Starting phenix.real_space_refine on Thu Feb 22 08:26:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afi_11766/02_2024/7afi_11766_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afi_11766/02_2024/7afi_11766.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afi_11766/02_2024/7afi_11766_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afi_11766/02_2024/7afi_11766_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afi_11766/02_2024/7afi_11766_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afi_11766/02_2024/7afi_11766.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afi_11766/02_2024/7afi_11766.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afi_11766/02_2024/7afi_11766_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afi_11766/02_2024/7afi_11766_updated.pdb" } resolution = 3.53 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1066 5.49 5 Mg 46 5.21 5 S 45 5.16 5 C 16997 2.51 5 N 6274 2.21 5 O 9375 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33803 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 22908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 22908 Classifications: {'RNA': 1066} Modifications used: {'rna2p_pur': 81, 'rna2p_pyr': 58, 'rna3p': 5, 'rna3p_pur': 532, 'rna3p_pyr': 390} Link IDs: {'rna2p': 138, 'rna3p': 927} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 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: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 866 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "X" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1174 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Unusual residues: {' MG': 46} Classifications: {'undetermined': 46} Link IDs: {None: 45} Time building chain proxies: 17.57, per 1000 atoms: 0.52 Number of scatterers: 33803 At special positions: 0 Unit cell: (146.475, 214.83, 139.965, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 45 16.00 P 1066 15.00 Mg 46 11.99 O 9375 8.00 N 6274 7.00 C 16997 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 24.06 Conformation dependent library (CDL) restraints added in 2.3 seconds 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2570 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 13 sheets defined 35.8% alpha, 15.8% beta 334 base pairs and 521 stacking pairs defined. Time for finding SS restraints: 22.19 Creating SS restraints... Processing helix chain 'D' and resid 8 through 14 removed outlier: 3.922A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 40 through 42 No H-bonds generated for 'chain 'D' and resid 40 through 42' Processing helix chain 'D' and resid 50 through 64 removed outlier: 3.541A pdb=" N GLN D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) 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 120 removed outlier: 3.522A pdb=" N LEU D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 151 removed outlier: 3.774A pdb=" N LYS D 151 " --> pdb=" O LYS D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 164 removed outlier: 3.947A pdb=" N GLN D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 205 removed outlier: 3.557A pdb=" N SER D 205 " --> pdb=" O VAL D 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 66 Processing helix chain 'E' and resid 109 through 118 removed outlier: 3.858A pdb=" N VAL E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 146 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 32 removed outlier: 4.522A pdb=" N GLU F 16 " --> pdb=" O ASP F 13 " (cutoff:3.500A) Proline residue: F 19 - end of helix removed outlier: 4.008A pdb=" N GLU F 23 " --> pdb=" O GLY F 20 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG F 24 " --> pdb=" O MET F 21 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ALA F 27 " --> pdb=" O ARG F 24 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY F 31 " --> pdb=" O ALA F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 80 removed outlier: 3.699A pdb=" N ASP F 72 " --> pdb=" O GLN F 68 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU F 74 " --> pdb=" O VAL F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 105 Processing helix chain 'H' and resid 6 through 20 Processing helix chain 'H' and resid 31 through 43 removed outlier: 3.688A pdb=" N VAL H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS H 41 " --> pdb=" O ALA H 37 " (cutoff:3.500A) 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 96 through 98 No H-bonds generated for 'chain 'H' and resid 96 through 98' Processing helix chain 'H' and resid 113 through 119 Processing helix chain 'K' and resid 47 through 50 No H-bonds generated for 'chain 'K' and resid 47 through 50' Processing helix chain 'K' and resid 56 through 58 No H-bonds generated for 'chain 'K' and resid 56 through 58' Processing helix chain 'K' and resid 60 through 71 Processing helix chain 'K' and resid 74 through 77 No H-bonds generated for 'chain 'K' and resid 74 through 77' Processing helix chain 'K' and resid 93 through 103 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 14 Processing helix chain 'O' and resid 25 through 45 removed outlier: 3.566A pdb=" N GLN O 40 " --> pdb=" O ILE O 36 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE O 43 " --> pdb=" O LEU O 39 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 73 removed outlier: 3.552A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 85 removed outlier: 4.077A pdb=" N GLU O 83 " --> pdb=" O THR O 79 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ARG O 84 " --> pdb=" O GLN O 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 54 through 62 Processing helix chain 'P' and resid 69 through 80 Processing helix chain 'Q' and resid 49 through 51 No H-bonds generated for 'chain 'Q' and resid 49 through 51' Processing helix chain 'R' and resid 12 through 16 Processing helix chain 'R' and resid 26 through 31 removed outlier: 3.915A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (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 removed outlier: 3.760A pdb=" N GLN R 54 " --> pdb=" O LYS R 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 41 removed outlier: 3.506A pdb=" N ILE T 12 " --> pdb=" O LYS T 8 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU T 15 " --> pdb=" O ALA T 11 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS T 20 " --> pdb=" O LYS T 16 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE T 32 " --> pdb=" O MET T 28 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL T 35 " --> pdb=" O PHE T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 63 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 69 through 84 Processing helix chain 'X' and resid 5 through 18 removed outlier: 3.578A pdb=" N ALA X 14 " --> pdb=" O GLU X 10 " (cutoff:3.500A) Proline residue: X 15 - end of helix Processing helix chain 'X' and resid 48 through 64 removed outlier: 4.293A pdb=" N VAL X 64 " --> pdb=" O ALA X 60 " (cutoff:3.500A) Processing helix chain 'X' and resid 88 through 93 Processing sheet with id= A, first strand: chain 'D' and resid 123 through 125 Processing sheet with id= B, first strand: chain 'D' and resid 171 through 174 Processing sheet with id= C, first strand: chain 'E' and resid 46 through 53 removed outlier: 3.561A pdb=" N ALA E 17 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 85 through 89 removed outlier: 3.671A pdb=" N ARG E 93 " --> pdb=" O TYR E 128 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'F' and resid 89 through 91 removed outlier: 3.591A pdb=" N VAL F 64 " --> pdb=" O TYR F 4 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU F 65 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ILE F 36 " --> pdb=" O GLU F 65 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 24 through 27 removed outlier: 3.602A pdb=" N VAL H 25 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU H 61 " --> pdb=" O VAL H 25 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 75 through 77 removed outlier: 6.859A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N TYR H 128 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE H 101 " --> pdb=" O TYR H 128 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'K' and resid 110 through 112 removed outlier: 5.934A pdb=" N VAL K 84 " --> pdb=" O THR K 111 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ALA K 21 " --> pdb=" O MET K 85 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LYS K 87 " --> pdb=" O ALA K 21 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE K 23 " --> pdb=" O LYS K 87 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'L' and resid 79 through 83 removed outlier: 6.484A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N VAL L 37 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL L 52 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR L 39 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG L 50 " --> pdb=" O THR L 39 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'P' and resid 2 through 11 removed outlier: 6.552A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'Q' and resid 58 through 61 removed outlier: 7.665A pdb=" N GLN Q 9 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLU Q 26 " --> pdb=" O GLN Q 9 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL Q 22 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE Q 25 " --> pdb=" O THR Q 42 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR Q 42 " --> pdb=" O ILE Q 25 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL Q 29 " --> pdb=" O ILE Q 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'X' and resid 74 through 77 removed outlier: 7.244A pdb=" N LEU X 36 " --> pdb=" O GLU X 75 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N SER X 77 " --> pdb=" O LEU X 36 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE X 38 " --> pdb=" O SER X 77 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY X 25 " --> pdb=" O TYR X 39 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'X' and resid 143 through 147 removed outlier: 4.220A pdb=" N GLU X 98 " --> pdb=" O VAL X 147 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL X 116 " --> pdb=" O THR X 128 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR X 126 " --> pdb=" O LYS X 118 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N VAL X 120 " --> pdb=" O MET X 124 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N MET X 124 " --> pdb=" O VAL X 120 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1080 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 775 hydrogen bonds 992 hydrogen bond angles 0 basepair planarities 334 basepair parallelities 521 stacking parallelities Total time for adding SS restraints: 26.67 Time building geometry restraints manager: 25.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3733 1.32 - 1.44: 15878 1.44 - 1.57: 14839 1.57 - 1.69: 2128 1.69 - 1.82: 78 Bond restraints: 36656 Sorted by residual: bond pdb=" C2 G7M A 527 " pdb=" N3 G7M A 527 " ideal model delta sigma weight residual 1.462 1.309 0.153 2.00e-02 2.50e+03 5.85e+01 bond pdb=" N3 2MG A1516 " pdb=" C4 2MG A1516 " ideal model delta sigma weight residual 1.496 1.346 0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N3 G7M A 527 " pdb=" C4 G7M A 527 " ideal model delta sigma weight residual 1.492 1.350 0.142 2.00e-02 2.50e+03 5.05e+01 bond pdb=" C2 2MG A1516 " pdb=" N2 2MG A1516 " ideal model delta sigma weight residual 1.475 1.344 0.131 2.00e-02 2.50e+03 4.27e+01 bond pdb=" C2 G7M A 527 " pdb=" N2 G7M A 527 " ideal model delta sigma weight residual 1.452 1.326 0.126 2.00e-02 2.50e+03 3.95e+01 ... (remaining 36651 not shown) Histogram of bond angle deviations from ideal: 97.13 - 105.16: 5169 105.16 - 113.19: 23073 113.19 - 121.22: 17335 121.22 - 129.25: 8129 129.25 - 137.28: 1103 Bond angle restraints: 54809 Sorted by residual: angle pdb=" C1' G7M A 527 " pdb=" N9 G7M A 527 " pdb=" C8 G7M A 527 " ideal model delta sigma weight residual 94.96 127.74 -32.78 3.00e+00 1.11e-01 1.19e+02 angle pdb=" CA PHE K 52 " pdb=" C PHE K 52 " pdb=" O PHE K 52 " ideal model delta sigma weight residual 121.05 111.12 9.93 1.14e+00 7.69e-01 7.59e+01 angle pdb=" C HIS Q 31 " pdb=" N PRO Q 32 " pdb=" CA PRO Q 32 " ideal model delta sigma weight residual 119.05 110.82 8.23 1.11e+00 8.12e-01 5.50e+01 angle pdb=" N ASN Q 51 " pdb=" CA ASN Q 51 " pdb=" C ASN Q 51 " ideal model delta sigma weight residual 111.39 101.78 9.61 1.38e+00 5.25e-01 4.85e+01 angle pdb=" C3' C A 528 " pdb=" C2' C A 528 " pdb=" O2' C A 528 " ideal model delta sigma weight residual 110.70 101.51 9.19 1.50e+00 4.44e-01 3.75e+01 ... (remaining 54804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 20397 35.99 - 71.98: 2740 71.98 - 107.97: 308 107.97 - 143.96: 8 143.96 - 179.94: 6 Dihedral angle restraints: 23459 sinusoidal: 19479 harmonic: 3980 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 52.39 147.61 1 1.50e+01 4.44e-03 7.87e+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 58.38 141.62 1 1.50e+01 4.44e-03 7.61e+01 dihedral pdb=" O4' U A 85 " pdb=" C1' U A 85 " pdb=" N1 U A 85 " pdb=" C2 U A 85 " ideal model delta sinusoidal sigma weight residual -128.00 51.94 -179.94 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 23456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 6626 0.121 - 0.243: 344 0.243 - 0.364: 17 0.364 - 0.485: 2 0.485 - 0.607: 2 Chirality restraints: 6991 Sorted by residual: chirality pdb=" CA ARG K 69 " pdb=" N ARG K 69 " pdb=" C ARG K 69 " pdb=" CB ARG K 69 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.20e+00 chirality pdb=" CA ASP K 72 " pdb=" N ASP K 72 " pdb=" C ASP K 72 " pdb=" CB ASP K 72 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.06e+00 chirality pdb=" CA GLU K 68 " pdb=" N GLU K 68 " pdb=" C GLU K 68 " pdb=" CB GLU K 68 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.13e+00 ... (remaining 6988 not shown) Planarity restraints: 2987 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " 0.057 2.00e-02 2.50e+03 6.14e-01 8.50e+03 pdb=" C4' 2MG A1516 " 0.451 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " 0.692 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " -0.593 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " -0.644 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " -0.184 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " 0.974 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " 0.206 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " -0.959 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 MA6 A1519 " 0.121 2.00e-02 2.50e+03 2.00e-01 3.98e+02 pdb=" N6 MA6 A1519 " -0.346 2.00e-02 2.50e+03 pdb=" C10 MA6 A1519 " 0.116 2.00e-02 2.50e+03 pdb=" C9 MA6 A1519 " 0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 MA6 A1518 " 0.121 2.00e-02 2.50e+03 1.97e-01 3.89e+02 pdb=" N6 MA6 A1518 " -0.341 2.00e-02 2.50e+03 pdb=" C10 MA6 A1518 " 0.114 2.00e-02 2.50e+03 pdb=" C9 MA6 A1518 " 0.106 2.00e-02 2.50e+03 ... (remaining 2984 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 525 2.45 - 3.06: 24368 3.06 - 3.67: 74166 3.67 - 4.29: 99332 4.29 - 4.90: 132136 Nonbonded interactions: 330527 Sorted by model distance: nonbonded pdb=" OP2 A A 560 " pdb="MG MG A1603 " model vdw 1.836 2.170 nonbonded pdb=" OP2 C A 175 " pdb="MG MG A1623 " model vdw 1.845 2.170 nonbonded pdb=" OP2 G A 117 " pdb="MG MG A1644 " model vdw 1.846 2.170 nonbonded pdb=" N7 G A 362 " pdb="MG MG A1611 " model vdw 1.852 2.250 nonbonded pdb=" OP2 A A 53 " pdb="MG MG A1624 " model vdw 1.867 2.170 ... (remaining 330522 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 group one per residue 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 13.460 Check model and map are aligned: 0.510 Set scattering table: 0.300 Process input model: 123.220 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.153 36656 Z= 0.641 Angle : 0.988 32.775 54809 Z= 0.598 Chirality : 0.059 0.607 6991 Planarity : 0.013 0.614 2987 Dihedral : 24.241 179.944 20889 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 33.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 0.00 % Allowed : 16.96 % Favored : 83.04 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.21), residues: 1360 helix: -1.89 (0.23), residues: 473 sheet: -1.88 (0.32), residues: 236 loop : -1.95 (0.21), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Q 73 HIS 0.009 0.002 HIS X 56 PHE 0.020 0.002 PHE K 61 TYR 0.014 0.002 TYR O 69 ARG 0.007 0.001 ARG X 110 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 399 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 135 TYR cc_start: 0.9415 (t80) cc_final: 0.9049 (t80) REVERT: E 14 LYS cc_start: 0.9037 (mttm) cc_final: 0.8550 (mmtm) REVERT: E 30 ILE cc_start: 0.9000 (mm) cc_final: 0.8732 (mm) REVERT: E 68 ARG cc_start: 0.9342 (mtt-85) cc_final: 0.8815 (mmt90) REVERT: E 103 THR cc_start: 0.9431 (m) cc_final: 0.9173 (p) REVERT: E 116 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8158 (tm-30) REVERT: F 5 GLU cc_start: 0.8805 (tt0) cc_final: 0.8602 (tm-30) REVERT: F 17 GLN cc_start: 0.9307 (tp-100) cc_final: 0.9089 (tp-100) REVERT: F 80 PHE cc_start: 0.9099 (t80) cc_final: 0.8779 (t80) REVERT: F 88 MET cc_start: 0.9061 (tpt) cc_final: 0.8808 (tpt) REVERT: H 3 MET cc_start: 0.8909 (tmm) cc_final: 0.8511 (tmm) REVERT: H 27 MET cc_start: 0.8665 (ptp) cc_final: 0.8437 (ptp) REVERT: H 80 ARG cc_start: 0.9536 (mtm110) cc_final: 0.9151 (mtp-110) REVERT: H 88 ARG cc_start: 0.8664 (mtp-110) cc_final: 0.8016 (mtp85) REVERT: K 42 LEU cc_start: 0.9065 (mm) cc_final: 0.8784 (mt) REVERT: K 70 CYS cc_start: 0.8854 (t) cc_final: 0.8462 (m) REVERT: L 41 THR cc_start: 0.8335 (p) cc_final: 0.8064 (p) REVERT: P 76 LYS cc_start: 0.9686 (ttmm) cc_final: 0.9479 (tptt) REVERT: Q 8 LEU cc_start: 0.9319 (tp) cc_final: 0.8795 (tt) REVERT: Q 60 GLU cc_start: 0.8680 (tt0) cc_final: 0.8333 (tp30) REVERT: Q 81 LYS cc_start: 0.8698 (tppt) cc_final: 0.8244 (tppt) REVERT: R 26 ILE cc_start: 0.9686 (pt) cc_final: 0.9301 (mt) REVERT: R 57 ARG cc_start: 0.9304 (mtm-85) cc_final: 0.9093 (mmm160) REVERT: T 24 ARG cc_start: 0.9222 (tpp-160) cc_final: 0.8914 (mmm-85) REVERT: T 59 ASP cc_start: 0.8608 (m-30) cc_final: 0.8392 (m-30) REVERT: X 40 ILE cc_start: 0.9485 (mp) cc_final: 0.9183 (pt) REVERT: X 136 PHE cc_start: 0.8165 (m-80) cc_final: 0.7899 (m-80) REVERT: X 143 LYS cc_start: 0.8853 (tptp) cc_final: 0.8613 (mtmm) outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 0.5881 time to fit residues: 344.7319 Evaluate side-chains 271 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 201 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 187 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 217 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 GLN ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 ASN E 148 ASN F 14 GLN ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN K 119 ASN O 28 GLN O 35 GLN O 40 GLN Q 9 GLN Q 50 ASN Q 51 ASN R 19 GLN R 52 GLN ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 ASN X 47 ASN ** X 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 109 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 36656 Z= 0.254 Angle : 0.631 12.663 54809 Z= 0.328 Chirality : 0.035 0.273 6991 Planarity : 0.005 0.115 2987 Dihedral : 24.517 177.854 18191 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 26.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.98 % Allowed : 21.77 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.21), residues: 1360 helix: -0.99 (0.21), residues: 500 sheet: -1.80 (0.29), residues: 278 loop : -1.08 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP X 113 HIS 0.011 0.001 HIS X 56 PHE 0.023 0.002 PHE F 8 TYR 0.034 0.002 TYR K 77 ARG 0.007 0.001 ARG L 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 320 time to evaluate : 2.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 71 GLN cc_start: 0.9319 (tt0) cc_final: 0.9080 (tt0) REVERT: D 206 LYS cc_start: 0.8976 (ttpp) cc_final: 0.8509 (ttmm) REVERT: E 14 LYS cc_start: 0.9134 (mttm) cc_final: 0.8867 (mmtm) REVERT: E 54 ARG cc_start: 0.4548 (mtt180) cc_final: 0.4059 (mpt180) REVERT: E 96 MET cc_start: 0.8776 (mpp) cc_final: 0.8511 (mpp) REVERT: E 103 THR cc_start: 0.9450 (m) cc_final: 0.9126 (p) REVERT: E 116 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8175 (tm-30) REVERT: F 62 MET cc_start: 0.7800 (mpp) cc_final: 0.7585 (mpp) REVERT: F 69 GLU cc_start: 0.9380 (pm20) cc_final: 0.9085 (pm20) REVERT: F 88 MET cc_start: 0.9142 (tpt) cc_final: 0.8905 (tpp) REVERT: F 93 LYS cc_start: 0.9279 (mttt) cc_final: 0.9056 (tttt) REVERT: H 3 MET cc_start: 0.8935 (tmm) cc_final: 0.8641 (tmm) REVERT: H 42 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8721 (mt-10) REVERT: H 58 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7642 (mm-30) REVERT: H 80 ARG cc_start: 0.9352 (mtm110) cc_final: 0.9018 (mtp-110) REVERT: H 88 ARG cc_start: 0.8598 (mtp-110) cc_final: 0.7846 (mtp85) REVERT: H 96 MET cc_start: 0.9070 (mtp) cc_final: 0.8263 (ttm) REVERT: H 121 LEU cc_start: 0.9349 (tp) cc_final: 0.9053 (tp) REVERT: K 24 HIS cc_start: 0.8541 (t70) cc_final: 0.8338 (t70) REVERT: K 94 GLU cc_start: 0.9316 (tt0) cc_final: 0.8676 (tm-30) REVERT: O 59 MET cc_start: 0.9152 (mtm) cc_final: 0.8831 (mtm) REVERT: P 76 LYS cc_start: 0.9530 (ttmm) cc_final: 0.9301 (tptt) REVERT: Q 8 LEU cc_start: 0.9309 (tp) cc_final: 0.8859 (tp) REVERT: Q 39 LYS cc_start: 0.9136 (ptpp) cc_final: 0.8889 (mtmm) REVERT: Q 61 ILE cc_start: 0.9459 (mm) cc_final: 0.9112 (tp) REVERT: Q 81 LYS cc_start: 0.8468 (tppt) cc_final: 0.7998 (tppt) REVERT: R 32 TYR cc_start: 0.8668 (m-80) cc_final: 0.8446 (m-80) REVERT: T 24 ARG cc_start: 0.9152 (tpp-160) cc_final: 0.8870 (mmm-85) REVERT: T 59 ASP cc_start: 0.8746 (m-30) cc_final: 0.8490 (m-30) REVERT: X 82 ASP cc_start: 0.9186 (m-30) cc_final: 0.8723 (t0) REVERT: X 113 TRP cc_start: 0.8423 (m-90) cc_final: 0.7552 (m-90) outliers start: 57 outliers final: 29 residues processed: 351 average time/residue: 0.5305 time to fit residues: 283.7312 Evaluate side-chains 287 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 258 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain X residue 44 ASP Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 89 GLU Chi-restraints excluded: chain X residue 125 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 120 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 147 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 217 optimal weight: 9.9990 chunk 234 optimal weight: 8.9990 chunk 193 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 174 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 54 GLN D 126 ASN ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 GLN ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 ASN K 81 ASN O 28 GLN ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 109 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 36656 Z= 0.352 Angle : 0.658 12.608 54809 Z= 0.343 Chirality : 0.037 0.273 6991 Planarity : 0.005 0.119 2987 Dihedral : 24.437 175.945 18191 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 29.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 6.21 % Allowed : 23.43 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.21), residues: 1360 helix: -0.44 (0.22), residues: 488 sheet: -1.59 (0.29), residues: 265 loop : -1.09 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 44 HIS 0.008 0.002 HIS L 72 PHE 0.013 0.002 PHE D 107 TYR 0.024 0.002 TYR R 70 ARG 0.007 0.001 ARG O 58 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 279 time to evaluate : 2.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 71 GLN cc_start: 0.9363 (tt0) cc_final: 0.9094 (tt0) REVERT: D 75 TYR cc_start: 0.9124 (m-80) cc_final: 0.8693 (m-80) REVERT: D 105 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.8831 (mtp) REVERT: D 124 MET cc_start: 0.9223 (ttm) cc_final: 0.9022 (tpp) REVERT: D 202 GLU cc_start: 0.8836 (pt0) cc_final: 0.8607 (pp20) REVERT: E 12 GLN cc_start: 0.8827 (mp10) cc_final: 0.8414 (mp10) REVERT: E 14 LYS cc_start: 0.9052 (mttm) cc_final: 0.8851 (mmtm) REVERT: E 103 THR cc_start: 0.9346 (m) cc_final: 0.8997 (p) REVERT: E 116 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8318 (tm-30) REVERT: F 17 GLN cc_start: 0.9395 (OUTLIER) cc_final: 0.9165 (tp-100) REVERT: F 35 LYS cc_start: 0.9405 (mptt) cc_final: 0.9019 (mmtt) REVERT: H 9 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8302 (t70) REVERT: H 58 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7802 (mm-30) REVERT: H 88 ARG cc_start: 0.8614 (mtp-110) cc_final: 0.8074 (mtp85) REVERT: H 96 MET cc_start: 0.9097 (mtp) cc_final: 0.8386 (ttm) REVERT: H 121 LEU cc_start: 0.9383 (tp) cc_final: 0.9009 (tp) REVERT: K 75 LYS cc_start: 0.9029 (pptt) cc_final: 0.8508 (mmtt) REVERT: O 80 GLN cc_start: 0.9119 (tp-100) cc_final: 0.8862 (tp-100) REVERT: P 47 GLU cc_start: 0.8138 (tt0) cc_final: 0.7481 (mt-10) REVERT: P 53 ASP cc_start: 0.8819 (t0) cc_final: 0.8618 (t0) REVERT: P 76 LYS cc_start: 0.9496 (ttmm) cc_final: 0.9273 (tptt) REVERT: Q 60 GLU cc_start: 0.8015 (tp30) cc_final: 0.7788 (tp30) REVERT: Q 81 LYS cc_start: 0.8521 (tppt) cc_final: 0.8121 (tppt) REVERT: R 32 TYR cc_start: 0.8826 (m-80) cc_final: 0.8538 (m-80) REVERT: T 24 ARG cc_start: 0.9175 (tpp-160) cc_final: 0.8939 (mmm-85) REVERT: T 59 ASP cc_start: 0.8680 (m-30) cc_final: 0.8434 (m-30) REVERT: X 37 ARG cc_start: 0.9130 (ttp80) cc_final: 0.8915 (ttp-170) REVERT: X 110 ARG cc_start: 0.3594 (OUTLIER) cc_final: 0.3317 (ptp90) REVERT: X 124 MET cc_start: 0.9051 (tmm) cc_final: 0.8729 (tmm) outliers start: 71 outliers final: 46 residues processed: 317 average time/residue: 0.5516 time to fit residues: 265.9980 Evaluate side-chains 302 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 252 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 70 CYS Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain X residue 41 ASP Chi-restraints excluded: chain X residue 44 ASP Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 74 LEU Chi-restraints excluded: chain X residue 89 GLU Chi-restraints excluded: chain X residue 91 TYR Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 110 ARG Chi-restraints excluded: chain X residue 114 GLN Chi-restraints excluded: chain X residue 146 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 214 optimal weight: 0.9990 chunk 163 optimal weight: 30.0000 chunk 112 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 146 optimal weight: 0.0670 chunk 218 optimal weight: 6.9990 chunk 231 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 206 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 overall best weight: 2.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 GLN ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 9 GLN ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 109 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36656 Z= 0.171 Angle : 0.553 12.119 54809 Z= 0.289 Chirality : 0.032 0.294 6991 Planarity : 0.005 0.116 2987 Dihedral : 24.163 179.617 18191 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 21.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 5.51 % Allowed : 25.96 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.22), residues: 1360 helix: 0.19 (0.23), residues: 500 sheet: -1.29 (0.30), residues: 257 loop : -0.87 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP X 113 HIS 0.008 0.001 HIS X 56 PHE 0.010 0.001 PHE X 28 TYR 0.027 0.002 TYR F 59 ARG 0.008 0.001 ARG Q 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 289 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 54 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8811 (mp10) REVERT: D 64 ILE cc_start: 0.9469 (tp) cc_final: 0.9166 (mt) REVERT: D 105 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8624 (mtp) REVERT: D 124 MET cc_start: 0.9107 (ttm) cc_final: 0.8905 (tpp) REVERT: D 132 ILE cc_start: 0.9269 (mm) cc_final: 0.9022 (mp) REVERT: D 206 LYS cc_start: 0.9119 (ttpp) cc_final: 0.8516 (ttmm) REVERT: E 66 LYS cc_start: 0.9722 (mtpp) cc_final: 0.9428 (mtpp) REVERT: E 71 MET cc_start: 0.8997 (mmm) cc_final: 0.8743 (tpp) REVERT: E 103 THR cc_start: 0.9451 (m) cc_final: 0.9142 (p) REVERT: F 1 MET cc_start: 0.8967 (ptp) cc_final: 0.8578 (ttt) REVERT: F 9 MET cc_start: 0.8822 (tpp) cc_final: 0.8597 (tpp) REVERT: F 35 LYS cc_start: 0.9380 (mptt) cc_final: 0.8987 (mmtm) REVERT: H 3 MET cc_start: 0.8973 (tmm) cc_final: 0.8427 (tmm) REVERT: H 58 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7910 (mm-30) REVERT: H 75 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8543 (pp) REVERT: H 80 ARG cc_start: 0.9247 (mtm110) cc_final: 0.8779 (mtp-110) REVERT: H 121 LEU cc_start: 0.9368 (tp) cc_final: 0.9001 (tp) REVERT: K 75 LYS cc_start: 0.9041 (pptt) cc_final: 0.8526 (mmtt) REVERT: K 85 MET cc_start: 0.8966 (mtm) cc_final: 0.8639 (pmm) REVERT: K 98 ARG cc_start: 0.9027 (tmm-80) cc_final: 0.8785 (ptt90) REVERT: O 58 ARG cc_start: 0.7820 (ttp80) cc_final: 0.7596 (ttp80) REVERT: O 59 MET cc_start: 0.8969 (mtm) cc_final: 0.8736 (mtm) REVERT: O 73 LYS cc_start: 0.9378 (tptp) cc_final: 0.9087 (tppt) REVERT: O 80 GLN cc_start: 0.9062 (tp-100) cc_final: 0.8826 (tp-100) REVERT: P 47 GLU cc_start: 0.7871 (tt0) cc_final: 0.7394 (mt-10) REVERT: P 76 LYS cc_start: 0.9499 (ttmm) cc_final: 0.9289 (tptt) REVERT: Q 11 ARG cc_start: 0.8914 (ttp80) cc_final: 0.8332 (ttp80) REVERT: Q 17 MET cc_start: 0.7843 (mtm) cc_final: 0.7572 (mtm) REVERT: Q 60 GLU cc_start: 0.8065 (tp30) cc_final: 0.7831 (tp30) REVERT: R 32 TYR cc_start: 0.8700 (m-80) cc_final: 0.8491 (m-80) REVERT: T 24 ARG cc_start: 0.9132 (tpp-160) cc_final: 0.8895 (mmm-85) REVERT: X 56 HIS cc_start: 0.8977 (OUTLIER) cc_final: 0.8363 (p-80) REVERT: X 118 LYS cc_start: 0.9199 (mmmt) cc_final: 0.8836 (mmtt) outliers start: 63 outliers final: 41 residues processed: 327 average time/residue: 0.5410 time to fit residues: 269.3328 Evaluate side-chains 305 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 260 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 70 CYS Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 59 HIS Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 56 HIS Chi-restraints excluded: chain X residue 89 GLU Chi-restraints excluded: chain X residue 91 TYR Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 110 ARG Chi-restraints excluded: chain X residue 114 GLN Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 132 LYS Chi-restraints excluded: chain X residue 145 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 192 optimal weight: 0.6980 chunk 131 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 197 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 36656 Z= 0.315 Angle : 0.628 12.290 54809 Z= 0.327 Chirality : 0.035 0.272 6991 Planarity : 0.005 0.117 2987 Dihedral : 24.236 179.446 18191 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 28.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 6.21 % Allowed : 25.35 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.22), residues: 1360 helix: 0.08 (0.23), residues: 483 sheet: -1.23 (0.30), residues: 259 loop : -0.85 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP F 42 HIS 0.007 0.001 HIS L 72 PHE 0.023 0.002 PHE H 66 TYR 0.029 0.002 TYR F 59 ARG 0.006 0.001 ARG X 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 264 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 54 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8865 (mp10) REVERT: D 64 ILE cc_start: 0.9496 (tp) cc_final: 0.9171 (mt) REVERT: D 105 MET cc_start: 0.9245 (mtp) cc_final: 0.8735 (mtp) REVERT: D 124 MET cc_start: 0.9148 (ttm) cc_final: 0.8879 (tpp) REVERT: D 132 ILE cc_start: 0.9340 (mm) cc_final: 0.9102 (mt) REVERT: E 66 LYS cc_start: 0.9744 (mtpp) cc_final: 0.9470 (mtpp) REVERT: E 86 LYS cc_start: 0.9334 (ttmm) cc_final: 0.9032 (mmmt) REVERT: E 103 THR cc_start: 0.9364 (m) cc_final: 0.9023 (p) REVERT: F 35 LYS cc_start: 0.9411 (mptt) cc_final: 0.8997 (mmtt) REVERT: H 3 MET cc_start: 0.8901 (tmm) cc_final: 0.8474 (tmm) REVERT: H 75 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8563 (pp) REVERT: H 96 MET cc_start: 0.9144 (mtp) cc_final: 0.8393 (ttm) REVERT: H 121 LEU cc_start: 0.9368 (tp) cc_final: 0.9114 (tp) REVERT: K 75 LYS cc_start: 0.9018 (pptt) cc_final: 0.8497 (mmtt) REVERT: K 98 ARG cc_start: 0.8991 (tmm-80) cc_final: 0.8755 (ttp80) REVERT: L 20 ASN cc_start: 0.9302 (p0) cc_final: 0.9046 (p0) REVERT: O 59 MET cc_start: 0.9044 (mtm) cc_final: 0.8813 (mtm) REVERT: O 73 LYS cc_start: 0.9389 (OUTLIER) cc_final: 0.9149 (tppt) REVERT: O 80 GLN cc_start: 0.9144 (tp-100) cc_final: 0.8907 (tp-100) REVERT: P 47 GLU cc_start: 0.8103 (tt0) cc_final: 0.7613 (mt-10) REVERT: P 76 LYS cc_start: 0.9498 (ttmm) cc_final: 0.9286 (tptt) REVERT: Q 60 GLU cc_start: 0.8097 (tp30) cc_final: 0.7862 (tp30) REVERT: Q 81 LYS cc_start: 0.8317 (tppt) cc_final: 0.7930 (tppt) REVERT: R 38 LYS cc_start: 0.9138 (mmmt) cc_final: 0.8605 (mmmt) REVERT: X 56 HIS cc_start: 0.9056 (OUTLIER) cc_final: 0.8441 (p-80) REVERT: X 103 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7595 (pp) REVERT: X 118 LYS cc_start: 0.9228 (mmmt) cc_final: 0.8856 (mmtt) outliers start: 71 outliers final: 56 residues processed: 307 average time/residue: 0.5235 time to fit residues: 246.0576 Evaluate side-chains 310 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 249 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 24 HIS Chi-restraints excluded: chain K residue 70 CYS Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 73 LYS Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 59 HIS Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 41 ASP Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 56 HIS Chi-restraints excluded: chain X residue 89 GLU Chi-restraints excluded: chain X residue 91 TYR Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 103 LEU Chi-restraints excluded: chain X residue 105 MET Chi-restraints excluded: chain X residue 109 ASN Chi-restraints excluded: chain X residue 110 ARG Chi-restraints excluded: chain X residue 114 GLN Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 145 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/iotbx/cli_parser.py", line 939, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.2822 > 50: distance: 70 - 76: 14.687 distance: 76 - 77: 24.672 distance: 77 - 78: 28.057 distance: 77 - 80: 21.517 distance: 78 - 79: 28.137 distance: 78 - 85: 26.689 distance: 80 - 81: 14.699 distance: 81 - 82: 50.293 distance: 82 - 83: 41.371 distance: 83 - 84: 4.038 distance: 85 - 86: 14.393 distance: 86 - 87: 9.315 distance: 86 - 89: 12.570 distance: 87 - 88: 12.774 distance: 87 - 94: 21.948 distance: 89 - 90: 29.111 distance: 90 - 91: 11.157 distance: 91 - 92: 5.312 distance: 91 - 93: 29.291 distance: 94 - 95: 34.265 distance: 95 - 96: 7.730 distance: 95 - 98: 39.093 distance: 96 - 97: 5.254 distance: 96 - 100: 4.212 distance: 97 - 127: 19.602 distance: 98 - 99: 9.763 distance: 100 - 101: 4.828 distance: 101 - 102: 4.524 distance: 101 - 104: 3.893 distance: 102 - 111: 13.267 distance: 103 - 132: 20.137 distance: 104 - 105: 8.907 distance: 105 - 106: 4.392 distance: 106 - 107: 26.818 distance: 107 - 108: 12.944 distance: 108 - 109: 8.717 distance: 108 - 110: 11.521 distance: 111 - 112: 42.532 distance: 112 - 113: 22.392 distance: 112 - 115: 17.742 distance: 113 - 114: 21.945 distance: 113 - 118: 24.739 distance: 114 - 137: 17.393 distance: 115 - 116: 40.369 distance: 115 - 117: 18.345 distance: 118 - 119: 11.399 distance: 119 - 120: 14.008 distance: 119 - 122: 12.660 distance: 120 - 121: 18.224 distance: 120 - 127: 9.436 distance: 121 - 145: 23.618 distance: 122 - 123: 11.260 distance: 123 - 124: 18.281 distance: 124 - 125: 12.080 distance: 125 - 126: 17.301 distance: 127 - 128: 14.392 distance: 128 - 129: 6.113 distance: 128 - 131: 35.281 distance: 129 - 130: 5.453 distance: 129 - 132: 28.108 distance: 130 - 154: 28.661 distance: 132 - 133: 23.190 distance: 133 - 134: 14.000 distance: 133 - 136: 24.576 distance: 134 - 137: 19.308 distance: 135 - 162: 31.350 distance: 137 - 138: 9.280 distance: 138 - 139: 14.650 distance: 138 - 141: 17.358 distance: 139 - 140: 13.624 distance: 139 - 145: 12.880 distance: 140 - 166: 31.499 distance: 141 - 142: 15.438 distance: 142 - 143: 16.365 distance: 142 - 144: 26.915 distance: 145 - 146: 18.929 distance: 146 - 147: 17.620 distance: 146 - 149: 5.429 distance: 147 - 148: 12.561 distance: 147 - 154: 23.684 distance: 149 - 150: 15.250 distance: 151 - 153: 10.300