003 TYR D 51 ARG 0.008 0.001 ARG E 157 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 255 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 8 LYS cc_start: 0.7155 (mmtt) cc_final: 0.6800 (mmtp) REVERT: D 25 VAL cc_start: 0.6829 (p) cc_final: 0.6560 (m) REVERT: D 30 THR cc_start: 0.7125 (m) cc_final: 0.6823 (p) REVERT: D 151 LYS cc_start: 0.5952 (pttp) cc_final: 0.5412 (pttp) REVERT: D 156 LYS cc_start: 0.6419 (tmtp) cc_final: 0.6083 (mttt) REVERT: D 160 GLU cc_start: 0.5583 (mt-10) cc_final: 0.5204 (mm-30) REVERT: D 185 LYS cc_start: 0.6534 (mmtt) cc_final: 0.6139 (mttm) REVERT: D 187 GLU cc_start: 0.6434 (mm-30) cc_final: 0.6230 (mm-30) REVERT: E 12 GLN cc_start: 0.7055 (mt0) cc_final: 0.6251 (tt0) REVERT: E 14 LYS cc_start: 0.7595 (mtpp) cc_final: 0.7189 (mttm) REVERT: E 23 LYS cc_start: 0.7954 (ptmm) cc_final: 0.7507 (ptmt) REVERT: E 26 LYS cc_start: 0.6954 (tttm) cc_final: 0.6381 (pttm) REVERT: E 55 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6633 (mp0) REVERT: E 61 GLN cc_start: 0.7172 (tt0) cc_final: 0.6833 (tp40) REVERT: E 65 GLU cc_start: 0.7307 (mt-10) cc_final: 0.7086 (mt-10) REVERT: E 70 ASN cc_start: 0.6767 (m-40) cc_final: 0.6329 (m-40) REVERT: E 134 ILE cc_start: 0.7628 (mt) cc_final: 0.7274 (pt) REVERT: E 146 ASN cc_start: 0.6053 (m-40) cc_final: 0.5501 (p0) REVERT: E 151 GLU cc_start: 0.6530 (mp0) cc_final: 0.6128 (mm-30) REVERT: H 21 ASN cc_start: 0.7829 (m-40) cc_final: 0.7612 (m110) REVERT: H 22 LYS cc_start: 0.7119 (mmmm) cc_final: 0.6870 (mmmt) REVERT: H 31 LYS cc_start: 0.7416 (mmmm) cc_final: 0.6981 (mtmt) REVERT: H 60 GLU cc_start: 0.7705 (tt0) cc_final: 0.7457 (tt0) REVERT: H 88 ARG cc_start: 0.7387 (mtm-85) cc_final: 0.7172 (mtp180) REVERT: H 90 ASP cc_start: 0.7208 (p0) cc_final: 0.6923 (p0) REVERT: H 114 ARG cc_start: 0.7000 (ttp80) cc_final: 0.6300 (ttm110) REVERT: K 40 ASN cc_start: 0.6897 (m-40) cc_final: 0.6656 (m-40) REVERT: K 68 GLU cc_start: 0.6508 (mt-10) cc_final: 0.6199 (mt-10) REVERT: K 126 LYS cc_start: 0.7872 (tttt) cc_final: 0.7268 (ttmm) REVERT: L 10 LYS cc_start: 0.7226 (tttt) cc_final: 0.6905 (ttpp) REVERT: L 43 LYS cc_start: 0.7236 (ttpt) cc_final: 0.6872 (ttmm) REVERT: L 54 ARG cc_start: 0.7061 (ttm-80) cc_final: 0.6664 (ttm-80) REVERT: L 56 ARG cc_start: 0.6547 (ttm-80) cc_final: 0.6085 (ttm110) REVERT: L 62 GLU cc_start: 0.6775 (tt0) cc_final: 0.6541 (tp30) REVERT: L 75 GLN cc_start: 0.6080 (mt0) cc_final: 0.5730 (pt0) REVERT: L 108 LYS cc_start: 0.6353 (mptt) cc_final: 0.6073 (tttm) REVERT: L 121 ARG cc_start: 0.7514 (ttt-90) cc_final: 0.7239 (ttt90) REVERT: O 77 ARG cc_start: 0.7039 (mtp180) cc_final: 0.6675 (mtm110) REVERT: P 53 ASP cc_start: 0.7668 (t0) cc_final: 0.7454 (t70) REVERT: Q 19 LYS cc_start: 0.7476 (mttp) cc_final: 0.6927 (mmtt) REVERT: Q 39 LYS cc_start: 0.7524 (mttt) cc_final: 0.7161 (mttp) REVERT: R 24 LYS cc_start: 0.6773 (OUTLIER) cc_final: 0.6432 (mtpt) REVERT: R 30 LYS cc_start: 0.7447 (mttp) cc_final: 0.7232 (mtmm) REVERT: R 43 ARG cc_start: 0.6726 (ptm160) cc_final: 0.6478 (ptt90) REVERT: R 48 ARG cc_start: 0.6542 (mmt-90) cc_final: 0.5858 (mtp-110) REVERT: T 48 GLN cc_start: 0.7298 (tp40) cc_final: 0.6979 (tp-100) REVERT: T 53 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6895 (mt-10) outliers start: 8 outliers final: 2 residues processed: 256 average time/residue: 2.0060 time to fit residues: 590.6931 Evaluate side-chains 252 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 248 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain T residue 53 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 204 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 138 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 219 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 ASN E 78 ASN E 121 HIS F 11 HIS L 20 ASN O 35 GLN O 40 GLN T 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 36168 Z= 0.240 Angle : 0.714 12.976 54205 Z= 0.375 Chirality : 0.040 0.333 6931 Planarity : 0.006 0.131 2832 Dihedral : 22.701 175.243 18474 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.96 % Allowed : 8.85 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.01 (0.23), residues: 1233 helix: 1.64 (0.22), residues: 501 sheet: 0.25 (0.33), residues: 229 loop : -0.00 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP P 60 HIS 0.009 0.002 HIS F 58 PHE 0.023 0.002 PHE F 8 TYR 0.018 0.003 TYR D 51 ARG 0.005 0.001 ARG E 157 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 251 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 8 LYS cc_start: 0.7192 (mmtt) cc_final: 0.6818 (mmtp) REVERT: D 25 VAL cc_start: 0.6840 (p) cc_final: 0.6562 (m) REVERT: D 30 THR cc_start: 0.7150 (m) cc_final: 0.6850 (p) REVERT: D 151 LYS cc_start: 0.5949 (pttp) cc_final: 0.5608 (ptmm) REVERT: D 156 LYS cc_start: 0.6384 (tmtp) cc_final: 0.5910 (mmmt) REVERT: D 160 GLU cc_start: 0.5574 (mt-10) cc_final: 0.5202 (mm-30) REVERT: D 177 LYS cc_start: 0.5352 (OUTLIER) cc_final: 0.5125 (mttp) REVERT: D 185 LYS cc_start: 0.6539 (mmtt) cc_final: 0.6140 (mttm) REVERT: E 12 GLN cc_start: 0.7020 (mt0) cc_final: 0.6198 (tt0) REVERT: E 14 LYS cc_start: 0.7639 (mtpp) cc_final: 0.7228 (mttm) REVERT: E 23 LYS cc_start: 0.7967 (ptmm) cc_final: 0.7547 (ptmt) REVERT: E 26 LYS cc_start: 0.6968 (tttm) cc_final: 0.6683 (ptmm) REVERT: E 55 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6632 (mp0) REVERT: E 61 GLN cc_start: 0.7190 (tt0) cc_final: 0.6849 (tp40) REVERT: E 65 GLU cc_start: 0.7282 (mt-10) cc_final: 0.7056 (mt-10) REVERT: E 70 ASN cc_start: 0.6724 (m-40) cc_final: 0.6309 (m-40) REVERT: E 134 ILE cc_start: 0.7626 (mt) cc_final: 0.7283 (pt) REVERT: E 146 ASN cc_start: 0.6016 (m-40) cc_final: 0.5545 (p0) REVERT: E 151 GLU cc_start: 0.6576 (mp0) cc_final: 0.6187 (mm-30) REVERT: H 21 ASN cc_start: 0.7781 (m-40) cc_final: 0.7566 (m110) REVERT: H 22 LYS cc_start: 0.7121 (mmmm) cc_final: 0.6864 (mmmt) REVERT: H 31 LYS cc_start: 0.7392 (mmmm) cc_final: 0.6980 (mtpt) REVERT: H 60 GLU cc_start: 0.7737 (tt0) cc_final: 0.7488 (tt0) REVERT: H 88 ARG cc_start: 0.7421 (mtm-85) cc_final: 0.7189 (mtp180) REVERT: H 114 ARG cc_start: 0.7007 (ttp80) cc_final: 0.6303 (ttm110) REVERT: K 40 ASN cc_start: 0.6921 (m-40) cc_final: 0.6674 (m-40) REVERT: K 68 GLU cc_start: 0.6474 (mt-10) cc_final: 0.6118 (mt-10) REVERT: K 126 LYS cc_start: 0.7873 (tttt) cc_final: 0.7267 (ttmm) REVERT: L 10 LYS cc_start: 0.7227 (tttt) cc_final: 0.6910 (ttpp) REVERT: L 43 LYS cc_start: 0.7207 (ttpt) cc_final: 0.6836 (ttmm) REVERT: L 54 ARG cc_start: 0.7053 (ttm-80) cc_final: 0.6733 (ttm-80) REVERT: L 56 ARG cc_start: 0.6578 (ttm-80) cc_final: 0.6117 (ttm110) REVERT: L 108 LYS cc_start: 0.6352 (mptt) cc_final: 0.6067 (tttm) REVERT: L 121 ARG cc_start: 0.7502 (ttt-90) cc_final: 0.7212 (ttt90) REVERT: O 77 ARG cc_start: 0.6996 (mtp180) cc_final: 0.6637 (mtm110) REVERT: P 53 ASP cc_start: 0.7666 (t0) cc_final: 0.7441 (t70) REVERT: Q 9 GLN cc_start: 0.7257 (mt0) cc_final: 0.6725 (tt0) REVERT: Q 19 LYS cc_start: 0.7437 (mttp) cc_final: 0.6903 (mmtt) REVERT: Q 25 ILE cc_start: 0.7661 (OUTLIER) cc_final: 0.7360 (mm) REVERT: Q 39 LYS cc_start: 0.7553 (mttt) cc_final: 0.7219 (mttp) REVERT: R 24 LYS cc_start: 0.6744 (OUTLIER) cc_final: 0.6439 (mtpt) REVERT: R 30 LYS cc_start: 0.7452 (mttp) cc_final: 0.7154 (mtmt) REVERT: R 43 ARG cc_start: 0.6738 (ptm160) cc_final: 0.6509 (ptt90) REVERT: R 48 ARG cc_start: 0.6570 (mmt-90) cc_final: 0.5908 (mtp-110) REVERT: T 48 GLN cc_start: 0.7256 (tp40) cc_final: 0.7032 (tp-100) REVERT: T 53 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6894 (mt-10) outliers start: 10 outliers final: 3 residues processed: 254 average time/residue: 2.0284 time to fit residues: 593.0146 Evaluate side-chains 254 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 247 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain T residue 53 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 182 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 163 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 187 optimal weight: 7.9990 chunk 151 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 196 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 ASN E 78 ASN E 121 HIS F 11 HIS L 20 ASN O 35 GLN O 40 GLN T 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 36168 Z= 0.405 Angle : 0.939 13.424 54205 Z= 0.469 Chirality : 0.048 0.317 6931 Planarity : 0.008 0.139 2832 Dihedral : 22.780 173.601 18474 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.35 % Allowed : 8.66 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 (0.23), residues: 1233 helix: 1.13 (0.22), residues: 501 sheet: 0.15 (0.33), residues: 237 loop : -0.10 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP P 60 HIS 0.011 0.003 HIS P 9 PHE 0.027 0.003 PHE F 8 TYR 0.022 0.004 TYR D 51 ARG 0.010 0.001 ARG E 157 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 248 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 8 LYS cc_start: 0.7207 (mmtt) cc_final: 0.6962 (mppt) REVERT: D 25 VAL cc_start: 0.6737 (p) cc_final: 0.6438 (m) REVERT: D 30 THR cc_start: 0.7162 (m) cc_final: 0.6861 (p) REVERT: D 47 ARG cc_start: 0.5806 (ttm170) cc_final: 0.5458 (ttp80) REVERT: D 151 LYS cc_start: 0.5879 (pttp) cc_final: 0.5437 (pttp) REVERT: D 177 LYS cc_start: 0.5320 (OUTLIER) cc_final: 0.5099 (mttp) REVERT: D 185 LYS cc_start: 0.6428 (mmtt) cc_final: 0.6138 (mttm) REVERT: E 12 GLN cc_start: 0.6993 (mt0) cc_final: 0.6237 (tt0) REVERT: E 14 LYS cc_start: 0.7554 (mtpp) cc_final: 0.7138 (mttm) REVERT: E 26 LYS cc_start: 0.6907 (tttm) cc_final: 0.6381 (pttt) REVERT: E 55 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6596 (mp0) REVERT: E 61 GLN cc_start: 0.7171 (tt0) cc_final: 0.6835 (tp40) REVERT: E 65 GLU cc_start: 0.7207 (mt-10) cc_final: 0.7006 (mt-10) REVERT: E 70 ASN cc_start: 0.6705 (m-40) cc_final: 0.6289 (m-40) REVERT: E 134 ILE cc_start: 0.7712 (mt) cc_final: 0.7371 (pt) REVERT: E 142 ASP cc_start: 0.7458 (t70) cc_final: 0.7240 (t70) REVERT: E 146 ASN cc_start: 0.6015 (m-40) cc_final: 0.5479 (p0) REVERT: E 151 GLU cc_start: 0.6496 (mp0) cc_final: 0.6104 (mm-30) REVERT: H 21 ASN cc_start: 0.7783 (m-40) cc_final: 0.7503 (m110) REVERT: H 31 LYS cc_start: 0.7418 (mmmm) cc_final: 0.6989 (mtpt) REVERT: H 60 GLU cc_start: 0.7732 (tt0) cc_final: 0.7512 (tt0) REVERT: K 40 ASN cc_start: 0.7110 (m-40) cc_final: 0.6848 (m-40) REVERT: K 68 GLU cc_start: 0.6446 (mt-10) cc_final: 0.6071 (mt-10) REVERT: K 126 LYS cc_start: 0.7865 (tttt) cc_final: 0.7264 (ttmm) REVERT: L 10 LYS cc_start: 0.7273 (tttt) cc_final: 0.7000 (ttpp) REVERT: L 43 LYS cc_start: 0.7217 (ttpt) cc_final: 0.6868 (ttmm) REVERT: L 54 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.6711 (ttm-80) REVERT: L 56 ARG cc_start: 0.6453 (ttm-80) cc_final: 0.6038 (ttm110) REVERT: L 108 LYS cc_start: 0.6379 (mptt) cc_final: 0.6072 (tttm) REVERT: L 121 ARG cc_start: 0.7525 (ttt-90) cc_final: 0.7248 (ttt90) REVERT: O 14 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6568 (mt-10) REVERT: O 77 ARG cc_start: 0.7000 (mtp180) cc_final: 0.6663 (mtm110) REVERT: P 53 ASP cc_start: 0.7652 (t0) cc_final: 0.7444 (t70) REVERT: Q 9 GLN cc_start: 0.7262 (mt0) cc_final: 0.6820 (tt0) REVERT: Q 19 LYS cc_start: 0.7505 (mttp) cc_final: 0.6994 (mttt) REVERT: Q 39 LYS cc_start: 0.7552 (mttt) cc_final: 0.7231 (mttp) REVERT: R 24 LYS cc_start: 0.6851 (OUTLIER) cc_final: 0.6581 (mtpt) REVERT: R 30 LYS cc_start: 0.7487 (mttp) cc_final: 0.7266 (mtmm) REVERT: R 43 ARG cc_start: 0.6737 (ptm160) cc_final: 0.6533 (ptt90) REVERT: R 48 ARG cc_start: 0.6584 (mmt-90) cc_final: 0.5903 (mtp-110) REVERT: T 53 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6971 (mt-10) outliers start: 14 outliers final: 7 residues processed: 252 average time/residue: 2.0728 time to fit residues: 600.5406 Evaluate side-chains 259 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 247 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 53 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 73 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 219 optimal weight: 2.9990 chunk 182 optimal weight: 0.2980 chunk 101 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 115 optimal weight: 0.5980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 ASN E 78 ASN E 121 HIS F 11 HIS L 20 ASN O 35 GLN T 48 GLN T 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 36168 Z= 0.246 Angle : 0.729 12.993 54205 Z= 0.381 Chirality : 0.040 0.333 6931 Planarity : 0.006 0.132 2832 Dihedral : 22.716 174.544 18474 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.25 % Allowed : 9.24 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.90 (0.23), residues: 1233 helix: 1.49 (0.22), residues: 501 sheet: 0.23 (0.33), residues: 236 loop : -0.02 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP P 60 HIS 0.008 0.002 HIS P 9 PHE 0.024 0.002 PHE F 8 TYR 0.019 0.003 TYR D 51 ARG 0.005 0.001 ARG E 157 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 248 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 8 LYS cc_start: 0.7198 (mmtt) cc_final: 0.6953 (mppt) REVERT: D 25 VAL cc_start: 0.6761 (p) cc_final: 0.6452 (m) REVERT: D 30 THR cc_start: 0.7154 (m) cc_final: 0.6847 (p) REVERT: D 47 ARG cc_start: 0.5796 (ttm170) cc_final: 0.5446 (ttp80) REVERT: D 151 LYS cc_start: 0.5790 (pttp) cc_final: 0.5469 (pttp) REVERT: D 177 LYS cc_start: 0.5332 (OUTLIER) cc_final: 0.5103 (mttp) REVERT: D 185 LYS cc_start: 0.6513 (mmtt) cc_final: 0.6139 (mttm) REVERT: E 12 GLN cc_start: 0.7039 (mt0) cc_final: 0.6218 (tt0) REVERT: E 14 LYS cc_start: 0.7600 (mtpp) cc_final: 0.7185 (mttm) REVERT: E 26 LYS cc_start: 0.6968 (tttm) cc_final: 0.6695 (ptmm) REVERT: E 55 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6612 (mp0) REVERT: E 61 GLN cc_start: 0.7196 (tt0) cc_final: 0.6854 (tp40) REVERT: E 65 GLU cc_start: 0.7230 (mt-10) cc_final: 0.7027 (mt-10) REVERT: E 70 ASN cc_start: 0.6655 (m-40) cc_final: 0.6213 (m-40) REVERT: E 134 ILE cc_start: 0.7687 (mt) cc_final: 0.7339 (pt) REVERT: E 142 ASP cc_start: 0.7479 (t70) cc_final: 0.7270 (t70) REVERT: E 146 ASN cc_start: 0.5992 (m-40) cc_final: 0.5494 (p0) REVERT: E 151 GLU cc_start: 0.6559 (mp0) cc_final: 0.6181 (mm-30) REVERT: H 21 ASN cc_start: 0.7787 (m-40) cc_final: 0.7569 (m110) REVERT: H 22 LYS cc_start: 0.7134 (mmmm) cc_final: 0.6862 (mmmt) REVERT: H 31 LYS cc_start: 0.7363 (mmmm) cc_final: 0.6933 (mtmt) REVERT: H 60 GLU cc_start: 0.7745 (tt0) cc_final: 0.7514 (tt0) REVERT: K 40 ASN cc_start: 0.7106 (m-40) cc_final: 0.6854 (m-40) REVERT: K 68 GLU cc_start: 0.6498 (mt-10) cc_final: 0.6115 (mt-10) REVERT: K 126 LYS cc_start: 0.7875 (tttt) cc_final: 0.7268 (ttmm) REVERT: L 10 LYS cc_start: 0.7233 (tttt) cc_final: 0.6960 (ttpp) REVERT: L 43 LYS cc_start: 0.7196 (ttpt) cc_final: 0.6830 (ttmm) REVERT: L 54 ARG cc_start: 0.6941 (OUTLIER) cc_final: 0.6562 (ttm-80) REVERT: L 56 ARG cc_start: 0.6458 (ttm-80) cc_final: 0.6084 (ttm110) REVERT: L 108 LYS cc_start: 0.6330 (mptt) cc_final: 0.6062 (tttm) REVERT: L 121 ARG cc_start: 0.7513 (ttt-90) cc_final: 0.7296 (ttt90) REVERT: O 77 ARG cc_start: 0.7002 (mtp180) cc_final: 0.6654 (mtm110) REVERT: P 53 ASP cc_start: 0.7664 (t0) cc_final: 0.7453 (t70) REVERT: Q 9 GLN cc_start: 0.7267 (mt0) cc_final: 0.6818 (tt0) REVERT: Q 19 LYS cc_start: 0.7432 (mttp) cc_final: 0.6880 (mmtt) REVERT: Q 39 LYS cc_start: 0.7521 (mttt) cc_final: 0.7200 (mttp) REVERT: R 24 LYS cc_start: 0.6773 (OUTLIER) cc_final: 0.6458 (mtpt) REVERT: R 30 LYS cc_start: 0.7458 (mttp) cc_final: 0.7225 (mtmm) REVERT: R 43 ARG cc_start: 0.6796 (ptm160) cc_final: 0.6560 (ptt90) REVERT: R 48 ARG cc_start: 0.6578 (mmt-90) cc_final: 0.5917 (mtp-110) REVERT: T 53 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6889 (mt-10) outliers start: 13 outliers final: 6 residues processed: 252 average time/residue: 2.0616 time to fit residues: 597.8445 Evaluate side-chains 255 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 245 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain U residue 4 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 211 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 184 optimal weight: 0.1980 chunk 122 optimal weight: 0.0270 chunk 218 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 overall best weight: 0.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 ASN E 78 ASN E 121 HIS F 11 HIS L 20 ASN O 35 GLN O 40 GLN T 48 GLN T 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 36168 Z= 0.134 Angle : 0.567 12.558 54205 Z= 0.313 Chirality : 0.034 0.330 6931 Planarity : 0.005 0.124 2832 Dihedral : 22.599 175.098 18474 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.77 % Allowed : 10.01 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.34 (0.24), residues: 1233 helix: 2.05 (0.23), residues: 494 sheet: 0.28 (0.33), residues: 231 loop : 0.12 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 60 HIS 0.007 0.001 HIS F 58 PHE 0.022 0.001 PHE F 8 TYR 0.013 0.001 TYR D 51 ARG 0.003 0.000 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 244 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 8 LYS cc_start: 0.7059 (mmtt) cc_final: 0.6823 (mppt) REVERT: D 25 VAL cc_start: 0.6789 (p) cc_final: 0.6462 (m) REVERT: D 30 THR cc_start: 0.7161 (m) cc_final: 0.6853 (p) REVERT: D 47 ARG cc_start: 0.5816 (ttm170) cc_final: 0.5438 (ttp80) REVERT: D 151 LYS cc_start: 0.5796 (pttp) cc_final: 0.5509 (pttp) REVERT: D 185 LYS cc_start: 0.6491 (mmtt) cc_final: 0.6125 (mttm) REVERT: E 12 GLN cc_start: 0.7097 (mt0) cc_final: 0.6311 (tt0) REVERT: E 14 LYS cc_start: 0.7620 (mtpp) cc_final: 0.7212 (mttm) REVERT: E 23 LYS cc_start: 0.7962 (ptmm) cc_final: 0.7583 (ptmt) REVERT: E 26 LYS cc_start: 0.7020 (tttm) cc_final: 0.6717 (ptmm) REVERT: E 55 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6325 (pt0) REVERT: E 61 GLN cc_start: 0.7170 (tt0) cc_final: 0.6833 (tp40) REVERT: E 65 GLU cc_start: 0.7284 (mt-10) cc_final: 0.7048 (mt-10) REVERT: E 134 ILE cc_start: 0.7646 (mt) cc_final: 0.7262 (pt) REVERT: E 142 ASP cc_start: 0.7498 (t70) cc_final: 0.7225 (t70) REVERT: E 146 ASN cc_start: 0.5993 (m-40) cc_final: 0.5520 (p0) REVERT: E 151 GLU cc_start: 0.6695 (mp0) cc_final: 0.6357 (mm-30) REVERT: E 159 LYS cc_start: 0.7051 (mmtp) cc_final: 0.6739 (mmtt) REVERT: F 21 MET cc_start: 0.6451 (mtt) cc_final: 0.6237 (mtp) REVERT: H 21 ASN cc_start: 0.7774 (m-40) cc_final: 0.7568 (m110) REVERT: H 22 LYS cc_start: 0.7176 (mmmm) cc_final: 0.6885 (mmmt) REVERT: H 31 LYS cc_start: 0.7322 (mmmm) cc_final: 0.6889 (mtmt) REVERT: H 60 GLU cc_start: 0.7697 (tt0) cc_final: 0.7471 (tt0) REVERT: H 90 ASP cc_start: 0.7294 (p0) cc_final: 0.7029 (p0) REVERT: K 31 ILE cc_start: 0.7900 (mt) cc_final: 0.7677 (mm) REVERT: K 40 ASN cc_start: 0.6973 (m-40) cc_final: 0.6734 (m-40) REVERT: K 68 GLU cc_start: 0.6489 (mt-10) cc_final: 0.6213 (mt-10) REVERT: K 126 LYS cc_start: 0.7890 (tttt) cc_final: 0.7277 (ttmm) REVERT: L 10 LYS cc_start: 0.7211 (tttt) cc_final: 0.6890 (ttpp) REVERT: L 43 LYS cc_start: 0.7142 (ttpt) cc_final: 0.6761 (ttmm) REVERT: L 54 ARG cc_start: 0.6945 (ttm-80) cc_final: 0.6633 (ttm-80) REVERT: L 56 ARG cc_start: 0.6471 (ttm-80) cc_final: 0.6090 (ttm110) REVERT: L 62 GLU cc_start: 0.6839 (tp30) cc_final: 0.6534 (tp30) REVERT: L 108 LYS cc_start: 0.6312 (mptt) cc_final: 0.6035 (tttm) REVERT: L 121 ARG cc_start: 0.7472 (ttt-90) cc_final: 0.7252 (ttt90) REVERT: O 77 ARG cc_start: 0.6945 (mtp180) cc_final: 0.6613 (mtm110) REVERT: Q 9 GLN cc_start: 0.7238 (mt0) cc_final: 0.6775 (tt0) REVERT: Q 19 LYS cc_start: 0.7344 (mttp) cc_final: 0.6833 (mmtt) REVERT: Q 39 LYS cc_start: 0.7472 (mttt) cc_final: 0.7202 (mttp) REVERT: Q 77 ARG cc_start: 0.5883 (ptm-80) cc_final: 0.5585 (ptt90) REVERT: R 30 LYS cc_start: 0.7493 (mttp) cc_final: 0.7193 (mtmt) REVERT: R 43 ARG cc_start: 0.6785 (ptm160) cc_final: 0.6549 (ptt90) REVERT: R 48 ARG cc_start: 0.6513 (mmt-90) cc_final: 0.5858 (mtp-110) REVERT: U 44 GLU cc_start: 0.6527 (tm-30) cc_final: 0.6147 (tm-30) outliers start: 8 outliers final: 3 residues processed: 249 average time/residue: 2.0665 time to fit residues: 591.3081 Evaluate side-chains 240 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 237 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain Q residue 6 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 135 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 130 optimal weight: 0.5980 chunk 65 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 139 optimal weight: 9.9990 chunk 149 optimal weight: 0.5980 chunk 108 optimal weight: 0.0170 chunk 20 optimal weight: 7.9990 chunk 171 optimal weight: 7.9990 chunk 199 optimal weight: 0.6980 overall best weight: 1.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 70 ASN E 73 ASN E 78 ASN E 121 HIS F 11 HIS H 38 ASN L 20 ASN O 35 GLN T 48 GLN T 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 36168 Z= 0.193 Angle : 0.641 12.813 54205 Z= 0.344 Chirality : 0.037 0.322 6931 Planarity : 0.006 0.129 2832 Dihedral : 22.636 174.171 18474 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.58 % Allowed : 10.39 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 (0.24), residues: 1233 helix: 1.93 (0.23), residues: 495 sheet: 0.31 (0.33), residues: 234 loop : 0.14 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP P 60 HIS 0.007 0.001 HIS F 58 PHE 0.022 0.002 PHE F 8 TYR 0.013 0.002 TYR D 135 ARG 0.004 0.001 ARG E 157 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 249 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 8 LYS cc_start: 0.7158 (mmtt) cc_final: 0.6923 (mppt) REVERT: D 25 VAL cc_start: 0.6811 (p) cc_final: 0.6494 (m) REVERT: D 30 THR cc_start: 0.7143 (m) cc_final: 0.6838 (p) REVERT: D 47 ARG cc_start: 0.5800 (ttm170) cc_final: 0.5438 (ttp80) REVERT: D 151 LYS cc_start: 0.5800 (pttp) cc_final: 0.5474 (pttp) REVERT: D 185 LYS cc_start: 0.6462 (mmtt) cc_final: 0.6102 (mttm) REVERT: E 12 GLN cc_start: 0.7096 (mt0) cc_final: 0.6306 (tt0) REVERT: E 14 LYS cc_start: 0.7600 (mtpp) cc_final: 0.7185 (mttm) REVERT: E 23 LYS cc_start: 0.7994 (ptmm) cc_final: 0.7592 (ptmt) REVERT: E 26 LYS cc_start: 0.6993 (tttm) cc_final: 0.6682 (ptmm) REVERT: E 55 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6335 (pt0) REVERT: E 61 GLN cc_start: 0.7172 (tt0) cc_final: 0.6844 (tp40) REVERT: E 65 GLU cc_start: 0.7288 (mt-10) cc_final: 0.7061 (mt-10) REVERT: E 68 ARG cc_start: 0.7021 (mtt90) cc_final: 0.6776 (mtm-85) REVERT: E 134 ILE cc_start: 0.7655 (mt) cc_final: 0.7280 (pt) REVERT: E 142 ASP cc_start: 0.7514 (t70) cc_final: 0.7234 (t70) REVERT: E 146 ASN cc_start: 0.5984 (m-40) cc_final: 0.5507 (p0) REVERT: E 151 GLU cc_start: 0.6676 (mp0) cc_final: 0.6335 (mm-30) REVERT: F 21 MET cc_start: 0.6442 (mtt) cc_final: 0.6212 (mtp) REVERT: H 21 ASN cc_start: 0.7805 (m-40) cc_final: 0.7597 (m110) REVERT: H 22 LYS cc_start: 0.7182 (mmmm) cc_final: 0.6890 (mmmt) REVERT: H 31 LYS cc_start: 0.7356 (mmmm) cc_final: 0.6927 (mtmt) REVERT: H 60 GLU cc_start: 0.7712 (tt0) cc_final: 0.7476 (tt0) REVERT: K 40 ASN cc_start: 0.7030 (m-40) cc_final: 0.6773 (m-40) REVERT: K 68 GLU cc_start: 0.6542 (mt-10) cc_final: 0.6270 (mt-10) REVERT: K 126 LYS cc_start: 0.7889 (tttt) cc_final: 0.7273 (ttmm) REVERT: L 10 LYS cc_start: 0.7238 (tttt) cc_final: 0.6917 (ttpp) REVERT: L 43 LYS cc_start: 0.7166 (ttpt) cc_final: 0.6780 (ttmm) REVERT: L 54 ARG cc_start: 0.6954 (ttm-80) cc_final: 0.6601 (ttm-80) REVERT: L 56 ARG cc_start: 0.6476 (ttm-80) cc_final: 0.6099 (ttm110) REVERT: L 108 LYS cc_start: 0.6344 (mptt) cc_final: 0.6054 (tttm) REVERT: L 121 ARG cc_start: 0.7492 (ttt-90) cc_final: 0.7270 (ttt90) REVERT: O 77 ARG cc_start: 0.6944 (mtp180) cc_final: 0.6637 (mtm110) REVERT: Q 9 GLN cc_start: 0.7275 (mt0) cc_final: 0.6681 (tt0) REVERT: Q 19 LYS cc_start: 0.7413 (mttp) cc_final: 0.6890 (mmtt) REVERT: Q 25 ILE cc_start: 0.7619 (OUTLIER) cc_final: 0.7300 (mm) REVERT: Q 39 LYS cc_start: 0.7493 (mttt) cc_final: 0.7227 (mttp) REVERT: Q 77 ARG cc_start: 0.5885 (ptm-80) cc_final: 0.5591 (ptt90) REVERT: R 30 LYS cc_start: 0.7505 (mttp) cc_final: 0.7202 (mtmt) REVERT: R 43 ARG cc_start: 0.6800 (ptm160) cc_final: 0.6558 (ptt90) REVERT: R 48 ARG cc_start: 0.6531 (mmt-90) cc_final: 0.5896 (mtp-110) REVERT: T 53 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6931 (mt-10) outliers start: 6 outliers final: 4 residues processed: 250 average time/residue: 2.1058 time to fit residues: 605.4856 Evaluate side-chains 251 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 245 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain T residue 53 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 209 optimal weight: 0.9980 chunk 191 optimal weight: 7.9990 chunk 203 optimal weight: 9.9990 chunk 122 optimal weight: 0.8980 chunk 88 optimal weight: 8.9990 chunk 160 optimal weight: 0.5980 chunk 62 optimal weight: 7.9990 chunk 184 optimal weight: 7.9990 chunk 192 optimal weight: 0.6980 chunk 133 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 overall best weight: 1.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 70 ASN E 73 ASN E 78 ASN E 121 HIS F 11 HIS H 38 ASN L 20 ASN O 35 GLN O 40 GLN T 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 36168 Z= 0.216 Angle : 0.676 12.901 54205 Z= 0.359 Chirality : 0.038 0.313 6931 Planarity : 0.006 0.130 2832 Dihedral : 22.643 174.135 18474 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.58 % Allowed : 10.78 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.22 (0.23), residues: 1233 helix: 1.84 (0.22), residues: 495 sheet: 0.30 (0.33), residues: 234 loop : 0.13 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP P 60 HIS 0.007 0.002 HIS F 58 PHE 0.022 0.002 PHE F 8 TYR 0.014 0.002 TYR D 135 ARG 0.004 0.001 ARG E 157 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 246 time to evaluate : 2.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 8 LYS cc_start: 0.7150 (mmtt) cc_final: 0.6917 (mppt) REVERT: D 25 VAL cc_start: 0.6763 (p) cc_final: 0.6447 (m) REVERT: D 30 THR cc_start: 0.7139 (m) cc_final: 0.6836 (p) REVERT: D 47 ARG cc_start: 0.5831 (ttm170) cc_final: 0.5455 (ttp80) REVERT: D 151 LYS cc_start: 0.5786 (pttp) cc_final: 0.5489 (pttp) REVERT: D 185 LYS cc_start: 0.6465 (mmtt) cc_final: 0.6104 (mttm) REVERT: E 12 GLN cc_start: 0.7095 (mt0) cc_final: 0.6309 (tt0) REVERT: E 14 LYS cc_start: 0.7590 (mtpp) cc_final: 0.7174 (mttm) REVERT: E 23 LYS cc_start: 0.7990 (ptmm) cc_final: 0.7574 (ptmt) REVERT: E 26 LYS cc_start: 0.6986 (tttm) cc_final: 0.6677 (ptmm) REVERT: E 55 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6344 (pt0) REVERT: E 61 GLN cc_start: 0.7172 (tt0) cc_final: 0.6846 (tp40) REVERT: E 65 GLU cc_start: 0.7282 (mt-10) cc_final: 0.7060 (mt-10) REVERT: E 68 ARG cc_start: 0.7028 (mtt90) cc_final: 0.6779 (mtm-85) REVERT: E 134 ILE cc_start: 0.7656 (mt) cc_final: 0.7275 (pt) REVERT: E 142 ASP cc_start: 0.7533 (t70) cc_final: 0.7250 (t70) REVERT: E 146 ASN cc_start: 0.5980 (m-40) cc_final: 0.5512 (p0) REVERT: E 151 GLU cc_start: 0.6648 (mp0) cc_final: 0.6310 (mm-30) REVERT: H 21 ASN cc_start: 0.7815 (m-40) cc_final: 0.7602 (m110) REVERT: H 22 LYS cc_start: 0.7167 (mmmm) cc_final: 0.6876 (mmmt) REVERT: H 31 LYS cc_start: 0.7347 (mmmm) cc_final: 0.6921 (mtmt) REVERT: H 60 GLU cc_start: 0.7740 (tt0) cc_final: 0.7507 (tt0) REVERT: K 40 ASN cc_start: 0.7066 (m-40) cc_final: 0.6810 (m-40) REVERT: K 68 GLU cc_start: 0.6545 (mt-10) cc_final: 0.6229 (mt-10) REVERT: K 126 LYS cc_start: 0.7879 (tttt) cc_final: 0.7266 (ttmm) REVERT: L 10 LYS cc_start: 0.7229 (tttt) cc_final: 0.6918 (ttpp) REVERT: L 43 LYS cc_start: 0.7197 (ttpt) cc_final: 0.6815 (ttmm) REVERT: L 54 ARG cc_start: 0.6980 (ttm-80) cc_final: 0.6586 (ttm-80) REVERT: L 56 ARG cc_start: 0.6457 (ttm-80) cc_final: 0.6083 (ttm110) REVERT: L 108 LYS cc_start: 0.6357 (mptt) cc_final: 0.6060 (tttm) REVERT: L 121 ARG cc_start: 0.7504 (ttt-90) cc_final: 0.7284 (ttt90) REVERT: O 77 ARG cc_start: 0.6951 (mtp180) cc_final: 0.6639 (mtm110) REVERT: Q 9 GLN cc_start: 0.7284 (mt0) cc_final: 0.6682 (tt0) REVERT: Q 19 LYS cc_start: 0.7429 (mttp) cc_final: 0.6947 (mmtt) REVERT: Q 25 ILE cc_start: 0.7622 (OUTLIER) cc_final: 0.7296 (mm) REVERT: Q 39 LYS cc_start: 0.7518 (mttt) cc_final: 0.7233 (mttp) REVERT: Q 77 ARG cc_start: 0.5901 (ptm-80) cc_final: 0.5599 (ptt90) REVERT: R 30 LYS cc_start: 0.7498 (mttp) cc_final: 0.7192 (mtmt) REVERT: R 43 ARG cc_start: 0.6788 (ptm160) cc_final: 0.6566 (ptt90) REVERT: R 48 ARG cc_start: 0.6545 (mmt-90) cc_final: 0.5908 (mtp-110) REVERT: T 53 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6909 (mt-10) outliers start: 6 outliers final: 4 residues processed: 247 average time/residue: 2.0813 time to fit residues: 593.4582 Evaluate side-chains 248 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 242 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain T residue 53 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 131 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 149 optimal weight: 0.7980 chunk 226 optimal weight: 9.9990 chunk 208 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 143 optimal weight: 0.0870 chunk 191 optimal weight: 8.9990 overall best weight: 3.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 ASN E 78 ASN E 121 HIS F 11 HIS H 38 ASN L 20 ASN O 35 GLN T 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 36168 Z= 0.362 Angle : 0.881 13.455 54205 Z= 0.445 Chirality : 0.046 0.315 6931 Planarity : 0.008 0.138 2832 Dihedral : 22.762 172.772 18474 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.67 % Allowed : 10.68 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.77 (0.23), residues: 1233 helix: 1.30 (0.22), residues: 501 sheet: 0.21 (0.34), residues: 235 loop : -0.02 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP P 60 HIS 0.009 0.003 HIS F 58 PHE 0.024 0.003 PHE F 8 TYR 0.022 0.004 TYR D 135 ARG 0.009 0.001 ARG E 157 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 244 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 8 LYS cc_start: 0.7209 (mmtt) cc_final: 0.6954 (mppt) REVERT: D 25 VAL cc_start: 0.6792 (p) cc_final: 0.6486 (m) REVERT: D 30 THR cc_start: 0.7130 (m) cc_final: 0.6829 (p) REVERT: D 47 ARG cc_start: 0.5853 (ttm170) cc_final: 0.5499 (ttm170) REVERT: D 151 LYS cc_start: 0.5765 (pttp) cc_final: 0.5471 (pttp) REVERT: D 185 LYS cc_start: 0.6508 (mmtt) cc_final: 0.6122 (mttm) REVERT: E 12 GLN cc_start: 0.7016 (mt0) cc_final: 0.6236 (tt0) REVERT: E 14 LYS cc_start: 0.7548 (mtpp) cc_final: 0.7135 (mttm) REVERT: E 26 LYS cc_start: 0.6934 (tttm) cc_final: 0.6644 (ptmm) REVERT: E 55 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6339 (pt0) REVERT: E 61 GLN cc_start: 0.7151 (tt0) cc_final: 0.6803 (tp40) REVERT: E 68 ARG cc_start: 0.7019 (mtt90) cc_final: 0.6744 (mtm-85) REVERT: E 134 ILE cc_start: 0.7704 (mt) cc_final: 0.7366 (pt) REVERT: E 146 ASN cc_start: 0.6091 (m-40) cc_final: 0.5560 (p0) REVERT: E 151 GLU cc_start: 0.6506 (mp0) cc_final: 0.6119 (mm-30) REVERT: H 21 ASN cc_start: 0.7790 (m-40) cc_final: 0.7583 (m110) REVERT: H 31 LYS cc_start: 0.7404 (mmmm) cc_final: 0.6976 (mtpt) REVERT: H 60 GLU cc_start: 0.7723 (tt0) cc_final: 0.7472 (tt0) REVERT: K 40 ASN cc_start: 0.7113 (m-40) cc_final: 0.6809 (m-40) REVERT: K 68 GLU cc_start: 0.6528 (mt-10) cc_final: 0.6206 (mt-10) REVERT: K 126 LYS cc_start: 0.7859 (tttt) cc_final: 0.7254 (ttmm) REVERT: L 10 LYS cc_start: 0.7241 (tttt) cc_final: 0.6947 (ttpp) REVERT: L 43 LYS cc_start: 0.7211 (ttpt) cc_final: 0.6841 (ttmm) REVERT: L 54 ARG cc_start: 0.7063 (ttm-80) cc_final: 0.6719 (ttm-80) REVERT: L 56 ARG cc_start: 0.6436 (ttm-80) cc_final: 0.6071 (ttm110) REVERT: L 108 LYS cc_start: 0.6386 (mptt) cc_final: 0.6079 (tttm) REVERT: L 121 ARG cc_start: 0.7521 (ttt-90) cc_final: 0.7233 (ttt90) REVERT: O 77 ARG cc_start: 0.6989 (mtp180) cc_final: 0.6667 (mtm110) REVERT: Q 9 GLN cc_start: 0.7251 (mt0) cc_final: 0.6745 (tt0) REVERT: Q 39 LYS cc_start: 0.7530 (mttt) cc_final: 0.7240 (mttp) REVERT: R 24 LYS cc_start: 0.6768 (OUTLIER) cc_final: 0.6515 (mtpt) REVERT: R 30 LYS cc_start: 0.7452 (mttp) cc_final: 0.7240 (mtmm) REVERT: R 43 ARG cc_start: 0.6826 (ptm160) cc_final: 0.6623 (ptt90) REVERT: R 48 ARG cc_start: 0.6570 (mmt-90) cc_final: 0.5887 (mtp-110) outliers start: 7 outliers final: 6 residues processed: 247 average time/residue: 2.0810 time to fit residues: 591.1322 Evaluate side-chains 249 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 242 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain U residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 55 optimal weight: 5.9990 chunk 166 optimal weight: 0.0970 chunk 26 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 180 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 overall best weight: 3.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 ASN E 78 ASN E 121 HIS F 11 HIS L 20 ASN O 35 GLN O 40 GLN T 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.136144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.105981 restraints weight = 27536.328| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 0.47 r_work: 0.3011 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work: 0.2725 rms_B_bonded: 4.69 restraints_weight: 0.1250 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 36168 Z= 0.327 Angle : 0.826 13.226 54205 Z= 0.422 Chirality : 0.044 0.318 6931 Planarity : 0.007 0.137 2832 Dihedral : 22.752 172.992 18474 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.87 % Allowed : 10.78 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.76 (0.23), residues: 1233 helix: 1.30 (0.22), residues: 495 sheet: 0.22 (0.34), residues: 234 loop : -0.02 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP P 60 HIS 0.009 0.002 HIS F 58 PHE 0.024 0.003 PHE F 8 TYR 0.020 0.003 TYR D 135 ARG 0.008 0.001 ARG E 157 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12547.35 seconds wall clock time: 225 minutes 56.05 seconds (13556.05 seconds total)