Starting phenix.real_space_refine on Sun Mar 24 09:36:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8y_4762/03_2024/6r8y_4762_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8y_4762/03_2024/6r8y_4762.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8y_4762/03_2024/6r8y_4762_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8y_4762/03_2024/6r8y_4762_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8y_4762/03_2024/6r8y_4762_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8y_4762/03_2024/6r8y_4762.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8y_4762/03_2024/6r8y_4762.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8y_4762/03_2024/6r8y_4762_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8y_4762/03_2024/6r8y_4762_trim_updated.pdb" } resolution = 4.3 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= 0.952 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 288 5.49 5 S 67 5.16 5 C 12810 2.51 5 N 3928 2.21 5 O 4624 1.98 5 H 19245 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 107": "OD1" <-> "OD2" Residue "A ASP 124": "OD1" <-> "OD2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "B ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 69": "OD1" <-> "OD2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B ASP 86": "OD1" <-> "OD2" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 73": "OD1" <-> "OD2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C GLU 122": "OE1" <-> "OE2" Residue "D ARG 30": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 36": "OE1" <-> "OE2" Residue "D TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 52": "OD1" <-> "OD2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D ARG 93": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 106": "OE1" <-> "OE2" Residue "E ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 107": "OD1" <-> "OD2" Residue "E ASP 124": "OD1" <-> "OD2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "F GLU 64": "OE1" <-> "OE2" Residue "F ASP 69": "OD1" <-> "OD2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 73": "OD1" <-> "OD2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "G GLU 122": "OE1" <-> "OE2" Residue "H ARG 30": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 36": "OE1" <-> "OE2" Residue "H TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 52": "OD1" <-> "OD2" Residue "H GLU 72": "OE1" <-> "OE2" Residue "H ARG 93": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 106": "OE1" <-> "OE2" Residue "K TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 54": "OE1" <-> "OE2" Residue "K TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 99": "OD1" <-> "OD2" Residue "K ASP 110": "OD1" <-> "OD2" Residue "K GLU 117": "OE1" <-> "OE2" Residue "K ASP 137": "OD1" <-> "OD2" Residue "K ASP 146": "OD1" <-> "OD2" Residue "K PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 166": "OD1" <-> "OD2" Residue "K TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 199": "OE1" <-> "OE2" Residue "K GLU 201": "OE1" <-> "OE2" Residue "K GLU 215": "OE1" <-> "OE2" Residue "K ASP 243": "OD1" <-> "OD2" Residue "K ASP 265": "OD1" <-> "OD2" Residue "K ASP 275": "OD1" <-> "OD2" Residue "K GLU 303": "OE1" <-> "OE2" Residue "K ASP 330": "OD1" <-> "OD2" Residue "K ASP 339": "OD1" <-> "OD2" Residue "K GLU 368": "OE1" <-> "OE2" Residue "K ASP 744": "OD1" <-> "OD2" Residue "K PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 779": "OE1" <-> "OE2" Residue "K PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 811": "OE1" <-> "OE2" Residue "K ASP 824": "OD1" <-> "OD2" Residue "K GLU 840": "OE1" <-> "OE2" Residue "K GLU 842": "OE1" <-> "OE2" Residue "K ASP 855": "OD1" <-> "OD2" Residue "K GLU 898": "OE1" <-> "OE2" Residue "K GLU 902": "OE1" <-> "OE2" Residue "K ASP 919": "OD1" <-> "OD2" Residue "K ASP 925": "OD1" <-> "OD2" Residue "K GLU 944": "OE1" <-> "OE2" Residue "K ASP 948": "OD1" <-> "OD2" Residue "K PHE 949": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 958": "OE1" <-> "OE2" Residue "K ASP 980": "OD1" <-> "OD2" Residue "K GLU 988": "OE1" <-> "OE2" Residue "K PHE 1030": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 1053": "OD1" <-> "OD2" Residue "K GLU 1079": "OE1" <-> "OE2" Residue "K ASP 1099": "OD1" <-> "OD2" Residue "K ASP 1115": "OD1" <-> "OD2" Residue "K ASP 1116": "OD1" <-> "OD2" Residue "L PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 255": "OD1" <-> "OD2" Residue "L PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 299": "OD1" <-> "OD2" Residue "L ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 376": "OD1" <-> "OD2" Residue "L GLU 390": "OE1" <-> "OE2" Residue "L TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 426": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40962 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1705 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "B" Number of atoms: 1434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1434 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "C" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1875 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "D" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1560 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1708 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "F" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1347 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1873 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "H" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1560 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "I" Number of atoms: 4612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 4612 Classifications: {'DNA': 145} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 4583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 4583 Unusual residues: {'T64': 1} Classifications: {'DNA': 143, 'undetermined': 1} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 141, None: 2} Not linked: pdbres=" DA J 94 " pdbres="T64 J 95 " Not linked: pdbres="T64 J 95 " pdbres=" DG J 97 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "K" Number of atoms: 12894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 825, 12894 Classifications: {'peptide': 825} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 797} Chain breaks: 1 Chain: "L" Number of atoms: 5811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 5811 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 349} Time building chain proxies: 17.76, per 1000 atoms: 0.43 Number of scatterers: 40962 At special positions: 0 Unit cell: (127.28, 180.6, 129, 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 67 16.00 P 288 15.00 O 4624 8.00 N 3928 7.00 C 12810 6.00 H 19245 1.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 37.45 Conformation dependent library (CDL) restraints added in 3.6 seconds 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3710 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 23 sheets defined 29.6% alpha, 21.4% beta 142 base pairs and 223 stacking pairs defined. Time for finding SS restraints: 21.25 Creating SS restraints... Processing helix chain 'A' and resid 46 through 57 Processing helix chain 'A' and resid 65 through 79 removed outlier: 3.606A pdb=" N PHE A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 115 Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'B' and resid 22 through 25 No H-bonds generated for 'chain 'B' and resid 22 through 25' Processing helix chain 'B' and resid 27 through 29 No H-bonds generated for 'chain 'B' and resid 27 through 29' Processing helix chain 'B' and resid 32 through 41 Processing helix chain 'B' and resid 51 through 77 removed outlier: 3.589A pdb=" N ALA B 77 " --> pdb=" O TYR B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 93 Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 29 through 36 Processing helix chain 'C' and resid 48 through 73 Processing helix chain 'C' and resid 81 through 90 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 114 through 116 No H-bonds generated for 'chain 'C' and resid 114 through 116' Processing helix chain 'D' and resid 39 through 49 Processing helix chain 'D' and resid 57 through 85 Processing helix chain 'D' and resid 92 through 102 Processing helix chain 'D' and resid 105 through 124 removed outlier: 3.574A pdb=" N SER D 124 " --> pdb=" O THR D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 Processing helix chain 'E' and resid 65 through 77 Processing helix chain 'E' and resid 87 through 115 Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'F' and resid 27 through 29 No H-bonds generated for 'chain 'F' and resid 27 through 29' Processing helix chain 'F' and resid 32 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.892A pdb=" N TYR F 52 " --> pdb=" O GLY F 49 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU F 53 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 93 Processing helix chain 'G' and resid 18 through 22 Processing helix chain 'G' and resid 29 through 36 Processing helix chain 'G' and resid 48 through 74 Processing helix chain 'G' and resid 81 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 114 through 116 No H-bonds generated for 'chain 'G' and resid 114 through 116' Processing helix chain 'H' and resid 39 through 49 Processing helix chain 'H' and resid 57 through 84 Processing helix chain 'H' and resid 92 through 102 Processing helix chain 'H' and resid 105 through 124 Processing helix chain 'K' and resid 251 through 255 removed outlier: 4.034A pdb=" N GLN K 255 " --> pdb=" O ILE K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 728 through 730 No H-bonds generated for 'chain 'K' and resid 728 through 730' Processing helix chain 'K' and resid 756 through 758 No H-bonds generated for 'chain 'K' and resid 756 through 758' Processing helix chain 'K' and resid 986 through 989 No H-bonds generated for 'chain 'K' and resid 986 through 989' Processing helix chain 'K' and resid 1045 through 1061 Processing helix chain 'K' and resid 1070 through 1074 Processing helix chain 'K' and resid 1091 through 1099 removed outlier: 3.679A pdb=" N PHE K1097 " --> pdb=" O LEU K1093 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU K1098 " --> pdb=" O ILE K1094 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASP K1099 " --> pdb=" O GLU K1095 " (cutoff:3.500A) Processing helix chain 'K' and resid 1102 through 1109 Processing helix chain 'K' and resid 1126 through 1139 removed outlier: 3.992A pdb=" N ILE K1139 " --> pdb=" O GLU K1135 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 78 Processing helix chain 'L' and resid 83 through 100 removed outlier: 4.006A pdb=" N SER L 100 " --> pdb=" O HIS L 96 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'K' and resid 1088 through 1090 removed outlier: 7.359A pdb=" N ASN K 4 " --> pdb=" O ILE K1089 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE K1037 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL K1006 " --> pdb=" O GLY K1031 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 17 through 21 removed outlier: 3.627A pdb=" N GLY K 17 " --> pdb=" O ALA K 34 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL K 43 " --> pdb=" O PRO K 51 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'K' and resid 61 through 67 removed outlier: 6.842A pdb=" N LEU K 80 " --> pdb=" O ALA K 62 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N MET K 64 " --> pdb=" O PHE K 78 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE K 78 " --> pdb=" O MET K 64 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU K 66 " --> pdb=" O LEU K 76 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU K 76 " --> pdb=" O LEU K 66 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASN K 85 " --> pdb=" O THR K 81 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU K 90 " --> pdb=" O THR K 102 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N THR K 102 " --> pdb=" O GLU K 90 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS K 92 " --> pdb=" O ILE K 100 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ILE K 100 " --> pdb=" O LYS K 92 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N SER K 94 " --> pdb=" O ILE K 98 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ILE K 98 " --> pdb=" O SER K 94 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'K' and resid 121 through 124 Processing sheet with id= E, first strand: chain 'K' and resid 201 through 204 removed outlier: 3.551A pdb=" N ASP K 166 " --> pdb=" O VAL K 181 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLN K 183 " --> pdb=" O VAL K 164 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL K 164 " --> pdb=" O GLN K 183 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'K' and resid 218 through 221 Processing sheet with id= G, first strand: chain 'K' and resid 258 through 263 removed outlier: 7.010A pdb=" N GLY K 274 " --> pdb=" O VAL K 259 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N HIS K 261 " --> pdb=" O LEU K 272 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU K 272 " --> pdb=" O HIS K 261 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ARG K 263 " --> pdb=" O ARG K 270 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ARG K 270 " --> pdb=" O ARG K 263 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG K 279 " --> pdb=" O ASP K 275 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N MET K 282 " --> pdb=" O LEU K 304 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU K 304 " --> pdb=" O MET K 282 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU K 284 " --> pdb=" O VAL K 302 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N VAL K 302 " --> pdb=" O LEU K 284 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLU K 286 " --> pdb=" O LEU K 300 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU K 300 " --> pdb=" O GLU K 286 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'K' and resid 287 through 289 Processing sheet with id= I, first strand: chain 'K' and resid 313 through 318 removed outlier: 6.674A pdb=" N VAL K 321 " --> pdb=" O LEU K 317 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LYS K 335 " --> pdb=" O ALA K 349 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ALA K 349 " --> pdb=" O LYS K 335 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'K' and resid 361 through 365 removed outlier: 4.075A pdb=" N ASP K 361 " --> pdb=" O CYS K 378 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'K' and resid 749 through 751 removed outlier: 6.932A pdb=" N ASP K 795 " --> pdb=" O VAL K 801 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL K 801 " --> pdb=" O ASP K 795 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'K' and resid 811 through 819 removed outlier: 6.710A pdb=" N GLY K 832 " --> pdb=" O LEU K 814 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU K 816 " --> pdb=" O ILE K 830 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE K 830 " --> pdb=" O LEU K 816 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER K 818 " --> pdb=" O TYR K 828 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR K 828 " --> pdb=" O SER K 818 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG K 847 " --> pdb=" O THR K 833 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLN K 852 " --> pdb=" O THR K 860 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N THR K 860 " --> pdb=" O GLN K 852 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N SER K 854 " --> pdb=" O LEU K 858 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LEU K 858 " --> pdb=" O SER K 854 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'K' and resid 872 through 876 removed outlier: 3.601A pdb=" N SER K 872 " --> pdb=" O SER K 883 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLU K 892 " --> pdb=" O THR K 901 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N THR K 901 " --> pdb=" O GLU K 892 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'K' and resid 911 through 917 removed outlier: 6.747A pdb=" N GLY K 924 " --> pdb=" O LEU K 912 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU K 914 " --> pdb=" O LEU K 922 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU K 922 " --> pdb=" O LEU K 914 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N THR K 916 " --> pdb=" O PHE K 920 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N PHE K 920 " --> pdb=" O THR K 916 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA K 934 " --> pdb=" O GLU K 944 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N GLU K 944 " --> pdb=" O ALA K 934 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'K' and resid 954 through 959 removed outlier: 6.795A pdb=" N ALA K 968 " --> pdb=" O SER K 955 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL K 957 " --> pdb=" O LEU K 966 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU K 966 " --> pdb=" O VAL K 957 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ILE K 959 " --> pdb=" O ASN K 964 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ASN K 964 " --> pdb=" O ILE K 959 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN K 973 " --> pdb=" O GLU K 969 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLN K 978 " --> pdb=" O GLU K 994 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N GLU K 994 " --> pdb=" O GLN K 978 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'K' and resid 720 through 727 removed outlier: 6.485A pdb=" N LEU K 736 " --> pdb=" O ARG K 722 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE K 724 " --> pdb=" O GLY K 734 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLY K 734 " --> pdb=" O ILE K 724 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N TYR K 726 " --> pdb=" O CYS K 732 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N CYS K 732 " --> pdb=" O TYR K 726 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= R, first strand: chain 'L' and resid 148 through 150 Processing sheet with id= S, first strand: chain 'L' and resid 171 through 174 removed outlier: 6.537A pdb=" N ASP L 185 " --> pdb=" O ILE L 190 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE L 190 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 225 through 228 Processing sheet with id= U, first strand: chain 'L' and resid 283 through 286 removed outlier: 4.720A pdb=" N THR L 266 " --> pdb=" O SER L 262 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER L 262 " --> pdb=" O THR L 266 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS L 247 " --> pdb=" O ALA L 261 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'L' and resid 325 through 327 removed outlier: 3.749A pdb=" N GLY L 325 " --> pdb=" O VAL L 314 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 350 through 354 removed outlier: 5.862A pdb=" N ASP L 376 " --> pdb=" O MET L 382 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N MET L 382 " --> pdb=" O ASP L 376 " (cutoff:3.500A) 649 hydrogen bonds defined for protein. 1764 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 342 hydrogen bonds 684 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 223 stacking parallelities Total time for adding SS restraints: 19.91 Time building geometry restraints manager: 38.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 19218 1.03 - 1.23: 291 1.23 - 1.43: 9962 1.43 - 1.62: 12388 1.62 - 1.82: 109 Bond restraints: 41968 Sorted by residual: bond pdb=" CB VAL L 248 " pdb=" CG2 VAL L 248 " ideal model delta sigma weight residual 1.521 1.417 0.104 3.30e-02 9.18e+02 9.90e+00 bond pdb=" CB TRP K 953 " pdb=" CG TRP K 953 " ideal model delta sigma weight residual 1.498 1.402 0.096 3.10e-02 1.04e+03 9.67e+00 bond pdb=" CB PHE D 71 " pdb=" CG PHE D 71 " ideal model delta sigma weight residual 1.502 1.433 0.069 2.30e-02 1.89e+03 9.06e+00 bond pdb=" P T64 J 95 " pdb=" O5' T64 J 95 " ideal model delta sigma weight residual 1.649 1.590 0.059 2.00e-02 2.50e+03 8.73e+00 bond pdb=" CZ ARG B 40 " pdb=" NH2 ARG B 40 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.57e+00 ... (remaining 41963 not shown) Histogram of bond angle deviations from ideal: 65.26 - 80.13: 24 80.13 - 95.00: 23 95.00 - 109.87: 32969 109.87 - 124.74: 40815 124.74 - 139.60: 2157 Bond angle restraints: 75988 Sorted by residual: angle pdb=" C SER L 68 " pdb=" N ILE L 69 " pdb=" H ILE L 69 " ideal model delta sigma weight residual 124.17 74.35 49.81 3.00e+00 1.11e-01 2.76e+02 angle pdb=" CA ILE L 69 " pdb=" N ILE L 69 " pdb=" H ILE L 69 " ideal model delta sigma weight residual 113.87 65.26 48.60 3.00e+00 1.11e-01 2.62e+02 angle pdb=" C ALA A 136 " pdb=" CA ALA A 136 " pdb=" HA ALA A 136 " ideal model delta sigma weight residual 109.00 68.66 40.34 3.00e+00 1.11e-01 1.81e+02 angle pdb=" C GLU L 421 " pdb=" CA GLU L 421 " pdb=" HA GLU L 421 " ideal model delta sigma weight residual 109.00 71.86 37.14 3.00e+00 1.11e-01 1.53e+02 angle pdb=" C CYS K 903 " pdb=" CA CYS K 903 " pdb=" HA CYS K 903 " ideal model delta sigma weight residual 109.00 73.13 35.87 3.00e+00 1.11e-01 1.43e+02 ... (remaining 75983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 16766 35.29 - 70.59: 1787 70.59 - 105.88: 26 105.88 - 141.18: 1 141.18 - 176.47: 4 Dihedral angle restraints: 18584 sinusoidal: 12007 harmonic: 6577 Sorted by residual: dihedral pdb=" CA LYS B 21 " pdb=" C LYS B 21 " pdb=" N VAL B 22 " pdb=" CA VAL B 22 " ideal model delta harmonic sigma weight residual -180.00 -127.35 -52.65 0 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" CA ARG K 928 " pdb=" C ARG K 928 " pdb=" N SER K 929 " pdb=" CA SER K 929 " ideal model delta harmonic sigma weight residual -180.00 -139.72 -40.28 0 5.00e+00 4.00e-02 6.49e+01 dihedral pdb=" CA ASP L 111 " pdb=" C ASP L 111 " pdb=" N ARG L 112 " pdb=" CA ARG L 112 " ideal model delta harmonic sigma weight residual 180.00 -148.07 -31.93 0 5.00e+00 4.00e-02 4.08e+01 ... (remaining 18581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.421: 3600 0.421 - 0.841: 0 0.841 - 1.262: 1 1.262 - 1.682: 2 1.682 - 2.103: 1 Chirality restraints: 3604 Sorted by residual: chirality pdb=" C5 T64 J 95 " pdb=" C4 T64 J 95 " pdb=" C6 T64 J 95 " pdb=" C5A T64 J 95 " both_signs ideal model delta sigma weight residual False -2.64 -0.53 -2.10 2.00e-01 2.50e+01 1.11e+02 chirality pdb=" CG LEU E 66 " pdb=" CB LEU E 66 " pdb=" CD1 LEU E 66 " pdb=" CD2 LEU E 66 " both_signs ideal model delta sigma weight residual False -2.59 -0.96 -1.63 2.00e-01 2.50e+01 6.68e+01 chirality pdb=" CB THR G 121 " pdb=" CA THR G 121 " pdb=" OG1 THR G 121 " pdb=" CG2 THR G 121 " both_signs ideal model delta sigma weight residual False 2.55 1.29 1.27 2.00e-01 2.50e+01 4.01e+01 ... (remaining 3601 not shown) Planarity restraints: 5184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE K 382 " -0.029 2.00e-02 2.50e+03 5.62e-02 3.16e+01 pdb=" C PHE K 382 " 0.097 2.00e-02 2.50e+03 pdb=" O PHE K 382 " -0.035 2.00e-02 2.50e+03 pdb=" N LYS K 383 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA K 381 " 0.023 2.00e-02 2.50e+03 4.76e-02 2.26e+01 pdb=" C ALA K 381 " -0.082 2.00e-02 2.50e+03 pdb=" O ALA K 381 " 0.031 2.00e-02 2.50e+03 pdb=" N PHE K 382 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA K 381 " -0.019 2.00e-02 2.50e+03 3.57e-02 1.27e+01 pdb=" N PHE K 382 " 0.062 2.00e-02 2.50e+03 pdb=" CA PHE K 382 " -0.017 2.00e-02 2.50e+03 pdb=" H PHE K 382 " -0.025 2.00e-02 2.50e+03 ... (remaining 5181 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.20: 3071 2.20 - 2.80: 81574 2.80 - 3.40: 104012 3.40 - 4.00: 149135 4.00 - 4.60: 220060 Nonbonded interactions: 557852 Sorted by model distance: nonbonded pdb=" H ILE L 69 " pdb=" HA ILE L 69 " model vdw 1.606 1.816 nonbonded pdb=" H VAL A 118 " pdb=" OP1 DT I 70 " model vdw 1.618 1.850 nonbonded pdb="HH21 ARG A 43 " pdb=" OP1 DG I 68 " model vdw 1.627 1.850 nonbonded pdb=" OG1 THR L 97 " pdb="HE22 GLN L 420 " model vdw 1.636 1.850 nonbonded pdb=" O PHE K 67 " pdb=" H LEU K 76 " model vdw 1.637 1.850 ... (remaining 557847 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' selection = (chain 'E' and (resid 36 through 42 or (resid 43 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 o \ r name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21)) or r \ esid 44 through 49 or (resid 50 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or nam \ e H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or na \ me HD3 or name HE or name HH21 or name HH22)) or resid 51 through 136)) } ncs_group { reference = (chain 'B' and ((resid 22 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name \ HG13 or name HG21 or name HG22 or name HG23)) or resid 23 through 35 or (resid 3 \ 6 and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name NE or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or \ name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 \ or name HH12 or name HH21)) or resid 37 through 103)) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 10 through 11 or (resid 12 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 o \ r name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE or name HH11 or name HH12)) or resid 13 throu \ gh 42 or (resid 43 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name H \ A or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or nam \ e HE or name HH12)) or resid 44 through 126)) selection = (chain 'G' and (resid 10 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ or name H or \ name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 \ or name HE2 or name HE3 or name HZ2)) or resid 15 through 17 or (resid 18 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD or name NE \ or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name \ HH12 or name HH22)) or resid 19 through 126)) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 1 through 49 or resid 51 through 71 or resid 75 through 94 \ or resid 96 or resid 98 through 145)) selection = (chain 'J' and ((resid 1 and (name O5' or name C5' or name C4' or name O4' or na \ me C3' or name O3' or name C2' or name C1' or name N9 or name C8 or name N7 or n \ ame C5 or name C6 or name N6 or name N1 or name C2 or name N3 or name C4 or name \ H5' or name H5'' or name H4' or name H3' or name H2' or name H2'' or name H1' o \ r name H8 or name H61 or name H2 or name HO5')) or resid 2 through 49 or resid 5 \ 1 through 71 or resid 75 through 94 or resid 97 through 145)) } 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.580 Extract box with map and model: 7.920 Check model and map are aligned: 0.620 Set scattering table: 0.380 Process input model: 146.280 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.130 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 161.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 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 : 0.015 0.139 22723 Z= 0.908 Angle : 1.074 23.299 31952 Z= 0.613 Chirality : 0.082 2.103 3604 Planarity : 0.007 0.080 3077 Dihedral : 23.129 176.472 9311 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.72 % Favored : 94.02 % Rotamer: Outliers : 0.47 % Allowed : 3.92 % Favored : 95.61 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.60 (0.17), residues: 1974 helix: 0.21 (0.19), residues: 618 sheet: -0.88 (0.22), residues: 456 loop : -2.07 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP K 207 HIS 0.013 0.003 HIS L 333 PHE 0.033 0.004 PHE K 382 TYR 0.025 0.003 TYR L 413 ARG 0.018 0.001 ARG L 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 14 is missing expected H atoms. Skipping. Residue TYR 906 is missing expected H atoms. Skipping. Evaluate side-chains 517 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 509 time to evaluate : 3.041 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ILE cc_start: 0.9172 (mt) cc_final: 0.8654 (mt) REVERT: B 50 LEU cc_start: 0.8748 (mt) cc_final: 0.7974 (tp) REVERT: B 79 ARG cc_start: 0.7064 (mtm110) cc_final: 0.6058 (mtm110) REVERT: G 42 GLU cc_start: 0.7909 (mp0) cc_final: 0.7652 (mt-10) REVERT: G 43 ARG cc_start: 0.7096 (ptp-170) cc_final: 0.6131 (ptp-170) REVERT: G 95 ASN cc_start: 0.8302 (t0) cc_final: 0.7979 (t0) REVERT: H 113 SER cc_start: 0.8557 (OUTLIER) cc_final: 0.8076 (p) REVERT: K 5 TYR cc_start: 0.7764 (t80) cc_final: 0.7507 (t80) REVERT: K 58 TYR cc_start: 0.7278 (m-10) cc_final: 0.6938 (m-10) REVERT: K 192 THR cc_start: 0.6490 (p) cc_final: 0.6096 (p) REVERT: K 301 ARG cc_start: 0.7168 (mtt90) cc_final: 0.6845 (mtt180) REVERT: K 375 LEU cc_start: 0.7918 (tp) cc_final: 0.7210 (tp) REVERT: K 377 THR cc_start: 0.7887 (p) cc_final: 0.7612 (p) REVERT: K 379 SER cc_start: 0.5370 (t) cc_final: 0.4593 (m) REVERT: K 727 GLN cc_start: 0.7133 (tt0) cc_final: 0.6930 (tt0) REVERT: K 1123 GLU cc_start: 0.2829 (tp30) cc_final: 0.2544 (tp30) REVERT: L 234 GLU cc_start: 0.7688 (pm20) cc_final: 0.7001 (pt0) REVERT: L 245 VAL cc_start: 0.7958 (t) cc_final: 0.7744 (m) REVERT: L 341 LYS cc_start: 0.8856 (mttt) cc_final: 0.8489 (tttp) outliers start: 8 outliers final: 5 residues processed: 514 average time/residue: 0.9695 time to fit residues: 700.1655 Evaluate side-chains 363 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 357 time to evaluate : 2.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 174 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 202 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 GLN E 94 GLN K 727 GLN ** K1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1059 ASN L 385 GLN L 420 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 22723 Z= 0.279 Angle : 0.749 26.826 31952 Z= 0.419 Chirality : 0.068 1.665 3604 Planarity : 0.005 0.081 3077 Dihedral : 26.377 171.054 5441 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.47 % Favored : 94.43 % Rotamer: Outliers : 0.06 % Allowed : 2.58 % Favored : 97.37 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.18), residues: 1974 helix: 0.88 (0.20), residues: 623 sheet: -0.56 (0.23), residues: 479 loop : -1.90 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 83 HIS 0.009 0.001 HIS L 333 PHE 0.025 0.002 PHE L 257 TYR 0.018 0.002 TYR K 906 ARG 0.013 0.001 ARG K1102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 14 is missing expected H atoms. Skipping. Residue TYR 906 is missing expected H atoms. Skipping. Evaluate side-chains 433 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 432 time to evaluate : 2.795 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: 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: symmetry clash REVERT: A 91 MET cc_start: 0.7604 (mmm) cc_final: 0.7300 (mmm) REVERT: B 50 LEU cc_start: 0.8659 (mt) cc_final: 0.8005 (tp) REVERT: B 85 MET cc_start: 0.6453 (mmm) cc_final: 0.6195 (tpt) REVERT: F 85 MET cc_start: 0.7482 (mmm) cc_final: 0.7097 (tpp) REVERT: G 43 ARG cc_start: 0.7283 (ptp-170) cc_final: 0.6188 (ptp-170) REVERT: G 75 LYS cc_start: 0.8800 (mtmm) cc_final: 0.7949 (tmtt) REVERT: G 76 LYS cc_start: 0.8240 (mttm) cc_final: 0.7969 (mtmt) REVERT: G 95 ASN cc_start: 0.8417 (t0) cc_final: 0.8094 (t0) REVERT: H 83 HIS cc_start: 0.8124 (t70) cc_final: 0.7903 (t70) REVERT: H 91 THR cc_start: 0.9042 (t) cc_final: 0.8759 (p) REVERT: H 113 SER cc_start: 0.8433 (m) cc_final: 0.8157 (p) REVERT: K 5 TYR cc_start: 0.7643 (t80) cc_final: 0.7372 (t80) REVERT: K 91 TYR cc_start: 0.7833 (t80) cc_final: 0.7557 (t80) REVERT: K 131 ILE cc_start: 0.9121 (mp) cc_final: 0.8894 (mt) REVERT: K 145 LEU cc_start: 0.8483 (mt) cc_final: 0.8269 (mt) REVERT: K 166 ASP cc_start: 0.6574 (t70) cc_final: 0.6329 (t70) REVERT: K 297 LEU cc_start: 0.5685 (tp) cc_final: 0.5472 (tp) REVERT: K 364 VAL cc_start: 0.8531 (p) cc_final: 0.8324 (m) REVERT: K 377 THR cc_start: 0.7771 (p) cc_final: 0.7492 (p) REVERT: K 379 SER cc_start: 0.5398 (t) cc_final: 0.4653 (m) REVERT: K 725 CYS cc_start: 0.8300 (m) cc_final: 0.8057 (m) REVERT: K 819 CYS cc_start: 0.5180 (p) cc_final: 0.4339 (p) REVERT: K 821 LEU cc_start: 0.6988 (mt) cc_final: 0.6528 (mp) REVERT: K 1089 ILE cc_start: 0.8869 (mm) cc_final: 0.8652 (mm) REVERT: L 324 LEU cc_start: 0.9318 (mp) cc_final: 0.9006 (tt) REVERT: L 341 LYS cc_start: 0.8916 (mttt) cc_final: 0.8631 (tttm) outliers start: 1 outliers final: 1 residues processed: 432 average time/residue: 0.8808 time to fit residues: 553.8392 Evaluate side-chains 353 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 352 time to evaluate : 2.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 112 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 168 optimal weight: 8.9990 chunk 137 optimal weight: 0.0010 chunk 55 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 219 optimal weight: 0.7980 chunk 180 optimal weight: 5.9990 chunk 201 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 162 optimal weight: 10.0000 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 74 ASN K 964 ASN ** K 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22723 Z= 0.213 Angle : 0.702 25.994 31952 Z= 0.391 Chirality : 0.067 1.697 3604 Planarity : 0.005 0.071 3077 Dihedral : 26.249 172.090 5441 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.42 % Favored : 94.48 % Rotamer: Outliers : 0.12 % Allowed : 1.17 % Favored : 98.71 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.57 (0.19), residues: 1974 helix: 1.38 (0.21), residues: 621 sheet: -0.36 (0.24), residues: 459 loop : -1.69 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 207 HIS 0.010 0.001 HIS K 789 PHE 0.018 0.001 PHE L 257 TYR 0.014 0.001 TYR L 413 ARG 0.017 0.000 ARG K 900 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 14 is missing expected H atoms. Skipping. Residue TYR 906 is missing expected H atoms. Skipping. Evaluate side-chains 409 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 407 time to evaluate : 2.820 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: 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: A 57 LYS cc_start: 0.8253 (tppt) cc_final: 0.8045 (tppt) REVERT: A 91 MET cc_start: 0.7459 (mmm) cc_final: 0.7070 (mmm) REVERT: B 50 LEU cc_start: 0.8714 (mt) cc_final: 0.7982 (tp) REVERT: B 85 MET cc_start: 0.6459 (mmm) cc_final: 0.6107 (tpt) REVERT: C 18 ARG cc_start: 0.8101 (mtm180) cc_final: 0.7892 (mtp85) REVERT: D 117 LYS cc_start: 0.8777 (mtpp) cc_final: 0.8532 (mtpp) REVERT: E 94 GLN cc_start: 0.8642 (mt0) cc_final: 0.8194 (tt0) REVERT: E 97 CYS cc_start: 0.8829 (m) cc_final: 0.8525 (p) REVERT: G 27 PRO cc_start: 0.8127 (Cg_endo) cc_final: 0.7906 (Cg_exo) REVERT: G 43 ARG cc_start: 0.7216 (ptp-170) cc_final: 0.6745 (mtt180) REVERT: G 75 LYS cc_start: 0.8730 (mtmm) cc_final: 0.7557 (tmtt) REVERT: G 95 ASN cc_start: 0.8423 (t0) cc_final: 0.8159 (t0) REVERT: H 83 HIS cc_start: 0.8175 (t70) cc_final: 0.7963 (t70) REVERT: H 91 THR cc_start: 0.9050 (t) cc_final: 0.8789 (p) REVERT: H 113 SER cc_start: 0.8306 (m) cc_final: 0.8068 (p) REVERT: K 5 TYR cc_start: 0.7692 (t80) cc_final: 0.7438 (t80) REVERT: K 10 GLN cc_start: 0.7109 (tp40) cc_final: 0.6489 (tm-30) REVERT: K 91 TYR cc_start: 0.7834 (t80) cc_final: 0.7407 (t80) REVERT: K 166 ASP cc_start: 0.6750 (t70) cc_final: 0.6415 (t70) REVERT: K 282 MET cc_start: 0.4071 (ttp) cc_final: 0.3837 (ttp) REVERT: K 364 VAL cc_start: 0.8420 (p) cc_final: 0.8190 (m) REVERT: K 377 THR cc_start: 0.7832 (p) cc_final: 0.7582 (p) REVERT: K 379 SER cc_start: 0.5541 (t) cc_final: 0.4850 (m) REVERT: K 725 CYS cc_start: 0.8280 (m) cc_final: 0.7993 (m) REVERT: K 812 TYR cc_start: 0.7310 (m-10) cc_final: 0.7096 (m-10) REVERT: K 819 CYS cc_start: 0.5138 (p) cc_final: 0.4335 (p) REVERT: K 821 LEU cc_start: 0.7051 (mt) cc_final: 0.6597 (mp) REVERT: L 234 GLU cc_start: 0.7928 (pm20) cc_final: 0.7386 (pt0) REVERT: L 324 LEU cc_start: 0.9347 (mp) cc_final: 0.9080 (tt) REVERT: L 341 LYS cc_start: 0.8894 (mttt) cc_final: 0.8587 (tttp) outliers start: 2 outliers final: 1 residues processed: 408 average time/residue: 0.8717 time to fit residues: 517.8453 Evaluate side-chains 351 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 350 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 200 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 136 optimal weight: 9.9990 chunk 203 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 25 GLN ** H 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 290 GLN ** K 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 826 ASN K 907 ASN ** K 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 22723 Z= 0.352 Angle : 0.780 27.024 31952 Z= 0.437 Chirality : 0.070 1.793 3604 Planarity : 0.005 0.068 3077 Dihedral : 26.234 173.664 5441 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.45 % Favored : 92.45 % Rotamer: Outliers : 0.06 % Allowed : 2.99 % Favored : 96.96 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.18), residues: 1974 helix: 0.69 (0.20), residues: 615 sheet: -0.62 (0.23), residues: 464 loop : -1.78 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP K 207 HIS 0.008 0.002 HIS K 991 PHE 0.017 0.002 PHE L 257 TYR 0.017 0.002 TYR C 58 ARG 0.041 0.001 ARG K 900 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 14 is missing expected H atoms. Skipping. Residue TYR 906 is missing expected H atoms. Skipping. Evaluate side-chains 408 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 407 time to evaluate : 2.854 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8303 (tppt) cc_final: 0.8092 (tppt) REVERT: A 91 MET cc_start: 0.7770 (mmm) cc_final: 0.7470 (mmm) REVERT: A 95 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8425 (mm-30) REVERT: B 50 LEU cc_start: 0.8938 (mt) cc_final: 0.8270 (tp) REVERT: B 78 LYS cc_start: 0.8797 (mmtt) cc_final: 0.8455 (mttm) REVERT: B 89 TYR cc_start: 0.8698 (m-10) cc_final: 0.8395 (m-80) REVERT: C 18 ARG cc_start: 0.8415 (mtm180) cc_final: 0.8121 (mtp85) REVERT: C 20 SER cc_start: 0.9139 (p) cc_final: 0.8866 (t) REVERT: C 93 GLU cc_start: 0.7328 (mp0) cc_final: 0.7078 (mm-30) REVERT: D 117 LYS cc_start: 0.8796 (mtpp) cc_final: 0.8583 (mtpp) REVERT: E 94 GLN cc_start: 0.8820 (mt0) cc_final: 0.8338 (tt0) REVERT: E 95 GLU cc_start: 0.8462 (tp30) cc_final: 0.8042 (tp30) REVERT: E 97 CYS cc_start: 0.9111 (m) cc_final: 0.8673 (p) REVERT: F 89 TYR cc_start: 0.8431 (m-10) cc_final: 0.8223 (m-10) REVERT: G 75 LYS cc_start: 0.8992 (mtmm) cc_final: 0.8075 (tmtt) REVERT: H 83 HIS cc_start: 0.8464 (t70) cc_final: 0.8204 (t70) REVERT: H 91 THR cc_start: 0.9334 (t) cc_final: 0.9123 (p) REVERT: H 113 SER cc_start: 0.8421 (m) cc_final: 0.8200 (p) REVERT: H 116 THR cc_start: 0.8552 (m) cc_final: 0.8327 (m) REVERT: K 5 TYR cc_start: 0.7602 (t80) cc_final: 0.7352 (t80) REVERT: K 91 TYR cc_start: 0.8086 (t80) cc_final: 0.7690 (t80) REVERT: K 131 ILE cc_start: 0.9225 (mp) cc_final: 0.9000 (mt) REVERT: K 166 ASP cc_start: 0.7144 (t70) cc_final: 0.6848 (t70) REVERT: K 297 LEU cc_start: 0.5828 (tp) cc_final: 0.5619 (tp) REVERT: L 251 ASN cc_start: 0.8748 (t0) cc_final: 0.8447 (t0) REVERT: L 329 HIS cc_start: 0.8318 (t70) cc_final: 0.8010 (t-90) REVERT: L 341 LYS cc_start: 0.9049 (mttt) cc_final: 0.8712 (tttt) REVERT: L 399 GLU cc_start: 0.8729 (tp30) cc_final: 0.8364 (mm-30) outliers start: 1 outliers final: 1 residues processed: 408 average time/residue: 0.8794 time to fit residues: 516.5630 Evaluate side-chains 361 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 360 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 179 optimal weight: 0.0970 chunk 122 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 193 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 39 ASN K 337 ASN K 964 ASN ** K1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 22723 Z= 0.237 Angle : 0.706 25.992 31952 Z= 0.393 Chirality : 0.068 1.755 3604 Planarity : 0.005 0.064 3077 Dihedral : 26.197 172.973 5441 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.43 % Favored : 93.47 % Rotamer: Outliers : 0.06 % Allowed : 1.23 % Favored : 98.71 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.19), residues: 1974 helix: 0.96 (0.21), residues: 620 sheet: -0.46 (0.24), residues: 447 loop : -1.78 (0.19), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 207 HIS 0.007 0.001 HIS K 991 PHE 0.017 0.001 PHE L 257 TYR 0.015 0.001 TYR L 413 ARG 0.004 0.000 ARG L 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 14 is missing expected H atoms. Skipping. Residue TYR 906 is missing expected H atoms. Skipping. Evaluate side-chains 410 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 409 time to evaluate : 2.902 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: 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: A 57 LYS cc_start: 0.8319 (tppt) cc_final: 0.7604 (tptp) REVERT: A 91 MET cc_start: 0.7682 (mmm) cc_final: 0.7425 (mmm) REVERT: A 107 ASP cc_start: 0.7833 (t0) cc_final: 0.7554 (t70) REVERT: B 50 LEU cc_start: 0.8934 (mt) cc_final: 0.8292 (tp) REVERT: B 78 LYS cc_start: 0.8764 (mmtt) cc_final: 0.8446 (mttm) REVERT: B 89 TYR cc_start: 0.8685 (m-10) cc_final: 0.8427 (m-80) REVERT: C 18 ARG cc_start: 0.8450 (mtm180) cc_final: 0.8154 (mtp85) REVERT: C 20 SER cc_start: 0.9056 (p) cc_final: 0.8822 (t) REVERT: C 93 GLU cc_start: 0.7465 (mp0) cc_final: 0.7137 (mm-30) REVERT: D 117 LYS cc_start: 0.8795 (mtpp) cc_final: 0.8594 (mtpp) REVERT: E 94 GLN cc_start: 0.8896 (mt0) cc_final: 0.8405 (tt0) REVERT: E 95 GLU cc_start: 0.8600 (tp30) cc_final: 0.8230 (tp30) REVERT: G 75 LYS cc_start: 0.8907 (mtmm) cc_final: 0.7955 (tmtt) REVERT: H 60 MET cc_start: 0.8419 (tpp) cc_final: 0.8213 (ttp) REVERT: H 83 HIS cc_start: 0.8489 (t70) cc_final: 0.8229 (t70) REVERT: H 91 THR cc_start: 0.9268 (t) cc_final: 0.9037 (p) REVERT: H 113 SER cc_start: 0.8336 (m) cc_final: 0.8072 (p) REVERT: K 5 TYR cc_start: 0.7602 (t80) cc_final: 0.7282 (t80) REVERT: K 84 TYR cc_start: 0.8486 (m-80) cc_final: 0.8089 (m-80) REVERT: K 91 TYR cc_start: 0.7949 (t80) cc_final: 0.7579 (t80) REVERT: K 166 ASP cc_start: 0.7200 (t70) cc_final: 0.6866 (t70) REVERT: K 305 LEU cc_start: 0.8578 (mp) cc_final: 0.8255 (mp) REVERT: K 375 LEU cc_start: 0.7973 (tp) cc_final: 0.7716 (mt) REVERT: K 377 THR cc_start: 0.7977 (p) cc_final: 0.7769 (p) REVERT: K 905 HIS cc_start: 0.4897 (t70) cc_final: 0.4590 (t70) REVERT: K 958 GLU cc_start: 0.7771 (tp30) cc_final: 0.7340 (tm-30) REVERT: K 959 ILE cc_start: 0.8128 (mt) cc_final: 0.7140 (mt) REVERT: K 1036 MET cc_start: 0.7975 (ttp) cc_final: 0.7660 (ttt) REVERT: L 251 ASN cc_start: 0.8851 (t0) cc_final: 0.8578 (t0) REVERT: L 307 ASP cc_start: 0.8350 (p0) cc_final: 0.8072 (p0) REVERT: L 329 HIS cc_start: 0.8293 (t70) cc_final: 0.7990 (t-90) REVERT: L 341 LYS cc_start: 0.9041 (mttt) cc_final: 0.8707 (tttp) REVERT: L 399 GLU cc_start: 0.8674 (tp30) cc_final: 0.8266 (mm-30) outliers start: 1 outliers final: 1 residues processed: 409 average time/residue: 0.8521 time to fit residues: 507.2984 Evaluate side-chains 357 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 356 time to evaluate : 3.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 72 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 126 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 215 optimal weight: 0.9980 chunk 179 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 39 ASN K 964 ASN K1025 GLN ** K1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 308 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22723 Z= 0.178 Angle : 0.675 25.893 31952 Z= 0.374 Chirality : 0.067 1.757 3604 Planarity : 0.004 0.061 3077 Dihedral : 26.156 174.131 5441 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.38 % Favored : 93.52 % Rotamer: Outliers : 0.06 % Allowed : 0.64 % Favored : 99.30 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.48 (0.19), residues: 1974 helix: 1.55 (0.21), residues: 619 sheet: -0.29 (0.25), residues: 431 loop : -1.69 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 207 HIS 0.005 0.001 HIS K 905 PHE 0.015 0.001 PHE L 257 TYR 0.031 0.001 TYR K 871 ARG 0.006 0.000 ARG C 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 14 is missing expected H atoms. Skipping. Residue TYR 906 is missing expected H atoms. Skipping. Evaluate side-chains 411 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 410 time to evaluate : 2.943 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: 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: A 57 LYS cc_start: 0.8346 (tppt) cc_final: 0.7566 (tptp) REVERT: A 91 MET cc_start: 0.7570 (mmm) cc_final: 0.7324 (mmm) REVERT: B 50 LEU cc_start: 0.8858 (mt) cc_final: 0.8207 (tp) REVERT: B 89 TYR cc_start: 0.8620 (m-10) cc_final: 0.8387 (m-80) REVERT: C 18 ARG cc_start: 0.8392 (mtm180) cc_final: 0.8059 (mtp85) REVERT: C 20 SER cc_start: 0.8996 (p) cc_final: 0.8733 (t) REVERT: C 93 GLU cc_start: 0.7389 (mp0) cc_final: 0.7069 (mm-30) REVERT: E 95 GLU cc_start: 0.8481 (tp30) cc_final: 0.8204 (tp30) REVERT: G 75 LYS cc_start: 0.8856 (mtmm) cc_final: 0.7988 (tmtt) REVERT: G 76 LYS cc_start: 0.8390 (mttm) cc_final: 0.8174 (mtpt) REVERT: H 83 HIS cc_start: 0.8487 (t70) cc_final: 0.8175 (t70) REVERT: H 113 SER cc_start: 0.8248 (m) cc_final: 0.8014 (t) REVERT: K 5 TYR cc_start: 0.7700 (t80) cc_final: 0.7457 (t80) REVERT: K 91 TYR cc_start: 0.7842 (t80) cc_final: 0.7599 (t80) REVERT: K 130 MET cc_start: 0.6995 (ppp) cc_final: 0.6124 (pmm) REVERT: K 305 LEU cc_start: 0.8549 (mp) cc_final: 0.8218 (mt) REVERT: K 377 THR cc_start: 0.7970 (p) cc_final: 0.7760 (p) REVERT: K 959 ILE cc_start: 0.8062 (mt) cc_final: 0.7203 (mt) REVERT: K 973 ASN cc_start: 0.8659 (m-40) cc_final: 0.8374 (m-40) REVERT: K 1036 MET cc_start: 0.7838 (ttp) cc_final: 0.7454 (ttt) REVERT: L 234 GLU cc_start: 0.8228 (pm20) cc_final: 0.7302 (pt0) REVERT: L 251 ASN cc_start: 0.8733 (t0) cc_final: 0.8515 (t0) REVERT: L 329 HIS cc_start: 0.8315 (t70) cc_final: 0.8038 (t-90) REVERT: L 341 LYS cc_start: 0.8995 (mttt) cc_final: 0.8633 (tttp) REVERT: L 399 GLU cc_start: 0.8592 (tp30) cc_final: 0.8174 (mm-30) outliers start: 1 outliers final: 1 residues processed: 410 average time/residue: 0.8324 time to fit residues: 502.0149 Evaluate side-chains 356 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 355 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 208 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 181 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 214 optimal weight: 1.9990 chunk 134 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 907 ASN K 964 ASN ** L 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 22723 Z= 0.302 Angle : 0.737 26.756 31952 Z= 0.411 Chirality : 0.069 1.801 3604 Planarity : 0.005 0.050 3077 Dihedral : 26.185 177.038 5441 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.65 % Favored : 92.25 % Rotamer: Outliers : 0.06 % Allowed : 1.41 % Favored : 98.54 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.19), residues: 1974 helix: 0.93 (0.21), residues: 618 sheet: -0.52 (0.25), residues: 449 loop : -1.77 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 418 HIS 0.008 0.001 HIS L 333 PHE 0.023 0.002 PHE L 257 TYR 0.014 0.002 TYR K 871 ARG 0.006 0.001 ARG L 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 14 is missing expected H atoms. Skipping. Residue TYR 906 is missing expected H atoms. Skipping. Evaluate side-chains 401 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 400 time to evaluate : 2.709 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8420 (tppt) cc_final: 0.7683 (tptp) REVERT: A 69 GLN cc_start: 0.8607 (pt0) cc_final: 0.8352 (pt0) REVERT: A 91 MET cc_start: 0.7752 (mmm) cc_final: 0.7508 (mmm) REVERT: B 50 LEU cc_start: 0.8998 (mt) cc_final: 0.8363 (tp) REVERT: B 85 MET cc_start: 0.7384 (mmm) cc_final: 0.7151 (tpt) REVERT: B 89 TYR cc_start: 0.8722 (m-10) cc_final: 0.8410 (m-80) REVERT: B 94 GLN cc_start: 0.8505 (mm-40) cc_final: 0.8130 (tt0) REVERT: C 93 GLU cc_start: 0.7488 (mp0) cc_final: 0.7167 (mm-30) REVERT: E 95 GLU cc_start: 0.8577 (tp30) cc_final: 0.8252 (tp30) REVERT: G 24 LEU cc_start: 0.8335 (mp) cc_final: 0.7989 (mp) REVERT: G 75 LYS cc_start: 0.8900 (mtmm) cc_final: 0.8080 (tmtt) REVERT: G 76 LYS cc_start: 0.8645 (mttm) cc_final: 0.8439 (mtpt) REVERT: H 91 THR cc_start: 0.9289 (t) cc_final: 0.9069 (p) REVERT: H 113 SER cc_start: 0.8351 (m) cc_final: 0.8065 (t) REVERT: K 5 TYR cc_start: 0.7577 (t80) cc_final: 0.7301 (t80) REVERT: K 91 TYR cc_start: 0.7959 (t80) cc_final: 0.7568 (t80) REVERT: K 111 ARG cc_start: 0.6435 (mmm160) cc_final: 0.6232 (mmm160) REVERT: K 130 MET cc_start: 0.7077 (ppp) cc_final: 0.6159 (pmm) REVERT: K 305 LEU cc_start: 0.8579 (mp) cc_final: 0.8246 (mt) REVERT: K 905 HIS cc_start: 0.5215 (t70) cc_final: 0.4873 (t70) REVERT: K 1036 MET cc_start: 0.8121 (ttp) cc_final: 0.7712 (ttt) REVERT: L 341 LYS cc_start: 0.9062 (mttt) cc_final: 0.8698 (tttp) REVERT: L 399 GLU cc_start: 0.8596 (tp30) cc_final: 0.8244 (mm-30) outliers start: 1 outliers final: 1 residues processed: 400 average time/residue: 0.8491 time to fit residues: 493.5190 Evaluate side-chains 362 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 361 time to evaluate : 2.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 85 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 136 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 195 optimal weight: 0.4980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 885 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 22723 Z= 0.271 Angle : 0.720 26.267 31952 Z= 0.401 Chirality : 0.069 1.804 3604 Planarity : 0.005 0.059 3077 Dihedral : 26.194 178.568 5441 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.24 % Favored : 92.65 % Rotamer: Outliers : 0.06 % Allowed : 0.59 % Favored : 99.36 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.06 (0.19), residues: 1974 helix: 0.81 (0.21), residues: 618 sheet: -0.51 (0.25), residues: 444 loop : -1.90 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 207 HIS 0.011 0.001 HIS L 120 PHE 0.029 0.002 PHE G 26 TYR 0.020 0.002 TYR K 871 ARG 0.011 0.000 ARG H 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 14 is missing expected H atoms. Skipping. Residue TYR 906 is missing expected H atoms. Skipping. Evaluate side-chains 401 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 400 time to evaluate : 3.086 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8420 (tppt) cc_final: 0.7690 (tptp) REVERT: A 69 GLN cc_start: 0.8568 (pt0) cc_final: 0.8335 (pt0) REVERT: A 91 MET cc_start: 0.7819 (mmm) cc_final: 0.7614 (mmm) REVERT: B 50 LEU cc_start: 0.9006 (mt) cc_final: 0.8398 (tp) REVERT: B 85 MET cc_start: 0.7313 (mmm) cc_final: 0.7101 (tpt) REVERT: B 89 TYR cc_start: 0.8676 (m-10) cc_final: 0.8382 (m-80) REVERT: B 94 GLN cc_start: 0.8473 (mm-40) cc_final: 0.8124 (tt0) REVERT: C 93 GLU cc_start: 0.7534 (mp0) cc_final: 0.7221 (mm-30) REVERT: D 117 LYS cc_start: 0.8802 (mtpp) cc_final: 0.8563 (ttmm) REVERT: E 95 GLU cc_start: 0.8623 (tp30) cc_final: 0.8348 (tp30) REVERT: G 24 LEU cc_start: 0.8443 (mp) cc_final: 0.8163 (mp) REVERT: G 75 LYS cc_start: 0.8909 (mtmm) cc_final: 0.8160 (tmtt) REVERT: G 76 LYS cc_start: 0.8650 (mttm) cc_final: 0.8415 (mtpt) REVERT: G 116 LEU cc_start: 0.9285 (pp) cc_final: 0.9081 (pp) REVERT: H 57 SER cc_start: 0.8796 (p) cc_final: 0.8319 (t) REVERT: K 5 TYR cc_start: 0.7485 (t80) cc_final: 0.7276 (t80) REVERT: K 57 MET cc_start: 0.6626 (mtm) cc_final: 0.6047 (ptp) REVERT: K 91 TYR cc_start: 0.7916 (t80) cc_final: 0.7523 (t80) REVERT: K 130 MET cc_start: 0.7169 (ppp) cc_final: 0.6203 (pmm) REVERT: K 166 ASP cc_start: 0.7400 (t70) cc_final: 0.7012 (t0) REVERT: K 305 LEU cc_start: 0.8561 (mp) cc_final: 0.8236 (mt) REVERT: K 905 HIS cc_start: 0.5240 (t70) cc_final: 0.4931 (t70) REVERT: K 953 TRP cc_start: 0.8437 (m100) cc_final: 0.8095 (m100) REVERT: K 973 ASN cc_start: 0.8325 (m-40) cc_final: 0.8025 (m-40) REVERT: K 977 CYS cc_start: 0.8156 (m) cc_final: 0.7940 (t) REVERT: K 1054 MET cc_start: 0.8506 (mmp) cc_final: 0.8301 (mmm) REVERT: K 1089 ILE cc_start: 0.8976 (mm) cc_final: 0.8772 (mp) REVERT: L 251 ASN cc_start: 0.8947 (t0) cc_final: 0.8684 (t0) REVERT: L 341 LYS cc_start: 0.9086 (mttt) cc_final: 0.8713 (tttp) REVERT: L 399 GLU cc_start: 0.8633 (tp30) cc_final: 0.8220 (mm-30) outliers start: 1 outliers final: 1 residues processed: 400 average time/residue: 0.8331 time to fit residues: 486.3879 Evaluate side-chains 359 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 358 time to evaluate : 2.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 205 optimal weight: 0.6980 chunk 187 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 180 optimal weight: 7.9990 chunk 189 optimal weight: 0.8980 chunk 199 optimal weight: 3.9990 chunk 131 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 907 ASN K 908 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 22723 Z= 0.233 Angle : 0.700 26.209 31952 Z= 0.388 Chirality : 0.067 1.775 3604 Planarity : 0.004 0.050 3077 Dihedral : 26.179 179.239 5441 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.80 % Favored : 92.10 % Rotamer: Outliers : 0.06 % Allowed : 0.18 % Favored : 99.77 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.87 (0.19), residues: 1974 helix: 1.08 (0.21), residues: 616 sheet: -0.45 (0.25), residues: 442 loop : -1.85 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 207 HIS 0.007 0.001 HIS K 991 PHE 0.018 0.001 PHE L 257 TYR 0.017 0.001 TYR K 871 ARG 0.004 0.000 ARG H 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 14 is missing expected H atoms. Skipping. Residue TYR 906 is missing expected H atoms. Skipping. Evaluate side-chains 403 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 402 time to evaluate : 2.704 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8471 (tppt) cc_final: 0.7742 (tptp) REVERT: A 69 GLN cc_start: 0.8557 (pt0) cc_final: 0.8312 (pt0) REVERT: A 91 MET cc_start: 0.7792 (mmm) cc_final: 0.7567 (mmm) REVERT: B 50 LEU cc_start: 0.8983 (mt) cc_final: 0.8221 (tp) REVERT: B 85 MET cc_start: 0.7287 (mmm) cc_final: 0.7052 (tpt) REVERT: B 89 TYR cc_start: 0.8689 (m-10) cc_final: 0.8385 (m-80) REVERT: B 94 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8106 (tt0) REVERT: C 93 GLU cc_start: 0.7508 (mp0) cc_final: 0.7165 (mm-30) REVERT: D 117 LYS cc_start: 0.8774 (mtpp) cc_final: 0.8465 (ttmm) REVERT: E 60 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7955 (tm-30) REVERT: E 95 GLU cc_start: 0.8584 (tp30) cc_final: 0.8352 (tp30) REVERT: G 24 LEU cc_start: 0.8533 (mp) cc_final: 0.8233 (mp) REVERT: G 75 LYS cc_start: 0.8913 (mtmm) cc_final: 0.8227 (tmtt) REVERT: H 57 SER cc_start: 0.8755 (p) cc_final: 0.8326 (t) REVERT: K 91 TYR cc_start: 0.7906 (t80) cc_final: 0.7485 (t80) REVERT: K 96 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7744 (tm-30) REVERT: K 130 MET cc_start: 0.7095 (ppp) cc_final: 0.6198 (pmm) REVERT: K 166 ASP cc_start: 0.7505 (t70) cc_final: 0.7118 (t0) REVERT: K 305 LEU cc_start: 0.8547 (mp) cc_final: 0.8214 (mt) REVERT: K 844 LYS cc_start: 0.8686 (mmtt) cc_final: 0.8314 (tppt) REVERT: K 905 HIS cc_start: 0.5082 (t70) cc_final: 0.4747 (t70) REVERT: K 953 TRP cc_start: 0.8522 (m100) cc_final: 0.8094 (m100) REVERT: K 973 ASN cc_start: 0.8376 (m-40) cc_final: 0.8043 (m-40) REVERT: K 1089 ILE cc_start: 0.8952 (mm) cc_final: 0.8733 (mp) REVERT: L 251 ASN cc_start: 0.8869 (t0) cc_final: 0.8648 (t0) REVERT: L 341 LYS cc_start: 0.9057 (mttt) cc_final: 0.8746 (tttp) outliers start: 1 outliers final: 1 residues processed: 402 average time/residue: 0.8167 time to fit residues: 481.8126 Evaluate side-chains 364 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 363 time to evaluate : 3.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 211 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 222 optimal weight: 3.9990 chunk 204 optimal weight: 0.0970 chunk 176 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 885 ASN ** L 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.5782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 22723 Z= 0.331 Angle : 0.755 26.838 31952 Z= 0.422 Chirality : 0.069 1.823 3604 Planarity : 0.005 0.062 3077 Dihedral : 26.239 179.120 5441 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.02 % Favored : 90.83 % Rotamer: Outliers : 0.06 % Allowed : 0.18 % Favored : 99.77 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.18), residues: 1974 helix: 0.50 (0.21), residues: 616 sheet: -0.59 (0.25), residues: 442 loop : -1.99 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 418 HIS 0.010 0.002 HIS L 333 PHE 0.026 0.002 PHE L 334 TYR 0.058 0.002 TYR F 89 ARG 0.017 0.001 ARG K 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 14 is missing expected H atoms. Skipping. Residue TYR 906 is missing expected H atoms. Skipping. Evaluate side-chains 413 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 412 time to evaluate : 2.925 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8529 (tppt) cc_final: 0.7808 (tptp) REVERT: A 69 GLN cc_start: 0.8661 (pt0) cc_final: 0.8400 (pt0) REVERT: A 91 MET cc_start: 0.7907 (mmm) cc_final: 0.7684 (mmm) REVERT: B 50 LEU cc_start: 0.9023 (mt) cc_final: 0.8263 (tp) REVERT: B 85 MET cc_start: 0.7414 (mmm) cc_final: 0.7214 (tpt) REVERT: B 89 TYR cc_start: 0.8708 (m-10) cc_final: 0.8360 (m-80) REVERT: B 94 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8187 (tt0) REVERT: C 93 GLU cc_start: 0.7483 (mp0) cc_final: 0.7210 (mm-30) REVERT: D 117 LYS cc_start: 0.8837 (mtpp) cc_final: 0.8521 (ttmm) REVERT: E 95 GLU cc_start: 0.8728 (tp30) cc_final: 0.8486 (tp30) REVERT: G 24 LEU cc_start: 0.8594 (mp) cc_final: 0.8335 (mp) REVERT: G 75 LYS cc_start: 0.8927 (mtmm) cc_final: 0.8272 (tmtt) REVERT: G 76 LYS cc_start: 0.8673 (mttm) cc_final: 0.8378 (mtpt) REVERT: H 57 SER cc_start: 0.8801 (p) cc_final: 0.8338 (t) REVERT: H 89 THR cc_start: 0.8624 (p) cc_final: 0.8360 (p) REVERT: K 91 TYR cc_start: 0.8034 (t80) cc_final: 0.7480 (t80) REVERT: K 96 GLU cc_start: 0.8483 (mm-30) cc_final: 0.7751 (tm-30) REVERT: K 130 MET cc_start: 0.7144 (ppp) cc_final: 0.6172 (pmm) REVERT: K 840 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7675 (mt-10) REVERT: K 905 HIS cc_start: 0.5289 (t70) cc_final: 0.5001 (t70) REVERT: K 1054 MET cc_start: 0.8521 (mmp) cc_final: 0.8266 (mmm) REVERT: L 265 GLN cc_start: 0.8265 (mt0) cc_final: 0.7840 (mp10) REVERT: L 268 LYS cc_start: 0.8378 (mttm) cc_final: 0.7921 (mttp) REVERT: L 341 LYS cc_start: 0.9117 (mttt) cc_final: 0.8837 (tttt) outliers start: 1 outliers final: 1 residues processed: 412 average time/residue: 0.8515 time to fit residues: 513.1142 Evaluate side-chains 371 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 370 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 163 optimal weight: 6.9990 chunk 26 optimal weight: 0.2980 chunk 49 optimal weight: 0.4980 chunk 177 optimal weight: 7.9990 chunk 74 optimal weight: 0.0970 chunk 181 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.150307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.123946 restraints weight = 95346.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.127763 restraints weight = 45407.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.130199 restraints weight = 27163.598| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.5841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22723 Z= 0.179 Angle : 0.678 25.718 31952 Z= 0.375 Chirality : 0.066 1.733 3604 Planarity : 0.004 0.055 3077 Dihedral : 26.179 178.855 5441 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.74 % Favored : 93.11 % Rotamer: Outliers : 0.06 % Allowed : 0.18 % Favored : 99.77 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.19), residues: 1974 helix: 1.36 (0.21), residues: 614 sheet: -0.38 (0.25), residues: 437 loop : -1.81 (0.19), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 320 HIS 0.010 0.001 HIS L 123 PHE 0.023 0.001 PHE K 972 TYR 0.013 0.001 TYR K 871 ARG 0.006 0.000 ARG L 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11247.00 seconds wall clock time: 198 minutes 18.83 seconds (11898.83 seconds total)