Starting phenix.real_space_refine on Mon Mar 18 19:32:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwd_30232/03_2024/7bwd_30232_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwd_30232/03_2024/7bwd_30232.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwd_30232/03_2024/7bwd_30232.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwd_30232/03_2024/7bwd_30232.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwd_30232/03_2024/7bwd_30232_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwd_30232/03_2024/7bwd_30232_updated.pdb" } resolution = 4.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5986 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 29 5.16 5 C 9189 2.51 5 N 2962 2.21 5 O 3570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K GLU 16": "OE1" <-> "OE2" Residue "K ASP 28": "OD1" <-> "OD2" Residue "K ASP 32": "OD1" <-> "OD2" Residue "K GLU 39": "OE1" <-> "OE2" Residue "K ASP 50": "OD1" <-> "OD2" Residue "K GLU 69": "OE1" <-> "OE2" Residue "K TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 134": "OE1" <-> "OE2" Residue "K TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 138": "OE1" <-> "OE2" Residue "K ASP 142": "OD1" <-> "OD2" Residue "K ASP 155": "OD1" <-> "OD2" Residue "K ASP 161": "OD1" <-> "OD2" Residue "K ASP 189": "OD1" <-> "OD2" Residue "K GLU 201": "OE1" <-> "OE2" Residue "K GLU 248": "OE1" <-> "OE2" Residue "K ASP 250": "OD1" <-> "OD2" Residue "K GLU 255": "OE1" <-> "OE2" Residue "K ARG 278": "NH1" <-> "NH2" Residue "K ASP 286": "OD1" <-> "OD2" Residue "K TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 323": "OE1" <-> "OE2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "H ARG 33": "NH1" <-> "NH2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "E ARG 40": "NH1" <-> "NH2" Residue "E TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A ASP 106": "OD1" <-> "OD2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "C ARG 11": "NH1" <-> "NH2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "L GLU 18": "OE1" <-> "OE2" Residue "M GLU 18": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16042 Number of models: 1 Model: "" Number of chains: 14 Chain: "K" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2671 Classifications: {'peptide': 328} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 309} Chain: "F" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 844 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "A" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "C" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 866 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "B" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 673 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "L" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 594 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 594 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N LEU L 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU L 73 " occ=0.45 residue: pdb=" N ARG L 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG L 74 " occ=0.45 residue: pdb=" N GLY L 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY L 75 " occ=0.25 residue: pdb=" N LEU M 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU M 73 " occ=0.45 residue: pdb=" N ARG M 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG M 74 " occ=0.45 residue: pdb=" N GLY M 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY M 75 " occ=0.25 Time building chain proxies: 8.82, per 1000 atoms: 0.55 Number of scatterers: 16042 At special positions: 0 Unit cell: (114.48, 143.64, 136.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 P 292 15.00 O 3570 8.00 N 2962 7.00 C 9189 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=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.63 Conformation dependent library (CDL) restraints added in 1.8 seconds 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2358 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 3 sheets defined 43.4% alpha, 3.3% beta 76 base pairs and 184 stacking pairs defined. Time for finding SS restraints: 7.79 Creating SS restraints... Processing helix chain 'K' and resid 38 through 47 removed outlier: 4.176A pdb=" N ARG K 42 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TRP K 43 " --> pdb=" O GLU K 39 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL K 44 " --> pdb=" O THR K 40 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU K 46 " --> pdb=" O ARG K 42 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU K 47 " --> pdb=" O TRP K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 55 removed outlier: 3.665A pdb=" N LYS K 52 " --> pdb=" O PRO K 49 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET K 55 " --> pdb=" O LYS K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 89 removed outlier: 4.367A pdb=" N ARG K 73 " --> pdb=" O GLU K 69 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU K 74 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS K 77 " --> pdb=" O ARG K 73 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ASP K 83 " --> pdb=" O ASN K 79 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER K 84 " --> pdb=" O ARG K 80 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN K 87 " --> pdb=" O ASP K 83 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU K 88 " --> pdb=" O SER K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 113 removed outlier: 3.650A pdb=" N LEU K 111 " --> pdb=" O LEU K 107 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLN K 113 " --> pdb=" O HIS K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 125 No H-bonds generated for 'chain 'K' and resid 122 through 125' Processing helix chain 'K' and resid 170 through 176 removed outlier: 4.179A pdb=" N ALA K 175 " --> pdb=" O LEU K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 189 through 200 removed outlier: 3.621A pdb=" N TYR K 194 " --> pdb=" O ILE K 190 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA K 195 " --> pdb=" O PRO K 191 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N MET K 198 " --> pdb=" O TYR K 194 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 209 removed outlier: 3.576A pdb=" N MET K 206 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LYS K 207 " --> pdb=" O ARG K 203 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TRP K 208 " --> pdb=" O LYS K 204 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR K 209 " --> pdb=" O TRP K 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 202 through 209' Processing helix chain 'K' and resid 229 through 233 Processing helix chain 'K' and resid 247 through 254 removed outlier: 4.161A pdb=" N HIS K 251 " --> pdb=" O PRO K 247 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLN K 252 " --> pdb=" O GLU K 248 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 259 No H-bonds generated for 'chain 'K' and resid 257 through 259' Processing helix chain 'K' and resid 320 through 323 No H-bonds generated for 'chain 'K' and resid 320 through 323' Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 41 removed outlier: 3.538A pdb=" N ARG F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG F 39 " --> pdb=" O ARG F 35 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARG F 40 " --> pdb=" O ARG F 36 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 64 removed outlier: 3.755A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 75 removed outlier: 4.424A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 90 No H-bonds generated for 'chain 'F' and resid 87 through 90' Processing helix chain 'G' and resid 17 through 21 removed outlier: 3.693A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 17 through 21' Processing helix chain 'G' and resid 27 through 36 removed outlier: 4.009A pdb=" N ARG G 35 " --> pdb=" O HIS G 31 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS G 36 " --> pdb=" O ARG G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 71 removed outlier: 3.607A pdb=" N GLU G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU G 63 " --> pdb=" O THR G 59 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 87 removed outlier: 3.974A pdb=" N ALA G 86 " --> pdb=" O HIS G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 96 removed outlier: 3.706A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 91 through 96' Processing helix chain 'H' and resid 38 through 47 removed outlier: 3.812A pdb=" N TYR H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS H 43 " --> pdb=" O VAL H 39 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS H 46 " --> pdb=" O TYR H 42 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 78 removed outlier: 3.600A pdb=" N VAL H 66 " --> pdb=" O MET H 62 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN H 67 " --> pdb=" O ASN H 63 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASP H 68 " --> pdb=" O SER H 64 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLU H 71 " --> pdb=" O ASN H 67 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA H 74 " --> pdb=" O PHE H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 84 No H-bonds generated for 'chain 'H' and resid 81 through 84' Processing helix chain 'H' and resid 93 through 101 removed outlier: 3.698A pdb=" N ARG H 99 " --> pdb=" O GLN H 95 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU H 100 " --> pdb=" O THR H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 122 removed outlier: 3.856A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 54 removed outlier: 4.000A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 75 removed outlier: 3.508A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG E 72 " --> pdb=" O GLN E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 92 Processing helix chain 'E' and resid 94 through 96 No H-bonds generated for 'chain 'E' and resid 94 through 96' Processing helix chain 'E' and resid 101 through 113 removed outlier: 3.685A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA E 111 " --> pdb=" O THR E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 removed outlier: 3.637A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 removed outlier: 4.012A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 74 removed outlier: 3.644A pdb=" N GLU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 114 removed outlier: 3.602A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN A 93 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU A 94 " --> pdb=" O MET A 90 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN A 108 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 129 removed outlier: 3.830A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 47 removed outlier: 3.812A pdb=" N TYR D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS D 43 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS D 46 " --> pdb=" O TYR D 42 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 78 removed outlier: 3.601A pdb=" N VAL D 66 " --> pdb=" O MET D 62 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASP D 68 " --> pdb=" O SER D 64 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLU D 71 " --> pdb=" O ASN D 67 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA D 74 " --> pdb=" O PHE D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 84 No H-bonds generated for 'chain 'D' and resid 81 through 84' Processing helix chain 'D' and resid 93 through 101 removed outlier: 3.699A pdb=" N ARG D 99 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 122 removed outlier: 3.856A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 37 removed outlier: 4.237A pdb=" N ARG C 35 " --> pdb=" O HIS C 31 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLY C 37 " --> pdb=" O LEU C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 71 removed outlier: 3.658A pdb=" N ALA C 53 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 41 removed outlier: 3.585A pdb=" N ARG B 35 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 75 removed outlier: 4.599A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 90 removed outlier: 4.578A pdb=" N ALA B 89 " --> pdb=" O ASP B 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 34 Processing helix chain 'L' and resid 57 through 59 No H-bonds generated for 'chain 'L' and resid 57 through 59' Processing helix chain 'M' and resid 23 through 34 Processing helix chain 'M' and resid 57 through 59 No H-bonds generated for 'chain 'M' and resid 57 through 59' Processing sheet with id= A, first strand: chain 'K' and resid 237 through 239 removed outlier: 6.318A pdb=" N ARG K 265 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'L' and resid 12 through 16 removed outlier: 6.314A pdb=" N SER L 65 " --> pdb=" O PHE L 4 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LYS L 6 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU L 67 " --> pdb=" O LYS L 6 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'M' and resid 12 through 16 removed outlier: 6.314A pdb=" N SER M 65 " --> pdb=" O PHE M 4 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LYS M 6 " --> pdb=" O SER M 65 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU M 67 " --> pdb=" O LYS M 6 " (cutoff:3.500A) 229 hydrogen bonds defined for protein. 678 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 184 hydrogen bonds 356 hydrogen bond angles 0 basepair planarities 76 basepair parallelities 184 stacking parallelities Total time for adding SS restraints: 4.54 Time building geometry restraints manager: 9.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3060 1.33 - 1.45: 5184 1.45 - 1.57: 8057 1.57 - 1.69: 583 1.69 - 1.81: 51 Bond restraints: 16935 Sorted by residual: bond pdb=" C8 SAH K 501 " pdb=" N7 SAH K 501 " ideal model delta sigma weight residual 1.299 1.374 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" CA TYR K 136 " pdb=" CB TYR K 136 " ideal model delta sigma weight residual 1.526 1.582 -0.056 1.53e-02 4.27e+03 1.33e+01 bond pdb=" C2 SAH K 501 " pdb=" N3 SAH K 501 " ideal model delta sigma weight residual 1.322 1.374 -0.052 2.00e-02 2.50e+03 6.76e+00 bond pdb=" C6 SAH K 501 " pdb=" N1 SAH K 501 " ideal model delta sigma weight residual 1.338 1.383 -0.045 2.00e-02 2.50e+03 5.15e+00 bond pdb=" C3' DC J 75 " pdb=" O3' DC J 75 " ideal model delta sigma weight residual 1.422 1.486 -0.064 3.00e-02 1.11e+03 4.56e+00 ... (remaining 16930 not shown) Histogram of bond angle deviations from ideal: 90.01 - 98.99: 13 98.99 - 107.96: 2999 107.96 - 116.94: 10303 116.94 - 125.91: 9783 125.91 - 134.89: 1031 Bond angle restraints: 24129 Sorted by residual: angle pdb=" C THR F 30 " pdb=" N LYS F 31 " pdb=" CA LYS F 31 " ideal model delta sigma weight residual 120.09 126.73 -6.64 1.25e+00 6.40e-01 2.82e+01 angle pdb=" C THR B 30 " pdb=" N LYS B 31 " pdb=" CA LYS B 31 " ideal model delta sigma weight residual 120.09 125.62 -5.53 1.25e+00 6.40e-01 1.96e+01 angle pdb=" C PRO K 274 " pdb=" N LEU K 275 " pdb=" CA LEU K 275 " ideal model delta sigma weight residual 121.54 129.45 -7.91 1.91e+00 2.74e-01 1.72e+01 angle pdb=" CG SAH K 501 " pdb=" SD SAH K 501 " pdb=" C5' SAH K 501 " ideal model delta sigma weight residual 101.77 90.01 11.76 3.00e+00 1.11e-01 1.54e+01 angle pdb=" C LEU F 22 " pdb=" N ARG F 23 " pdb=" CA ARG F 23 " ideal model delta sigma weight residual 120.38 126.10 -5.72 1.46e+00 4.69e-01 1.53e+01 ... (remaining 24124 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 8016 35.64 - 71.28: 1400 71.28 - 106.92: 41 106.92 - 142.57: 0 142.57 - 178.21: 6 Dihedral angle restraints: 9463 sinusoidal: 5813 harmonic: 3650 Sorted by residual: dihedral pdb=" CA LYS C 13 " pdb=" C LYS C 13 " pdb=" N ALA C 14 " pdb=" CA ALA C 14 " ideal model delta harmonic sigma weight residual 180.00 146.55 33.45 0 5.00e+00 4.00e-02 4.48e+01 dihedral pdb=" CA GLN E 85 " pdb=" C GLN E 85 " pdb=" N SER E 86 " pdb=" CA SER E 86 " ideal model delta harmonic sigma weight residual -180.00 -153.85 -26.15 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA VAL L 17 " pdb=" C VAL L 17 " pdb=" N GLU L 18 " pdb=" CA GLU L 18 " ideal model delta harmonic sigma weight residual 180.00 156.08 23.92 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 9460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 2633 0.117 - 0.233: 92 0.233 - 0.350: 2 0.350 - 0.466: 1 0.466 - 0.583: 1 Chirality restraints: 2729 Sorted by residual: chirality pdb=" C3' SAH K 501 " pdb=" C2' SAH K 501 " pdb=" C4' SAH K 501 " pdb=" O3' SAH K 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.12 -0.58 2.00e-01 2.50e+01 8.49e+00 chirality pdb=" CB VAL K 169 " pdb=" CA VAL K 169 " pdb=" CG1 VAL K 169 " pdb=" CG2 VAL K 169 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" CB ILE K 190 " pdb=" CA ILE K 190 " pdb=" CG1 ILE K 190 " pdb=" CG2 ILE K 190 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 2726 not shown) Planarity restraints: 2052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE K 223 " -0.022 2.00e-02 2.50e+03 2.11e-02 7.79e+00 pdb=" CG PHE K 223 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE K 223 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE K 223 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE K 223 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE K 223 " -0.021 2.00e-02 2.50e+03 pdb=" CZ PHE K 223 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA K 273 " 0.044 5.00e-02 4.00e+02 6.61e-02 6.98e+00 pdb=" N PRO K 274 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO K 274 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO K 274 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 65 " -0.038 5.00e-02 4.00e+02 5.73e-02 5.26e+00 pdb=" N PRO A 66 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " -0.033 5.00e-02 4.00e+02 ... (remaining 2049 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 6 2.06 - 2.77: 3220 2.77 - 3.48: 20982 3.48 - 4.19: 41559 4.19 - 4.90: 61044 Nonbonded interactions: 126811 Sorted by model distance: nonbonded pdb=" OP2 DC J 126 " pdb=" CB ARG L 72 " model vdw 1.348 3.440 nonbonded pdb=" C4' DG J 125 " pdb=" NH2 ARG L 72 " model vdw 1.674 3.550 nonbonded pdb=" N ARG D 31 " pdb=" N CYS M 76 " model vdw 1.735 3.200 nonbonded pdb=" O4' DG J 125 " pdb=" NH2 ARG L 72 " model vdw 1.914 2.520 nonbonded pdb=" N ARG D 31 " pdb=" C CYS M 76 " model vdw 1.963 3.350 ... (remaining 126806 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 37 through 133) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 19 through 102) } ncs_group { reference = (chain 'C' and resid 11 through 119) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'L' selection = chain 'M' } 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=0.25 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.010 Extract box with map and model: 2.570 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 50.390 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 0.079 16935 Z= 0.503 Angle : 0.927 13.611 24129 Z= 0.521 Chirality : 0.054 0.583 2729 Planarity : 0.007 0.066 2052 Dihedral : 26.469 178.206 7105 Min Nonbonded Distance : 1.348 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.98 % Allowed : 9.04 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -5.07 (0.17), residues: 1234 helix: -4.36 (0.10), residues: 555 sheet: -1.47 (0.83), residues: 45 loop : -2.50 (0.21), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 305 HIS 0.006 0.002 HIS K 86 PHE 0.042 0.003 PHE K 223 TYR 0.022 0.002 TYR K 128 ARG 0.006 0.001 ARG G 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 272 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 153 MET cc_start: 0.0123 (mpp) cc_final: -0.1388 (mtt) REVERT: F 29 ILE cc_start: 0.9049 (mm) cc_final: 0.8763 (mm) REVERT: F 50 ILE cc_start: 0.9271 (mm) cc_final: 0.8987 (mm) REVERT: G 15 LYS cc_start: 0.8178 (ttpt) cc_final: 0.7441 (mmtt) REVERT: G 84 GLN cc_start: 0.8994 (tp-100) cc_final: 0.8583 (tp40) REVERT: H 111 VAL cc_start: 0.9189 (OUTLIER) cc_final: 0.8890 (t) REVERT: E 68 GLN cc_start: 0.9028 (tt0) cc_final: 0.8128 (tm-30) REVERT: E 79 LYS cc_start: 0.8793 (tptt) cc_final: 0.8366 (tptp) REVERT: A 50 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8141 (mt-10) REVERT: A 73 GLU cc_start: 0.8388 (pp20) cc_final: 0.7928 (pp20) REVERT: D 120 LYS cc_start: 0.8157 (mtpp) cc_final: 0.7793 (mttp) REVERT: C 90 ASP cc_start: 0.8087 (m-30) cc_final: 0.7855 (m-30) REVERT: C 95 LYS cc_start: 0.8998 (mtpp) cc_final: 0.8706 (mttt) REVERT: B 35 ARG cc_start: 0.7818 (ttm-80) cc_final: 0.7494 (ttm-80) REVERT: B 44 LYS cc_start: 0.9460 (tttt) cc_final: 0.9203 (ttmm) REVERT: B 66 ILE cc_start: 0.9442 (mt) cc_final: 0.9180 (mm) REVERT: B 85 ASP cc_start: 0.8719 (m-30) cc_final: 0.8165 (m-30) REVERT: B 92 ARG cc_start: 0.8400 (ptm160) cc_final: 0.7845 (ttp80) REVERT: B 98 TYR cc_start: 0.9064 (m-10) cc_final: 0.8806 (m-80) outliers start: 32 outliers final: 6 residues processed: 291 average time/residue: 0.3536 time to fit residues: 139.6513 Evaluate side-chains 213 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 206 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 133 optimal weight: 30.0000 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 57 ASN K 113 GLN ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 252 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN H 63 ASN H 84 ASN H 95 GLN A 68 GLN A 76 GLN A 85 GLN D 84 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN C 112 GLN ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 ASN ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 60 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16935 Z= 0.216 Angle : 0.660 8.584 24129 Z= 0.384 Chirality : 0.041 0.276 2729 Planarity : 0.005 0.051 2052 Dihedral : 29.722 177.208 4582 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.09 % Allowed : 3.73 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.78 (0.19), residues: 1234 helix: -2.94 (0.16), residues: 556 sheet: -0.67 (0.66), residues: 65 loop : -2.22 (0.22), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 305 HIS 0.003 0.000 HIS K 181 PHE 0.021 0.002 PHE K 245 TYR 0.022 0.001 TYR H 40 ARG 0.009 0.000 ARG G 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 269 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 153 MET cc_start: 0.0245 (mpp) cc_final: -0.1035 (mtt) REVERT: F 29 ILE cc_start: 0.9015 (mm) cc_final: 0.8800 (mm) REVERT: F 50 ILE cc_start: 0.9377 (mm) cc_final: 0.9012 (mm) REVERT: G 11 ARG cc_start: 0.7275 (ttt-90) cc_final: 0.7066 (ttt-90) REVERT: G 25 PHE cc_start: 0.8743 (m-10) cc_final: 0.8369 (m-10) REVERT: G 84 GLN cc_start: 0.8903 (tp-100) cc_final: 0.8466 (tp40) REVERT: H 67 ASN cc_start: 0.8969 (m-40) cc_final: 0.8159 (t0) REVERT: E 79 LYS cc_start: 0.8725 (tptt) cc_final: 0.7852 (tppt) REVERT: E 84 PHE cc_start: 0.8781 (m-80) cc_final: 0.8395 (m-10) REVERT: E 108 ASN cc_start: 0.9063 (t0) cc_final: 0.8820 (t0) REVERT: E 126 LEU cc_start: 0.8977 (tp) cc_final: 0.7970 (mp) REVERT: A 73 GLU cc_start: 0.8535 (pp20) cc_final: 0.8281 (pp20) REVERT: D 118 VAL cc_start: 0.9327 (t) cc_final: 0.9034 (p) REVERT: B 66 ILE cc_start: 0.9395 (mt) cc_final: 0.9155 (mm) REVERT: B 73 THR cc_start: 0.9575 (p) cc_final: 0.9373 (t) REVERT: B 92 ARG cc_start: 0.8282 (ptm160) cc_final: 0.7937 (ttp80) REVERT: B 98 TYR cc_start: 0.9199 (m-10) cc_final: 0.8944 (m-80) outliers start: 1 outliers final: 1 residues processed: 270 average time/residue: 0.3106 time to fit residues: 118.1002 Evaluate side-chains 217 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 216 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 133 optimal weight: 50.0000 chunk 144 optimal weight: 50.0000 chunk 119 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN H 95 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS C 38 ASN C 112 GLN ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16935 Z= 0.245 Angle : 0.629 8.327 24129 Z= 0.362 Chirality : 0.040 0.264 2729 Planarity : 0.005 0.044 2052 Dihedral : 29.807 175.486 4582 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -2.92 (0.21), residues: 1234 helix: -2.06 (0.19), residues: 568 sheet: 0.13 (0.68), residues: 56 loop : -1.96 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 305 HIS 0.003 0.001 HIS A 39 PHE 0.033 0.002 PHE K 245 TYR 0.021 0.002 TYR H 40 ARG 0.004 0.000 ARG K 220 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 153 MET cc_start: 0.0001 (mpp) cc_final: -0.1183 (mtt) REVERT: F 29 ILE cc_start: 0.9093 (mm) cc_final: 0.8808 (mm) REVERT: F 50 ILE cc_start: 0.9337 (mm) cc_final: 0.9051 (mm) REVERT: F 52 GLU cc_start: 0.8220 (tp30) cc_final: 0.7874 (tp30) REVERT: G 25 PHE cc_start: 0.8705 (m-10) cc_final: 0.8439 (m-10) REVERT: G 84 GLN cc_start: 0.8894 (tp-100) cc_final: 0.8295 (tp-100) REVERT: G 104 GLN cc_start: 0.8838 (mp10) cc_final: 0.8324 (mp10) REVERT: H 67 ASN cc_start: 0.8930 (m-40) cc_final: 0.8268 (t0) REVERT: H 96 THR cc_start: 0.9609 (m) cc_final: 0.9238 (t) REVERT: D 118 VAL cc_start: 0.9336 (t) cc_final: 0.9055 (p) REVERT: C 74 LYS cc_start: 0.9222 (mmtt) cc_final: 0.8213 (tppt) REVERT: B 35 ARG cc_start: 0.7917 (ttm-80) cc_final: 0.7562 (mtp85) REVERT: B 92 ARG cc_start: 0.8369 (ptm160) cc_final: 0.7934 (ttp80) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.3197 time to fit residues: 112.6886 Evaluate side-chains 205 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 134 optimal weight: 20.0000 chunk 142 optimal weight: 50.0000 chunk 70 optimal weight: 4.9990 chunk 127 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 109 HIS K 172 GLN ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN H 95 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS D 84 ASN C 24 GLN C 38 ASN C 112 GLN L 31 GLN ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 16935 Z= 0.372 Angle : 0.719 9.571 24129 Z= 0.403 Chirality : 0.044 0.252 2729 Planarity : 0.005 0.042 2052 Dihedral : 29.818 177.112 4582 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.09 % Allowed : 5.78 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.57 (0.22), residues: 1234 helix: -1.67 (0.20), residues: 571 sheet: -0.18 (0.63), residues: 60 loop : -1.84 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 305 HIS 0.005 0.001 HIS A 39 PHE 0.025 0.002 PHE K 245 TYR 0.021 0.002 TYR E 54 ARG 0.007 0.001 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 227 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 153 MET cc_start: -0.0038 (mpp) cc_final: -0.1622 (mtt) REVERT: F 52 GLU cc_start: 0.8225 (tp30) cc_final: 0.7942 (tp30) REVERT: G 25 PHE cc_start: 0.8804 (m-10) cc_final: 0.8599 (m-10) REVERT: G 84 GLN cc_start: 0.8938 (tp-100) cc_final: 0.8379 (tp-100) REVERT: D 95 GLN cc_start: 0.9294 (tm-30) cc_final: 0.8773 (tm-30) REVERT: D 118 VAL cc_start: 0.9465 (t) cc_final: 0.9248 (p) REVERT: C 74 LYS cc_start: 0.9176 (mmtt) cc_final: 0.8262 (tppt) REVERT: B 68 ASP cc_start: 0.7682 (m-30) cc_final: 0.7360 (m-30) REVERT: B 85 ASP cc_start: 0.8722 (m-30) cc_final: 0.8516 (m-30) REVERT: B 92 ARG cc_start: 0.8721 (ptm160) cc_final: 0.8230 (ttp80) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.3070 time to fit residues: 98.9144 Evaluate side-chains 192 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 2 optimal weight: 50.0000 chunk 105 optimal weight: 10.0000 chunk 58 optimal weight: 0.5980 chunk 121 optimal weight: 10.0000 chunk 98 optimal weight: 0.8980 chunk 0 optimal weight: 50.0000 chunk 72 optimal weight: 0.8980 chunk 127 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN H 95 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16935 Z= 0.184 Angle : 0.587 9.362 24129 Z= 0.336 Chirality : 0.038 0.186 2729 Planarity : 0.004 0.041 2052 Dihedral : 29.608 177.127 4582 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.14 (0.23), residues: 1234 helix: -1.27 (0.21), residues: 575 sheet: -0.61 (0.58), residues: 79 loop : -1.59 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 89 HIS 0.003 0.001 HIS B 75 PHE 0.037 0.002 PHE K 223 TYR 0.011 0.001 TYR B 98 ARG 0.006 0.000 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 153 MET cc_start: 0.0052 (mpp) cc_final: -0.1538 (mtt) REVERT: K 260 MET cc_start: 0.2068 (mmp) cc_final: 0.1728 (mmp) REVERT: F 50 ILE cc_start: 0.9297 (mm) cc_final: 0.9091 (mm) REVERT: F 52 GLU cc_start: 0.8228 (tp30) cc_final: 0.7838 (tp30) REVERT: G 84 GLN cc_start: 0.8918 (tp-100) cc_final: 0.8363 (tp-100) REVERT: G 104 GLN cc_start: 0.8855 (mp10) cc_final: 0.8612 (mp10) REVERT: H 67 ASN cc_start: 0.9000 (m-40) cc_final: 0.8451 (t0) REVERT: H 80 LEU cc_start: 0.9380 (tp) cc_final: 0.9179 (tp) REVERT: H 96 THR cc_start: 0.9726 (m) cc_final: 0.9369 (t) REVERT: E 87 SER cc_start: 0.8710 (m) cc_final: 0.8029 (t) REVERT: E 108 ASN cc_start: 0.9196 (t0) cc_final: 0.8964 (t0) REVERT: E 129 ARG cc_start: 0.7593 (tpt170) cc_final: 0.7195 (tpt170) REVERT: A 123 ASP cc_start: 0.8858 (m-30) cc_final: 0.8616 (m-30) REVERT: D 118 VAL cc_start: 0.9354 (t) cc_final: 0.9088 (p) REVERT: C 74 LYS cc_start: 0.8970 (mmtt) cc_final: 0.8082 (tppt) REVERT: B 35 ARG cc_start: 0.7913 (ttm-80) cc_final: 0.7623 (mtp85) REVERT: B 92 ARG cc_start: 0.8442 (ptm160) cc_final: 0.7988 (ttp80) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.3077 time to fit residues: 111.3357 Evaluate side-chains 207 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 0.4980 chunk 127 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 11 optimal weight: 0.0040 chunk 74 optimal weight: 0.9990 chunk 137 optimal weight: 30.0000 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN D 49 HIS L 41 GLN ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16935 Z= 0.178 Angle : 0.565 9.005 24129 Z= 0.324 Chirality : 0.037 0.203 2729 Planarity : 0.004 0.040 2052 Dihedral : 29.447 176.154 4582 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.67 (0.23), residues: 1234 helix: -0.94 (0.22), residues: 572 sheet: -0.42 (0.60), residues: 74 loop : -1.28 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 89 HIS 0.004 0.001 HIS D 49 PHE 0.024 0.002 PHE K 223 TYR 0.024 0.001 TYR H 40 ARG 0.009 0.000 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.316 Fit side-chains revert: symmetry clash REVERT: K 153 MET cc_start: -0.0321 (mpp) cc_final: -0.1728 (mtt) REVERT: F 29 ILE cc_start: 0.9120 (mm) cc_final: 0.8882 (mm) REVERT: F 52 GLU cc_start: 0.8244 (tp30) cc_final: 0.7867 (tp30) REVERT: G 61 GLU cc_start: 0.8155 (tp30) cc_final: 0.7949 (tp30) REVERT: G 84 GLN cc_start: 0.8885 (tp-100) cc_final: 0.8405 (tp-100) REVERT: H 67 ASN cc_start: 0.8896 (m-40) cc_final: 0.8540 (t0) REVERT: H 96 THR cc_start: 0.9707 (m) cc_final: 0.9347 (t) REVERT: E 84 PHE cc_start: 0.8409 (m-80) cc_final: 0.8122 (m-10) REVERT: E 87 SER cc_start: 0.8729 (m) cc_final: 0.8287 (t) REVERT: E 93 GLN cc_start: 0.8466 (tm-30) cc_final: 0.8049 (tm-30) REVERT: E 97 GLU cc_start: 0.8269 (mp0) cc_final: 0.7983 (mm-30) REVERT: E 129 ARG cc_start: 0.7579 (tpt170) cc_final: 0.7368 (tpt170) REVERT: A 45 THR cc_start: 0.8932 (m) cc_final: 0.8631 (t) REVERT: A 50 GLU cc_start: 0.8526 (tp30) cc_final: 0.8183 (tp30) REVERT: D 118 VAL cc_start: 0.9329 (t) cc_final: 0.9055 (p) REVERT: C 74 LYS cc_start: 0.8957 (mmtt) cc_final: 0.8087 (tppt) REVERT: B 35 ARG cc_start: 0.7788 (ttm-80) cc_final: 0.7453 (mtp85) REVERT: B 63 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7697 (mt-10) REVERT: B 92 ARG cc_start: 0.8437 (ptm160) cc_final: 0.7959 (ttp80) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.2864 time to fit residues: 103.4006 Evaluate side-chains 212 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 30.0000 chunk 81 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 119 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 141 optimal weight: 20.0000 chunk 88 optimal weight: 0.8980 chunk 86 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 68 ASN G 84 GLN ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN H 63 ASN H 95 GLN D 84 ASN C 24 GLN ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16935 Z= 0.169 Angle : 0.556 9.233 24129 Z= 0.317 Chirality : 0.037 0.254 2729 Planarity : 0.004 0.043 2052 Dihedral : 29.364 176.010 4582 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.56 (0.24), residues: 1234 helix: -0.78 (0.22), residues: 576 sheet: -0.42 (0.60), residues: 79 loop : -1.30 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 89 HIS 0.003 0.000 HIS K 181 PHE 0.034 0.002 PHE K 245 TYR 0.027 0.001 TYR B 88 ARG 0.004 0.000 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.457 Fit side-chains revert: symmetry clash REVERT: K 153 MET cc_start: -0.0243 (mpp) cc_final: -0.1734 (mtt) REVERT: F 29 ILE cc_start: 0.9183 (mm) cc_final: 0.8886 (mm) REVERT: F 30 THR cc_start: 0.9022 (t) cc_final: 0.8680 (m) REVERT: F 52 GLU cc_start: 0.8249 (tp30) cc_final: 0.7869 (tp30) REVERT: G 61 GLU cc_start: 0.8229 (tp30) cc_final: 0.7968 (tp30) REVERT: G 84 GLN cc_start: 0.8876 (tp40) cc_final: 0.8468 (tp-100) REVERT: H 67 ASN cc_start: 0.8816 (m-40) cc_final: 0.8559 (t0) REVERT: H 96 THR cc_start: 0.9711 (m) cc_final: 0.9304 (t) REVERT: E 87 SER cc_start: 0.8744 (m) cc_final: 0.8225 (t) REVERT: E 93 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8286 (tm-30) REVERT: E 97 GLU cc_start: 0.8383 (mp0) cc_final: 0.8116 (mm-30) REVERT: E 113 HIS cc_start: 0.8616 (t-90) cc_final: 0.8317 (t-90) REVERT: E 126 LEU cc_start: 0.9124 (tt) cc_final: 0.7532 (mp) REVERT: E 129 ARG cc_start: 0.7645 (tpt170) cc_final: 0.7321 (tpt170) REVERT: A 45 THR cc_start: 0.8983 (m) cc_final: 0.8772 (t) REVERT: D 118 VAL cc_start: 0.9307 (t) cc_final: 0.9024 (p) REVERT: C 74 LYS cc_start: 0.8906 (mmtt) cc_final: 0.8018 (tppt) REVERT: C 110 ASN cc_start: 0.8264 (t0) cc_final: 0.7873 (m-40) REVERT: B 35 ARG cc_start: 0.7704 (ttm-80) cc_final: 0.7449 (mtp85) REVERT: B 63 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7694 (mt-10) REVERT: B 84 MET cc_start: 0.8664 (tpp) cc_final: 0.8456 (tpp) REVERT: B 92 ARG cc_start: 0.8466 (ptm160) cc_final: 0.8042 (ttp80) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.2890 time to fit residues: 102.5432 Evaluate side-chains 208 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 135 optimal weight: 40.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN E 55 GLN D 49 HIS ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16935 Z= 0.302 Angle : 0.638 9.293 24129 Z= 0.359 Chirality : 0.041 0.273 2729 Planarity : 0.004 0.043 2052 Dihedral : 29.440 173.801 4582 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.56 (0.24), residues: 1234 helix: -0.73 (0.22), residues: 575 sheet: -0.27 (0.60), residues: 72 loop : -1.37 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 43 HIS 0.004 0.001 HIS A 39 PHE 0.021 0.002 PHE K 223 TYR 0.025 0.002 TYR B 88 ARG 0.007 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 1.316 Fit side-chains REVERT: K 153 MET cc_start: -0.0035 (mpp) cc_final: -0.1367 (mtt) REVERT: F 29 ILE cc_start: 0.9113 (mm) cc_final: 0.8849 (mm) REVERT: F 52 GLU cc_start: 0.8350 (tp30) cc_final: 0.8057 (tp30) REVERT: G 25 PHE cc_start: 0.8793 (m-10) cc_final: 0.8413 (m-10) REVERT: G 84 GLN cc_start: 0.8899 (tp40) cc_final: 0.8551 (tp-100) REVERT: G 100 VAL cc_start: 0.9085 (t) cc_final: 0.8807 (t) REVERT: H 96 THR cc_start: 0.9670 (m) cc_final: 0.9342 (t) REVERT: E 54 TYR cc_start: 0.8729 (m-80) cc_final: 0.8487 (m-80) REVERT: E 87 SER cc_start: 0.8838 (m) cc_final: 0.8154 (t) REVERT: E 113 HIS cc_start: 0.8732 (t-90) cc_final: 0.8527 (t-90) REVERT: E 129 ARG cc_start: 0.7640 (tpt170) cc_final: 0.7336 (tpt170) REVERT: A 45 THR cc_start: 0.8995 (m) cc_final: 0.8770 (t) REVERT: D 111 VAL cc_start: 0.9553 (m) cc_final: 0.9196 (p) REVERT: D 118 VAL cc_start: 0.9441 (t) cc_final: 0.9187 (p) REVERT: C 74 LYS cc_start: 0.8997 (mmtt) cc_final: 0.8175 (tppt) REVERT: B 84 MET cc_start: 0.8631 (tpp) cc_final: 0.8410 (tpp) REVERT: B 92 ARG cc_start: 0.8710 (ptm160) cc_final: 0.8283 (ttp80) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.2805 time to fit residues: 95.2497 Evaluate side-chains 201 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 135 optimal weight: 40.0000 chunk 79 optimal weight: 0.7980 chunk 57 optimal weight: 0.0170 chunk 103 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 overall best weight: 3.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN H 63 ASN H 67 ASN H 95 GLN D 84 ASN ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16935 Z= 0.294 Angle : 0.639 9.243 24129 Z= 0.360 Chirality : 0.041 0.263 2729 Planarity : 0.004 0.044 2052 Dihedral : 29.439 174.418 4582 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.09 % Allowed : 0.65 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.50 (0.24), residues: 1234 helix: -0.65 (0.22), residues: 576 sheet: -0.26 (0.60), residues: 72 loop : -1.37 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 305 HIS 0.005 0.001 HIS A 39 PHE 0.017 0.002 PHE K 223 TYR 0.026 0.002 TYR A 54 ARG 0.007 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 233 time to evaluate : 1.336 Fit side-chains revert: symmetry clash REVERT: K 153 MET cc_start: 0.0001 (mpp) cc_final: -0.1377 (mtt) REVERT: F 29 ILE cc_start: 0.9186 (mm) cc_final: 0.8919 (mm) REVERT: F 52 GLU cc_start: 0.8372 (tp30) cc_final: 0.8065 (tp30) REVERT: G 84 GLN cc_start: 0.8928 (tp40) cc_final: 0.8636 (tp40) REVERT: G 112 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8560 (mm-40) REVERT: H 67 ASN cc_start: 0.9033 (OUTLIER) cc_final: 0.8827 (t0) REVERT: H 96 THR cc_start: 0.9671 (m) cc_final: 0.9325 (t) REVERT: E 50 GLU cc_start: 0.7996 (tp30) cc_final: 0.7749 (tp30) REVERT: E 54 TYR cc_start: 0.8750 (m-80) cc_final: 0.8474 (m-80) REVERT: E 87 SER cc_start: 0.8898 (m) cc_final: 0.8284 (t) REVERT: E 93 GLN cc_start: 0.8571 (tm-30) cc_final: 0.7867 (tm-30) REVERT: E 120 MET cc_start: 0.8399 (mtt) cc_final: 0.8149 (mtt) REVERT: E 129 ARG cc_start: 0.7736 (tpt170) cc_final: 0.7430 (tpt170) REVERT: A 45 THR cc_start: 0.9073 (m) cc_final: 0.8851 (t) REVERT: D 111 VAL cc_start: 0.9555 (m) cc_final: 0.9191 (p) REVERT: D 118 VAL cc_start: 0.9444 (t) cc_final: 0.9203 (p) REVERT: C 74 LYS cc_start: 0.8976 (mmtt) cc_final: 0.8129 (tppt) REVERT: B 92 ARG cc_start: 0.8755 (ptm160) cc_final: 0.8306 (ttp80) outliers start: 1 outliers final: 0 residues processed: 234 average time/residue: 0.2913 time to fit residues: 98.3484 Evaluate side-chains 198 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 197 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 50.0000 chunk 85 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 146 optimal weight: 20.0000 chunk 134 optimal weight: 30.0000 chunk 116 optimal weight: 10.0000 chunk 12 optimal weight: 0.0170 chunk 90 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 overall best weight: 1.0820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN H 95 GLN ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16935 Z= 0.174 Angle : 0.573 8.750 24129 Z= 0.325 Chirality : 0.037 0.220 2729 Planarity : 0.004 0.045 2052 Dihedral : 29.288 176.350 4582 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.20 (0.24), residues: 1234 helix: -0.38 (0.22), residues: 576 sheet: -0.10 (0.61), residues: 72 loop : -1.24 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 305 HIS 0.007 0.001 HIS E 113 PHE 0.018 0.002 PHE K 223 TYR 0.021 0.001 TYR E 54 ARG 0.008 0.000 ARG H 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.299 Fit side-chains revert: symmetry clash REVERT: K 153 MET cc_start: -0.0160 (mpp) cc_final: -0.1694 (mtt) REVERT: F 29 ILE cc_start: 0.9230 (mm) cc_final: 0.8872 (mm) REVERT: F 30 THR cc_start: 0.9042 (t) cc_final: 0.8630 (m) REVERT: F 52 GLU cc_start: 0.8334 (tp30) cc_final: 0.8041 (tp30) REVERT: G 25 PHE cc_start: 0.8752 (m-10) cc_final: 0.8497 (m-10) REVERT: G 84 GLN cc_start: 0.8891 (tp40) cc_final: 0.8524 (tp-100) REVERT: G 92 GLU cc_start: 0.7443 (tp30) cc_final: 0.7226 (tp30) REVERT: G 100 VAL cc_start: 0.8989 (t) cc_final: 0.8495 (t) REVERT: G 112 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8520 (mm-40) REVERT: E 50 GLU cc_start: 0.7875 (tp30) cc_final: 0.7576 (tp30) REVERT: E 54 TYR cc_start: 0.8697 (m-80) cc_final: 0.8382 (m-80) REVERT: E 87 SER cc_start: 0.8808 (m) cc_final: 0.8272 (t) REVERT: E 93 GLN cc_start: 0.8407 (tm-30) cc_final: 0.7672 (tm-30) REVERT: E 129 ARG cc_start: 0.7630 (tpt170) cc_final: 0.7358 (tpt170) REVERT: A 48 LEU cc_start: 0.9040 (mm) cc_final: 0.8816 (mm) REVERT: D 111 VAL cc_start: 0.9519 (m) cc_final: 0.9144 (p) REVERT: D 118 VAL cc_start: 0.9377 (t) cc_final: 0.9138 (p) REVERT: C 74 LYS cc_start: 0.8873 (mmtt) cc_final: 0.8050 (tppt) REVERT: B 35 ARG cc_start: 0.7841 (ttm-80) cc_final: 0.7579 (mtp85) REVERT: B 52 GLU cc_start: 0.7789 (pp20) cc_final: 0.7552 (pp20) REVERT: B 63 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7693 (mt-10) REVERT: B 92 ARG cc_start: 0.8512 (ptm160) cc_final: 0.7977 (ttp80) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.2967 time to fit residues: 101.3450 Evaluate side-chains 201 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 116 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 21 optimal weight: 40.0000 chunk 102 optimal weight: 0.9980 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN H 67 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.150934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.113081 restraints weight = 40840.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.110130 restraints weight = 46584.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.110588 restraints weight = 46835.627| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 16935 Z= 0.330 Angle : 0.655 9.203 24129 Z= 0.366 Chirality : 0.042 0.265 2729 Planarity : 0.004 0.044 2052 Dihedral : 29.361 174.354 4582 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.09 % Allowed : 0.75 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.24), residues: 1234 helix: -0.52 (0.22), residues: 577 sheet: -0.23 (0.61), residues: 72 loop : -1.33 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 205 HIS 0.004 0.001 HIS A 39 PHE 0.031 0.002 PHE K 245 TYR 0.025 0.002 TYR H 42 ARG 0.007 0.001 ARG H 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2770.32 seconds wall clock time: 50 minutes 53.02 seconds (3053.02 seconds total)