Starting phenix.real_space_refine on Mon Feb 19 07:13:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ven_21157/02_2024/6ven_21157_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ven_21157/02_2024/6ven_21157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ven_21157/02_2024/6ven_21157.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ven_21157/02_2024/6ven_21157.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ven_21157/02_2024/6ven_21157_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ven_21157/02_2024/6ven_21157_updated.pdb" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 292 5.49 5 S 73 5.16 5 C 14264 2.51 5 N 4291 2.21 5 O 5107 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 2": "NH1" <-> "NH2" Residue "A ARG 8": "NH1" <-> "NH2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "F PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K ARG 42": "NH1" <-> "NH2" Residue "K ASP 52": "OD1" <-> "OD2" Residue "K ASP 58": "OD1" <-> "OD2" Residue "K ARG 74": "NH1" <-> "NH2" Residue "L ARG 56": "NH1" <-> "NH2" Residue "L PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 106": "NH1" <-> "NH2" Residue "L ASP 117": "OD1" <-> "OD2" Residue "L ARG 185": "NH1" <-> "NH2" Residue "L ARG 202": "NH1" <-> "NH2" Residue "L ASP 210": "OD1" <-> "OD2" Residue "M GLU 14": "OE1" <-> "OE2" Residue "M ARG 28": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M ARG 73": "NH1" <-> "NH2" Residue "M GLU 110": "OE1" <-> "OE2" Residue "M ARG 112": "NH1" <-> "NH2" Residue "M ARG 128": "NH1" <-> "NH2" Residue "M TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 293": "OE1" <-> "OE2" Residue "M GLU 309": "OE1" <-> "OE2" Residue "M ARG 394": "NH1" <-> "NH2" Residue "M ARG 396": "NH1" <-> "NH2" Residue "M GLU 397": "OE1" <-> "OE2" Residue "M ARG 402": "NH1" <-> "NH2" Residue "M ARG 410": "NH1" <-> "NH2" Residue "M ARG 419": "NH1" <-> "NH2" Residue "N ARG 944": "NH1" <-> "NH2" Residue "N GLU 962": "OE1" <-> "OE2" Residue "N ARG 971": "NH1" <-> "NH2" Residue "N ARG 1034": "NH1" <-> "NH2" Residue "O ARG 53": "NH1" <-> "NH2" Residue "O ARG 61": "NH1" <-> "NH2" Residue "O ARG 67": "NH1" <-> "NH2" Residue "O GLU 84": "OE1" <-> "OE2" Residue "O GLU 99": "OE1" <-> "OE2" Residue "O ARG 188": "NH1" <-> "NH2" Residue "O GLU 194": "OE1" <-> "OE2" Residue "O GLU 212": "OE1" <-> "OE2" Residue "O GLU 253": "OE1" <-> "OE2" Residue "O ARG 257": "NH1" <-> "NH2" Residue "O ARG 258": "NH1" <-> "NH2" Residue "O GLU 294": "OE1" <-> "OE2" Residue "O ARG 297": "NH1" <-> "NH2" Residue "O PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 449": "NH1" <-> "NH2" Residue "O GLU 454": "OE1" <-> "OE2" Residue "O ARG 464": "NH1" <-> "NH2" Residue "O GLU 484": "OE1" <-> "OE2" Residue "P TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 139": "NH1" <-> "NH2" Residue "P ARG 151": "NH1" <-> "NH2" Residue "Q ARG 139": "NH1" <-> "NH2" Residue "Q ARG 151": "NH1" <-> "NH2" Residue "Q GLU 155": "OE1" <-> "OE2" Residue "R ASP 229": "OD1" <-> "OD2" Residue "R GLU 240": "OE1" <-> "OE2" Residue "R GLU 327": "OE1" <-> "OE2" Residue "R ARG 328": "NH1" <-> "NH2" Residue "R ARG 336": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24028 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 871 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'NLE:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 727 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'NLE:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "F" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 732 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 597 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "L" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2367 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 11, 'TRANS': 296} Chain breaks: 2 Chain: "M" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3183 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 377} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1710 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain breaks: 3 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "O" Number of atoms: 2595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2595 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 12, 'TRANS': 302} Chain breaks: 8 Chain: "P" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 336 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "Q" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 26} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 966 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19473 SG CYS N1019 84.930 78.071 29.381 1.00134.18 S ATOM 19794 SG CYS N1068 84.039 81.697 29.593 1.00129.18 S ATOM 19808 SG CYS N1070 87.089 80.901 27.747 1.00138.24 S Time building chain proxies: 12.86, per 1000 atoms: 0.54 Number of scatterers: 24028 At special positions: 0 Unit cell: (172.8, 143.64, 118.8, 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) Zn 1 29.99 S 73 16.00 P 292 15.00 O 5107 8.00 N 4291 7.00 C 14264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.89 Conformation dependent library (CDL) restraints added in 3.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN N1101 " pdb="ZN ZN N1101 " - pdb=" SG CYS N1019 " pdb="ZN ZN N1101 " - pdb=" SG CYS N1068 " pdb="ZN ZN N1101 " - pdb=" SG CYS N1070 " 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4278 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 23 sheets defined 32.4% alpha, 14.4% beta 142 base pairs and 244 stacking pairs defined. Time for finding SS restraints: 11.55 Creating SS restraints... Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.819A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.614A pdb=" N GLN A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 114 removed outlier: 4.106A pdb=" N TYR A 99 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N VAL A 101 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 131 removed outlier: 3.605A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 50 through 75 removed outlier: 4.464A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.899A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 21 No H-bonds generated for 'chain 'C' and resid 19 through 21' Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 47 through 72 removed outlier: 3.896A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 93 through 96 No H-bonds generated for 'chain 'C' and resid 93 through 96' Processing helix chain 'D' and resid 38 through 48 removed outlier: 3.642A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 83 Processing helix chain 'D' and resid 91 through 101 removed outlier: 3.528A pdb=" N GLN D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 121 removed outlier: 3.806A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.790A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 removed outlier: 3.572A pdb=" N ALA E 75 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 114 removed outlier: 4.478A pdb=" N TYR E 99 " --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL E 101 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASN E 108 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 130 removed outlier: 3.858A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.866A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.702A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 47 through 72 removed outlier: 3.817A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 93 through 96 No H-bonds generated for 'chain 'G' and resid 93 through 96' Processing helix chain 'H' and resid 38 through 48 removed outlier: 3.688A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 83 Processing helix chain 'H' and resid 93 through 101 Processing helix chain 'H' and resid 104 through 122 removed outlier: 4.244A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 34 Processing helix chain 'K' and resid 57 through 59 No H-bonds generated for 'chain 'K' and resid 57 through 59' Processing helix chain 'L' and resid 181 through 183 No H-bonds generated for 'chain 'L' and resid 181 through 183' Processing helix chain 'L' and resid 186 through 188 No H-bonds generated for 'chain 'L' and resid 186 through 188' Processing helix chain 'M' and resid 348 through 351 Processing helix chain 'M' and resid 418 through 420 No H-bonds generated for 'chain 'M' and resid 418 through 420' Processing helix chain 'N' and resid 804 through 824 Processing helix chain 'N' and resid 900 through 920 removed outlier: 4.518A pdb=" N ALA N 919 " --> pdb=" O GLU N 915 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ALA N 920 " --> pdb=" O ALA N 916 " (cutoff:3.500A) Processing helix chain 'N' and resid 974 through 986 Processing helix chain 'N' and resid 1011 through 1014 Processing helix chain 'O' and resid 244 through 260 removed outlier: 4.318A pdb=" N PHE O 260 " --> pdb=" O LYS O 256 " (cutoff:3.500A) Processing helix chain 'O' and resid 293 through 298 Processing helix chain 'O' and resid 385 through 391 Processing helix chain 'O' and resid 454 through 456 No H-bonds generated for 'chain 'O' and resid 454 through 456' Processing helix chain 'O' and resid 478 through 497 removed outlier: 3.582A pdb=" N GLU O 497 " --> pdb=" O ASP O 493 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 129 Processing helix chain 'P' and resid 131 through 143 Processing helix chain 'P' and resid 149 through 160 Processing helix chain 'Q' and resid 131 through 140 Processing helix chain 'Q' and resid 150 through 160 Processing helix chain 'R' and resid 203 through 240 removed outlier: 4.290A pdb=" N LEU R 209 " --> pdb=" O LYS R 205 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU R 210 " --> pdb=" O LYS R 206 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLU R 211 " --> pdb=" O LEU R 207 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LEU R 217 " --> pdb=" O TYR R 213 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASP R 218 " --> pdb=" O LEU R 214 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP R 228 " --> pdb=" O MET R 224 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASP R 229 " --> pdb=" O ARG R 225 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP R 230 " --> pdb=" O LYS R 226 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL R 235 " --> pdb=" O ALA R 231 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 282 No H-bonds generated for 'chain 'R' and resid 279 through 282' Processing helix chain 'R' and resid 311 through 348 removed outlier: 3.914A pdb=" N TYR R 315 " --> pdb=" O ASN R 311 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE R 342 " --> pdb=" O LYS R 338 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'K' and resid 12 through 16 Processing sheet with id= B, first strand: chain 'L' and resid 19 through 21 removed outlier: 3.558A pdb=" N LYS L 20 " --> pdb=" O ALA L 29 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA L 29 " --> pdb=" O LYS L 20 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL L 46 " --> pdb=" O ASP L 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'L' and resid 61 through 63 removed outlier: 3.560A pdb=" N CYS L 62 " --> pdb=" O ALA L 71 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA L 71 " --> pdb=" O CYS L 62 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N HIS L 83 " --> pdb=" O LEU L 88 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LEU L 88 " --> pdb=" O HIS L 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'L' and resid 101 through 104 removed outlier: 3.906A pdb=" N SER L 101 " --> pdb=" O SER L 114 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASP L 124 " --> pdb=" O LEU L 130 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU L 130 " --> pdb=" O ASP L 124 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 141 through 146 removed outlier: 6.876A pdb=" N GLY L 157 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL L 144 " --> pdb=" O SER L 155 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER L 155 " --> pdb=" O VAL L 144 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N VAL L 146 " --> pdb=" O ILE L 153 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ILE L 153 " --> pdb=" O VAL L 146 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS L 175 " --> pdb=" O ILE L 165 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ASP L 167 " --> pdb=" O CYS L 173 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N CYS L 173 " --> pdb=" O ASP L 167 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 192 through 197 removed outlier: 6.875A pdb=" N LYS L 207 " --> pdb=" O SER L 193 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N VAL L 195 " --> pdb=" O LEU L 205 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU L 205 " --> pdb=" O VAL L 195 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE L 197 " --> pdb=" O TYR L 203 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR L 203 " --> pdb=" O PHE L 197 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG L 225 " --> pdb=" O ILE L 215 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ASP L 217 " --> pdb=" O VAL L 223 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL L 223 " --> pdb=" O ASP L 217 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'L' and resid 243 through 246 removed outlier: 3.695A pdb=" N SER L 258 " --> pdb=" O TYR L 266 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN L 277 " --> pdb=" O CYS L 267 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ASN L 269 " --> pdb=" O LEU L 275 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU L 275 " --> pdb=" O ASN L 269 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 309 through 312 removed outlier: 3.929A pdb=" N MET L 300 " --> pdb=" O TRP L 312 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'M' and resid 40 through 44 Processing sheet with id= J, first strand: chain 'M' and resid 109 through 111 Processing sheet with id= K, first strand: chain 'M' and resid 140 through 143 removed outlier: 3.829A pdb=" N GLY M 119 " --> pdb=" O THR M 133 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'M' and resid 173 through 176 removed outlier: 3.821A pdb=" N VAL M 173 " --> pdb=" O GLY M 187 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS M 208 " --> pdb=" O PHE M 195 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LYS M 197 " --> pdb=" O CYS M 206 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N CYS M 206 " --> pdb=" O LYS M 197 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'M' and resid 220 through 222 removed outlier: 3.534A pdb=" N ILE M 221 " --> pdb=" O ALA M 230 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'M' and resid 244 through 246 removed outlier: 3.730A pdb=" N SER M 244 " --> pdb=" O GLU M 253 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU M 253 " --> pdb=" O SER M 244 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'M' and resid 269 through 274 removed outlier: 6.669A pdb=" N SER M 285 " --> pdb=" O ASN M 270 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE M 272 " --> pdb=" O VAL M 283 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL M 283 " --> pdb=" O ILE M 272 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'M' and resid 319 through 321 removed outlier: 3.717A pdb=" N HIS M 21 " --> pdb=" O VAL M 339 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N SER M 341 " --> pdb=" O LEU M 19 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LEU M 19 " --> pdb=" O SER M 341 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'N' and resid 940 through 944 Processing sheet with id= R, first strand: chain 'N' and resid 970 through 972 removed outlier: 3.720A pdb=" N THR N1001 " --> pdb=" O ASP N 998 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE N1003 " --> pdb=" O ARG N 996 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ARG N 996 " --> pdb=" O ILE N1003 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'N' and resid 1023 through 1030 removed outlier: 3.676A pdb=" N ILE N 965 " --> pdb=" O ILE N1038 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ALA N1040 " --> pdb=" O MET N 963 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N MET N 963 " --> pdb=" O ALA N1040 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'O' and resid 64 through 68 Processing sheet with id= U, first strand: chain 'O' and resid 69 through 71 Processing sheet with id= V, first strand: chain 'O' and resid 120 through 123 Processing sheet with id= W, first strand: chain 'O' and resid 449 through 451 removed outlier: 3.935A pdb=" N GLU O 136 " --> pdb=" O ILE O 451 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE O 368 " --> pdb=" O LEU O 355 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE O 357 " --> pdb=" O LYS O 366 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LYS O 366 " --> pdb=" O ILE O 357 " (cutoff:3.500A) 687 hydrogen bonds defined for protein. 1845 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 366 hydrogen bonds 732 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 244 stacking parallelities Total time for adding SS restraints: 12.92 Time building geometry restraints manager: 11.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6118 1.33 - 1.45: 6197 1.45 - 1.57: 12070 1.57 - 1.70: 582 1.70 - 1.82: 103 Bond restraints: 25070 Sorted by residual: bond pdb=" C THR K 14 " pdb=" N LEU K 15 " ideal model delta sigma weight residual 1.330 1.373 -0.043 1.31e-02 5.83e+03 1.06e+01 bond pdb=" CA PHE M 145 " pdb=" CB PHE M 145 " ideal model delta sigma weight residual 1.524 1.561 -0.037 1.33e-02 5.65e+03 7.77e+00 bond pdb=" C MET M 325 " pdb=" N SER M 326 " ideal model delta sigma weight residual 1.331 1.373 -0.042 1.51e-02 4.39e+03 7.64e+00 bond pdb=" N VAL Q 152 " pdb=" CA VAL Q 152 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.41e+00 bond pdb=" N ASN O 72 " pdb=" CA ASN O 72 " ideal model delta sigma weight residual 1.462 1.489 -0.027 1.05e-02 9.07e+03 6.79e+00 ... (remaining 25065 not shown) Histogram of bond angle deviations from ideal: 97.93 - 105.17: 1463 105.17 - 112.41: 13379 112.41 - 119.65: 8233 119.65 - 126.89: 11152 126.89 - 134.13: 922 Bond angle restraints: 35149 Sorted by residual: angle pdb=" CA VAL Q 152 " pdb=" C VAL Q 152 " pdb=" O VAL Q 152 " ideal model delta sigma weight residual 120.95 116.95 4.00 1.04e+00 9.25e-01 1.48e+01 angle pdb=" CA GLU O 324 " pdb=" CB GLU O 324 " pdb=" CG GLU O 324 " ideal model delta sigma weight residual 114.10 120.80 -6.70 2.00e+00 2.50e-01 1.12e+01 angle pdb=" CA LEU K 15 " pdb=" C LEU K 15 " pdb=" N GLU K 16 " ideal model delta sigma weight residual 115.51 119.72 -4.21 1.27e+00 6.20e-01 1.10e+01 angle pdb=" O LEU K 15 " pdb=" C LEU K 15 " pdb=" N GLU K 16 " ideal model delta sigma weight residual 122.86 119.01 3.85 1.18e+00 7.18e-01 1.07e+01 angle pdb=" C PHE O 323 " pdb=" N GLU O 324 " pdb=" CA GLU O 324 " ideal model delta sigma weight residual 122.72 127.15 -4.43 1.38e+00 5.25e-01 1.03e+01 ... (remaining 35144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.94: 12407 30.94 - 61.89: 1831 61.89 - 92.83: 70 92.83 - 123.78: 1 123.78 - 154.72: 2 Dihedral angle restraints: 14311 sinusoidal: 7706 harmonic: 6605 Sorted by residual: dihedral pdb=" CA ARG R 271 " pdb=" C ARG R 271 " pdb=" N ILE R 272 " pdb=" CA ILE R 272 " ideal model delta harmonic sigma weight residual 180.00 -154.97 -25.03 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA LEU R 207 " pdb=" C LEU R 207 " pdb=" N GLU R 208 " pdb=" CA GLU R 208 " ideal model delta harmonic sigma weight residual 180.00 155.78 24.22 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA PHE M 145 " pdb=" C PHE M 145 " pdb=" N SER M 146 " pdb=" CA SER M 146 " ideal model delta harmonic sigma weight residual 180.00 155.79 24.21 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 14308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3264 0.054 - 0.108: 604 0.108 - 0.162: 106 0.162 - 0.216: 3 0.216 - 0.270: 4 Chirality restraints: 3981 Sorted by residual: chirality pdb=" CB ILE H 89 " pdb=" CA ILE H 89 " pdb=" CG1 ILE H 89 " pdb=" CG2 ILE H 89 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA LEU Q 153 " pdb=" N LEU Q 153 " pdb=" C LEU Q 153 " pdb=" CB LEU Q 153 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB VAL Q 152 " pdb=" CA VAL Q 152 " pdb=" CG1 VAL Q 152 " pdb=" CG2 VAL Q 152 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 3978 not shown) Planarity restraints: 3455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN R 339 " -0.021 2.00e-02 2.50e+03 4.09e-02 1.67e+01 pdb=" C GLN R 339 " 0.071 2.00e-02 2.50e+03 pdb=" O GLN R 339 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU R 340 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 322 " -0.020 2.00e-02 2.50e+03 4.07e-02 1.65e+01 pdb=" C LEU R 322 " 0.070 2.00e-02 2.50e+03 pdb=" O LEU R 322 " -0.026 2.00e-02 2.50e+03 pdb=" N GLU R 323 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 341 " 0.019 2.00e-02 2.50e+03 3.75e-02 1.40e+01 pdb=" C ASN R 341 " -0.065 2.00e-02 2.50e+03 pdb=" O ASN R 341 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE R 342 " 0.022 2.00e-02 2.50e+03 ... (remaining 3452 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1799 2.73 - 3.27: 23189 3.27 - 3.81: 41459 3.81 - 4.36: 51055 4.36 - 4.90: 78874 Nonbonded interactions: 196376 Sorted by model distance: nonbonded pdb=" O LYS N1076 " pdb="ZN ZN N1101 " model vdw 2.184 2.230 nonbonded pdb=" OG SER L 114 " pdb=" O VAL L 141 " model vdw 2.216 2.440 nonbonded pdb=" OE1 GLN M 240 " pdb=" OH TYR M 260 " model vdw 2.234 2.440 nonbonded pdb=" OE1 GLU M 298 " pdb=" OG SER M 301 " model vdw 2.259 2.440 nonbonded pdb=" O PHE O 260 " pdb=" OG SER O 264 " model vdw 2.265 2.440 ... (remaining 196371 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 22 through 100) selection = (chain 'F' and resid 22 through 100) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 15 through 117) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 31 through 123) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 15.070 Check model and map are aligned: 0.370 Set scattering table: 0.240 Process input model: 79.430 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 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 : 0.004 0.043 25070 Z= 0.259 Angle : 0.695 8.942 35149 Z= 0.412 Chirality : 0.043 0.270 3981 Planarity : 0.005 0.085 3455 Dihedral : 23.367 154.722 10033 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.05 % Allowed : 8.49 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.15), residues: 2186 helix: -1.45 (0.16), residues: 767 sheet: -2.10 (0.25), residues: 369 loop : -3.05 (0.15), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 297 HIS 0.004 0.001 HIS F 75 PHE 0.030 0.002 PHE M 274 TYR 0.016 0.001 TYR O 482 ARG 0.005 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 292 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8135 (tt0) REVERT: D 68 ASP cc_start: 0.8198 (t0) cc_final: 0.7698 (t0) REVERT: K 39 ASP cc_start: 0.7554 (p0) cc_final: 0.7310 (p0) REVERT: K 42 ARG cc_start: 0.7393 (ttm170) cc_final: 0.6827 (ttp-170) REVERT: K 72 ARG cc_start: 0.6334 (ttp-110) cc_final: 0.5895 (ttp-170) REVERT: K 73 LEU cc_start: 0.5907 (tp) cc_final: 0.5378 (tt) REVERT: M 1 MET cc_start: 0.7776 (tpp) cc_final: 0.7304 (tpt) REVERT: M 94 TRP cc_start: 0.6718 (m-10) cc_final: 0.6291 (m-90) REVERT: N 815 ASP cc_start: 0.7848 (t0) cc_final: 0.7615 (p0) REVERT: N 974 GLN cc_start: 0.8246 (tp40) cc_final: 0.7967 (tp40) REVERT: N 979 MET cc_start: 0.7410 (tpt) cc_final: 0.7113 (tpp) REVERT: N 1000 ASN cc_start: 0.8602 (m110) cc_final: 0.8158 (m110) REVERT: O 135 TRP cc_start: 0.6220 (p90) cc_final: 0.5961 (p90) REVERT: O 224 GLU cc_start: 0.6616 (mp0) cc_final: 0.5242 (pm20) REVERT: R 214 LEU cc_start: 0.7961 (tt) cc_final: 0.7575 (pp) REVERT: R 327 GLU cc_start: 0.8127 (pp20) cc_final: 0.7869 (pp20) outliers start: 1 outliers final: 0 residues processed: 293 average time/residue: 0.4505 time to fit residues: 193.1151 Evaluate side-chains 205 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 2.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 208 optimal weight: 9.9990 chunk 187 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 126 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 193 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 chunk 224 optimal weight: 5.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN H 84 ASN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 ASN L 83 HIS L 172 HIS L 228 GLN M 15 HIS M 121 GLN M 199 HIS M 216 ASN M 268 GLN M 319 ASN ** M 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 821 ASN N 903 ASN N 912 GLN N 931 ASN N1080 ASN O 89 HIS O 181 HIS O 359 GLN P 127 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 25070 Z= 0.513 Angle : 0.729 11.034 35149 Z= 0.401 Chirality : 0.046 0.258 3981 Planarity : 0.005 0.080 3455 Dihedral : 27.003 158.143 5699 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.09 % Allowed : 15.53 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.16), residues: 2186 helix: -0.61 (0.17), residues: 767 sheet: -1.83 (0.25), residues: 380 loop : -2.54 (0.17), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 297 HIS 0.006 0.001 HIS F 75 PHE 0.037 0.002 PHE M 145 TYR 0.045 0.002 TYR Q 156 ARG 0.007 0.001 ARG O 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 199 time to evaluate : 2.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 6 LYS cc_start: 0.8404 (ttmm) cc_final: 0.7724 (tptp) REVERT: K 41 GLN cc_start: 0.6481 (pp30) cc_final: 0.6147 (pp30) REVERT: K 42 ARG cc_start: 0.7348 (ttm170) cc_final: 0.7136 (ttp-170) REVERT: K 43 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8529 (tt) REVERT: K 72 ARG cc_start: 0.6192 (ttp-110) cc_final: 0.5844 (ttp-170) REVERT: K 73 LEU cc_start: 0.5943 (tp) cc_final: 0.5273 (tt) REVERT: M 67 MET cc_start: 0.8021 (tpp) cc_final: 0.7734 (tpp) REVERT: M 145 PHE cc_start: 0.6831 (OUTLIER) cc_final: 0.6207 (p90) REVERT: M 325 MET cc_start: 0.9150 (tpp) cc_final: 0.8911 (ttm) REVERT: N 815 ASP cc_start: 0.7980 (t0) cc_final: 0.7599 (p0) REVERT: N 979 MET cc_start: 0.7616 (tpt) cc_final: 0.7255 (tpp) REVERT: O 135 TRP cc_start: 0.6209 (p90) cc_final: 0.5999 (p90) REVERT: Q 156 TYR cc_start: 0.6387 (p90) cc_final: 0.5865 (p90) REVERT: R 323 GLU cc_start: 0.8251 (mm-30) cc_final: 0.8015 (mm-30) REVERT: R 327 GLU cc_start: 0.8038 (pp20) cc_final: 0.7769 (pp20) outliers start: 60 outliers final: 36 residues processed: 247 average time/residue: 0.3815 time to fit residues: 144.3947 Evaluate side-chains 220 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 182 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 245 PHE Chi-restraints excluded: chain L residue 291 MET Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 145 PHE Chi-restraints excluded: chain M residue 174 CYS Chi-restraints excluded: chain M residue 180 HIS Chi-restraints excluded: chain M residue 199 HIS Chi-restraints excluded: chain M residue 249 ASN Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 265 ASN Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 319 ASN Chi-restraints excluded: chain N residue 821 ASN Chi-restraints excluded: chain N residue 968 VAL Chi-restraints excluded: chain N residue 1024 THR Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 199 PHE Chi-restraints excluded: chain O residue 352 ASP Chi-restraints excluded: chain O residue 440 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 124 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 186 optimal weight: 8.9990 chunk 152 optimal weight: 0.1980 chunk 61 optimal weight: 0.6980 chunk 224 optimal weight: 9.9990 chunk 242 optimal weight: 9.9990 chunk 200 optimal weight: 0.0670 chunk 222 optimal weight: 30.0000 chunk 76 optimal weight: 4.9990 chunk 180 optimal weight: 20.0000 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 149 ASN ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 224 GLN M 361 ASN ** N 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 127 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25070 Z= 0.168 Angle : 0.574 11.299 35149 Z= 0.323 Chirality : 0.039 0.162 3981 Planarity : 0.004 0.078 3455 Dihedral : 26.337 157.453 5699 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.52 % Allowed : 17.08 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.17), residues: 2186 helix: 0.36 (0.18), residues: 775 sheet: -1.43 (0.26), residues: 376 loop : -2.16 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 297 HIS 0.016 0.001 HIS M 199 PHE 0.019 0.001 PHE L 58 TYR 0.035 0.001 TYR Q 156 ARG 0.004 0.000 ARG L 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 232 time to evaluate : 2.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 80 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9174 (tp) REVERT: K 6 LYS cc_start: 0.8339 (ttmm) cc_final: 0.7732 (tptp) REVERT: K 41 GLN cc_start: 0.6688 (pp30) cc_final: 0.6351 (pp30) REVERT: K 42 ARG cc_start: 0.7301 (ttm170) cc_final: 0.7014 (ttp-170) REVERT: K 43 LEU cc_start: 0.9048 (tp) cc_final: 0.8592 (tt) REVERT: K 54 ARG cc_start: 0.7927 (mpt-90) cc_final: 0.7697 (mpt-90) REVERT: K 72 ARG cc_start: 0.6597 (ttp-110) cc_final: 0.6097 (ttp-170) REVERT: K 73 LEU cc_start: 0.6080 (tp) cc_final: 0.5548 (tt) REVERT: L 237 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7897 (pp) REVERT: N 815 ASP cc_start: 0.8072 (t0) cc_final: 0.7551 (p0) REVERT: N 963 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8557 (ttp) REVERT: N 979 MET cc_start: 0.7596 (tpt) cc_final: 0.7277 (tpp) REVERT: O 327 ASP cc_start: 0.6627 (OUTLIER) cc_final: 0.6110 (m-30) REVERT: O 381 LEU cc_start: 0.8455 (pt) cc_final: 0.8217 (pp) REVERT: Q 156 TYR cc_start: 0.6339 (OUTLIER) cc_final: 0.5998 (p90) REVERT: R 319 ILE cc_start: 0.5328 (mm) cc_final: 0.5042 (mm) REVERT: R 323 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8054 (mm-30) REVERT: R 327 GLU cc_start: 0.7989 (pp20) cc_final: 0.7698 (pp20) outliers start: 49 outliers final: 16 residues processed: 271 average time/residue: 0.3606 time to fit residues: 152.9357 Evaluate side-chains 216 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 195 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain L residue 237 LEU Chi-restraints excluded: chain L residue 245 PHE Chi-restraints excluded: chain L residue 256 VAL Chi-restraints excluded: chain M residue 200 SER Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 343 VAL Chi-restraints excluded: chain N residue 963 MET Chi-restraints excluded: chain N residue 1011 ILE Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 327 ASP Chi-restraints excluded: chain O residue 440 ILE Chi-restraints excluded: chain Q residue 156 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 222 optimal weight: 20.0000 chunk 168 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 chunk 107 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 225 optimal weight: 20.0000 chunk 238 optimal weight: 20.0000 chunk 117 optimal weight: 6.9990 chunk 213 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN ** L 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 821 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.068 25070 Z= 0.549 Angle : 0.716 8.782 35149 Z= 0.394 Chirality : 0.046 0.324 3981 Planarity : 0.005 0.068 3455 Dihedral : 26.882 159.168 5699 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.68 % Allowed : 17.70 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.17), residues: 2186 helix: 0.09 (0.18), residues: 768 sheet: -1.41 (0.26), residues: 373 loop : -2.17 (0.17), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 297 HIS 0.006 0.001 HIS L 137 PHE 0.036 0.002 PHE M 145 TYR 0.033 0.002 TYR Q 156 ARG 0.005 0.001 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 190 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 92 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8380 (ttt90) REVERT: D 85 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8613 (mmtp) REVERT: K 6 LYS cc_start: 0.8446 (ttmm) cc_final: 0.7661 (tptp) REVERT: K 34 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7124 (tp30) REVERT: K 41 GLN cc_start: 0.6719 (pp30) cc_final: 0.6323 (pp30) REVERT: K 42 ARG cc_start: 0.7277 (ttm170) cc_final: 0.7041 (ttp-170) REVERT: K 54 ARG cc_start: 0.7828 (mpt-90) cc_final: 0.7548 (mpt-90) REVERT: K 72 ARG cc_start: 0.6325 (ttp-110) cc_final: 0.5909 (ttp-170) REVERT: K 73 LEU cc_start: 0.6012 (tp) cc_final: 0.5455 (tt) REVERT: L 80 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6588 (mm-30) REVERT: L 237 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8118 (pp) REVERT: M 67 MET cc_start: 0.7881 (tpp) cc_final: 0.7618 (tpp) REVERT: N 815 ASP cc_start: 0.8159 (t0) cc_final: 0.7568 (p0) REVERT: N 979 MET cc_start: 0.7669 (tpt) cc_final: 0.7319 (tpp) REVERT: Q 156 TYR cc_start: 0.6444 (OUTLIER) cc_final: 0.6115 (p90) REVERT: R 323 GLU cc_start: 0.8280 (mm-30) cc_final: 0.8058 (mm-30) REVERT: R 327 GLU cc_start: 0.8119 (pp20) cc_final: 0.7790 (pp20) REVERT: R 329 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.7099 (mp) outliers start: 91 outliers final: 62 residues processed: 264 average time/residue: 0.3628 time to fit residues: 148.7080 Evaluate side-chains 251 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 184 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 237 LEU Chi-restraints excluded: chain L residue 245 PHE Chi-restraints excluded: chain L residue 256 VAL Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 53 TYR Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 180 HIS Chi-restraints excluded: chain M residue 216 ASN Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 225 ASN Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 255 THR Chi-restraints excluded: chain M residue 265 ASN Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain M residue 343 VAL Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain N residue 897 VAL Chi-restraints excluded: chain N residue 968 VAL Chi-restraints excluded: chain N residue 1011 ILE Chi-restraints excluded: chain N residue 1024 THR Chi-restraints excluded: chain O residue 125 ASP Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 199 PHE Chi-restraints excluded: chain O residue 331 THR Chi-restraints excluded: chain O residue 352 ASP Chi-restraints excluded: chain O residue 440 ILE Chi-restraints excluded: chain Q residue 127 ASN Chi-restraints excluded: chain Q residue 156 TYR Chi-restraints excluded: chain R residue 230 ASP Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 318 GLN Chi-restraints excluded: chain R residue 329 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 198 optimal weight: 0.0570 chunk 135 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 177 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 203 optimal weight: 9.9990 chunk 165 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 chunk 214 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.3500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN L 306 ASN ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25070 Z= 0.250 Angle : 0.591 10.996 35149 Z= 0.331 Chirality : 0.040 0.266 3981 Planarity : 0.004 0.064 3455 Dihedral : 26.486 159.941 5699 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.81 % Allowed : 18.72 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.17), residues: 2186 helix: 0.55 (0.19), residues: 768 sheet: -1.20 (0.26), residues: 376 loop : -1.98 (0.17), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 297 HIS 0.004 0.001 HIS F 75 PHE 0.025 0.001 PHE L 104 TYR 0.033 0.001 TYR Q 156 ARG 0.003 0.000 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 202 time to evaluate : 2.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 31 LYS cc_start: 0.7289 (mmpt) cc_final: 0.6759 (mmtt) REVERT: D 34 LYS cc_start: 0.8379 (mttm) cc_final: 0.8155 (tppt) REVERT: D 85 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8595 (mmtp) REVERT: K 6 LYS cc_start: 0.8395 (ttmm) cc_final: 0.7657 (tptp) REVERT: K 34 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7214 (tp30) REVERT: K 41 GLN cc_start: 0.6763 (pp30) cc_final: 0.6364 (pp30) REVERT: K 72 ARG cc_start: 0.6576 (ttp-110) cc_final: 0.6111 (ttp-170) REVERT: L 237 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8074 (pp) REVERT: M 67 MET cc_start: 0.7705 (tpp) cc_final: 0.7469 (tpp) REVERT: N 815 ASP cc_start: 0.8134 (t0) cc_final: 0.7546 (p0) REVERT: N 838 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6782 (pp20) REVERT: N 904 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7889 (ptp-110) REVERT: N 979 MET cc_start: 0.7596 (tpt) cc_final: 0.7250 (tpp) REVERT: O 381 LEU cc_start: 0.8421 (pt) cc_final: 0.8215 (pp) REVERT: Q 156 TYR cc_start: 0.6370 (OUTLIER) cc_final: 0.6074 (p90) REVERT: R 323 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8047 (mm-30) REVERT: R 327 GLU cc_start: 0.8073 (pp20) cc_final: 0.7655 (pp20) outliers start: 74 outliers final: 55 residues processed: 262 average time/residue: 0.3547 time to fit residues: 145.7447 Evaluate side-chains 250 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 190 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 104 PHE Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 237 LEU Chi-restraints excluded: chain L residue 245 PHE Chi-restraints excluded: chain L residue 256 VAL Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 249 ASN Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 265 ASN Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain M residue 343 VAL Chi-restraints excluded: chain N residue 821 ASN Chi-restraints excluded: chain N residue 838 GLU Chi-restraints excluded: chain N residue 897 VAL Chi-restraints excluded: chain N residue 904 ARG Chi-restraints excluded: chain N residue 968 VAL Chi-restraints excluded: chain N residue 1011 ILE Chi-restraints excluded: chain N residue 1070 CYS Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 331 THR Chi-restraints excluded: chain O residue 440 ILE Chi-restraints excluded: chain Q residue 127 ASN Chi-restraints excluded: chain Q residue 156 TYR Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 318 GLN Chi-restraints excluded: chain R residue 329 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 80 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 238 optimal weight: 20.0000 chunk 198 optimal weight: 0.8980 chunk 110 optimal weight: 0.0470 chunk 19 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 319 ASN N 912 GLN ** R 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25070 Z= 0.181 Angle : 0.553 11.054 35149 Z= 0.312 Chirality : 0.039 0.220 3981 Planarity : 0.004 0.061 3455 Dihedral : 26.174 159.202 5699 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.65 % Allowed : 19.34 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.18), residues: 2186 helix: 0.95 (0.19), residues: 765 sheet: -0.92 (0.27), residues: 365 loop : -1.84 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP O 135 HIS 0.003 0.001 HIS C 31 PHE 0.022 0.001 PHE N 910 TYR 0.033 0.001 TYR Q 156 ARG 0.003 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 205 time to evaluate : 2.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 31 LYS cc_start: 0.7306 (mmpt) cc_final: 0.6809 (mmtt) REVERT: D 85 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8625 (mmtp) REVERT: K 1 MET cc_start: 0.5777 (tpt) cc_final: 0.5576 (tpp) REVERT: K 6 LYS cc_start: 0.8340 (ttmm) cc_final: 0.7597 (tptp) REVERT: K 34 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7200 (tp30) REVERT: K 41 GLN cc_start: 0.6847 (pp30) cc_final: 0.6490 (pp30) REVERT: K 72 ARG cc_start: 0.6574 (ttp-110) cc_final: 0.6066 (ttp-170) REVERT: L 237 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7975 (pp) REVERT: M 262 ASP cc_start: 0.7071 (t0) cc_final: 0.6800 (t0) REVERT: M 325 MET cc_start: 0.9019 (tpp) cc_final: 0.8791 (ttm) REVERT: N 815 ASP cc_start: 0.8106 (t0) cc_final: 0.7579 (p0) REVERT: N 902 ASP cc_start: 0.8002 (m-30) cc_final: 0.7796 (m-30) REVERT: N 904 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7898 (ptp-110) REVERT: N 912 GLN cc_start: 0.7017 (pt0) cc_final: 0.6792 (pt0) REVERT: O 381 LEU cc_start: 0.8462 (pt) cc_final: 0.7756 (tt) REVERT: O 391 TYR cc_start: 0.4200 (OUTLIER) cc_final: 0.3629 (m-10) REVERT: Q 156 TYR cc_start: 0.6407 (OUTLIER) cc_final: 0.6065 (p90) REVERT: R 323 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8107 (mm-30) REVERT: R 327 GLU cc_start: 0.7976 (pp20) cc_final: 0.7639 (pp20) outliers start: 71 outliers final: 39 residues processed: 268 average time/residue: 0.3635 time to fit residues: 151.9867 Evaluate side-chains 241 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 197 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 104 PHE Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 237 LEU Chi-restraints excluded: chain L residue 256 VAL Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 216 ASN Chi-restraints excluded: chain M residue 265 ASN Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain N residue 904 ARG Chi-restraints excluded: chain N residue 968 VAL Chi-restraints excluded: chain N residue 1011 ILE Chi-restraints excluded: chain N residue 1070 CYS Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 331 THR Chi-restraints excluded: chain O residue 391 TYR Chi-restraints excluded: chain O residue 440 ILE Chi-restraints excluded: chain Q residue 127 ASN Chi-restraints excluded: chain Q residue 156 TYR Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 318 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 230 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 174 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 201 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 238 optimal weight: 20.0000 chunk 148 optimal weight: 0.4980 chunk 145 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 821 ASN R 326 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 25070 Z= 0.340 Angle : 0.617 10.593 35149 Z= 0.342 Chirality : 0.042 0.337 3981 Planarity : 0.004 0.057 3455 Dihedral : 26.478 160.257 5699 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.96 % Allowed : 19.34 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.18), residues: 2186 helix: 0.64 (0.19), residues: 779 sheet: -0.86 (0.28), residues: 360 loop : -1.79 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 297 HIS 0.006 0.001 HIS L 137 PHE 0.024 0.002 PHE M 145 TYR 0.032 0.001 TYR Q 156 ARG 0.004 0.000 ARG L 185 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 196 time to evaluate : 2.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 31 LYS cc_start: 0.7394 (mmpt) cc_final: 0.6740 (mmtt) REVERT: D 34 LYS cc_start: 0.8579 (tppt) cc_final: 0.8048 (mttm) REVERT: D 35 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8192 (mt-10) REVERT: D 85 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8617 (mmtp) REVERT: K 1 MET cc_start: 0.6288 (tpt) cc_final: 0.6079 (tpp) REVERT: K 6 LYS cc_start: 0.8370 (ttmm) cc_final: 0.7622 (tptp) REVERT: K 34 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7202 (tp30) REVERT: K 41 GLN cc_start: 0.7023 (pp30) cc_final: 0.6698 (pp30) REVERT: K 72 ARG cc_start: 0.6438 (ttp-110) cc_final: 0.6041 (ttp-170) REVERT: M 67 MET cc_start: 0.7758 (tpp) cc_final: 0.7399 (tpp) REVERT: M 145 PHE cc_start: 0.6448 (OUTLIER) cc_final: 0.6070 (p90) REVERT: M 325 MET cc_start: 0.9115 (tpp) cc_final: 0.8773 (ttm) REVERT: N 815 ASP cc_start: 0.7966 (t0) cc_final: 0.7400 (p0) REVERT: N 904 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7542 (ptp-110) REVERT: N 979 MET cc_start: 0.7467 (tpp) cc_final: 0.7205 (tpp) REVERT: O 381 LEU cc_start: 0.8429 (pt) cc_final: 0.7671 (tt) REVERT: O 391 TYR cc_start: 0.4258 (OUTLIER) cc_final: 0.3661 (m-10) REVERT: Q 156 TYR cc_start: 0.6262 (OUTLIER) cc_final: 0.5868 (p90) REVERT: R 323 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7769 (pp20) REVERT: R 327 GLU cc_start: 0.7999 (pp20) cc_final: 0.7668 (pp20) outliers start: 77 outliers final: 61 residues processed: 261 average time/residue: 0.3539 time to fit residues: 144.8309 Evaluate side-chains 255 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 189 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 104 PHE Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 256 VAL Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 145 PHE Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 216 ASN Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 249 ASN Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 265 ASN Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain N residue 821 ASN Chi-restraints excluded: chain N residue 904 ARG Chi-restraints excluded: chain N residue 968 VAL Chi-restraints excluded: chain N residue 1011 ILE Chi-restraints excluded: chain N residue 1070 CYS Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 125 ASP Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 199 PHE Chi-restraints excluded: chain O residue 264 SER Chi-restraints excluded: chain O residue 331 THR Chi-restraints excluded: chain O residue 391 TYR Chi-restraints excluded: chain O residue 440 ILE Chi-restraints excluded: chain Q residue 127 ASN Chi-restraints excluded: chain Q residue 156 TYR Chi-restraints excluded: chain R residue 230 ASP Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 318 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 147 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 151 optimal weight: 8.9990 chunk 162 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 187 optimal weight: 7.9990 chunk 216 optimal weight: 9.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 912 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25070 Z= 0.240 Angle : 0.579 10.761 35149 Z= 0.323 Chirality : 0.040 0.306 3981 Planarity : 0.004 0.056 3455 Dihedral : 26.294 160.791 5699 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.40 % Allowed : 20.01 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.18), residues: 2186 helix: 0.82 (0.19), residues: 778 sheet: -0.82 (0.27), residues: 375 loop : -1.68 (0.18), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 135 HIS 0.004 0.001 HIS C 31 PHE 0.018 0.001 PHE L 104 TYR 0.032 0.001 TYR Q 156 ARG 0.005 0.000 ARG L 185 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 194 time to evaluate : 2.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 31 LYS cc_start: 0.7386 (mmpt) cc_final: 0.6712 (mmmt) REVERT: D 34 LYS cc_start: 0.8650 (tppt) cc_final: 0.8034 (mttm) REVERT: D 85 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8572 (mmtp) REVERT: K 6 LYS cc_start: 0.8323 (ttmm) cc_final: 0.7585 (tptp) REVERT: K 34 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7221 (tp30) REVERT: K 41 GLN cc_start: 0.7073 (pp30) cc_final: 0.6838 (pp30) REVERT: K 72 ARG cc_start: 0.6363 (ttp-110) cc_final: 0.5964 (ttp-170) REVERT: M 67 MET cc_start: 0.7763 (tpp) cc_final: 0.7422 (tpp) REVERT: M 145 PHE cc_start: 0.6352 (OUTLIER) cc_final: 0.5938 (p90) REVERT: M 325 MET cc_start: 0.9093 (tpp) cc_final: 0.8749 (ttm) REVERT: N 904 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7728 (ptp-110) REVERT: N 979 MET cc_start: 0.7568 (tpp) cc_final: 0.7294 (tpp) REVERT: O 381 LEU cc_start: 0.8421 (pt) cc_final: 0.7666 (tt) REVERT: O 391 TYR cc_start: 0.4235 (OUTLIER) cc_final: 0.3595 (m-10) REVERT: Q 156 TYR cc_start: 0.6241 (OUTLIER) cc_final: 0.5864 (p90) REVERT: R 327 GLU cc_start: 0.8018 (pp20) cc_final: 0.7690 (pp20) outliers start: 66 outliers final: 55 residues processed: 249 average time/residue: 0.3640 time to fit residues: 141.4088 Evaluate side-chains 252 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 192 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 104 PHE Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 256 VAL Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 145 PHE Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 216 ASN Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 265 ASN Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain N residue 904 ARG Chi-restraints excluded: chain N residue 968 VAL Chi-restraints excluded: chain N residue 1011 ILE Chi-restraints excluded: chain N residue 1070 CYS Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 125 ASP Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 199 PHE Chi-restraints excluded: chain O residue 331 THR Chi-restraints excluded: chain O residue 391 TYR Chi-restraints excluded: chain O residue 440 ILE Chi-restraints excluded: chain Q residue 127 ASN Chi-restraints excluded: chain Q residue 156 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 318 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 228 optimal weight: 10.0000 chunk 208 optimal weight: 8.9990 chunk 221 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 200 optimal weight: 2.9990 chunk 209 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 234 optimal weight: 0.0050 overall best weight: 1.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 821 ASN N 912 GLN ** O 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 25070 Z= 0.323 Angle : 0.615 10.378 35149 Z= 0.339 Chirality : 0.041 0.314 3981 Planarity : 0.004 0.056 3455 Dihedral : 26.422 161.180 5699 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.55 % Allowed : 20.01 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.18), residues: 2186 helix: 0.72 (0.19), residues: 780 sheet: -0.71 (0.28), residues: 354 loop : -1.69 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 297 HIS 0.004 0.001 HIS L 137 PHE 0.022 0.002 PHE M 145 TYR 0.031 0.001 TYR Q 156 ARG 0.003 0.000 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 195 time to evaluate : 2.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 31 LYS cc_start: 0.7532 (mmpt) cc_final: 0.6815 (mmmt) REVERT: D 34 LYS cc_start: 0.8673 (tppt) cc_final: 0.8082 (mttm) REVERT: D 85 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8593 (mmtp) REVERT: G 99 ARG cc_start: 0.7998 (mmm-85) cc_final: 0.7792 (mmm160) REVERT: K 6 LYS cc_start: 0.8341 (ttmm) cc_final: 0.7596 (tptp) REVERT: K 41 GLN cc_start: 0.7115 (pp30) cc_final: 0.6875 (pp30) REVERT: K 72 ARG cc_start: 0.6373 (ttp-110) cc_final: 0.5994 (ttp-170) REVERT: M 145 PHE cc_start: 0.6473 (OUTLIER) cc_final: 0.6087 (p90) REVERT: N 904 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7516 (ptp-110) REVERT: N 979 MET cc_start: 0.7584 (tpp) cc_final: 0.7313 (tpp) REVERT: O 381 LEU cc_start: 0.8383 (pt) cc_final: 0.7650 (tt) REVERT: O 391 TYR cc_start: 0.4215 (OUTLIER) cc_final: 0.3641 (m-10) REVERT: Q 156 TYR cc_start: 0.6208 (OUTLIER) cc_final: 0.5914 (p90) REVERT: R 327 GLU cc_start: 0.8198 (pp20) cc_final: 0.7854 (pp20) outliers start: 69 outliers final: 64 residues processed: 254 average time/residue: 0.3695 time to fit residues: 145.5955 Evaluate side-chains 257 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 188 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 104 PHE Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 256 VAL Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 145 PHE Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 216 ASN Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 249 ASN Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 265 ASN Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain M residue 343 VAL Chi-restraints excluded: chain N residue 821 ASN Chi-restraints excluded: chain N residue 904 ARG Chi-restraints excluded: chain N residue 968 VAL Chi-restraints excluded: chain N residue 1011 ILE Chi-restraints excluded: chain N residue 1070 CYS Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 125 ASP Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 199 PHE Chi-restraints excluded: chain O residue 264 SER Chi-restraints excluded: chain O residue 331 THR Chi-restraints excluded: chain O residue 352 ASP Chi-restraints excluded: chain O residue 391 TYR Chi-restraints excluded: chain O residue 440 ILE Chi-restraints excluded: chain Q residue 127 ASN Chi-restraints excluded: chain Q residue 156 TYR Chi-restraints excluded: chain R residue 230 ASP Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 318 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 143 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 163 optimal weight: 1.9990 chunk 246 optimal weight: 0.6980 chunk 226 optimal weight: 0.4980 chunk 195 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 208 optimal weight: 9.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 168 HIS ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 821 ASN N 912 GLN ** O 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25070 Z= 0.261 Angle : 0.596 10.318 35149 Z= 0.330 Chirality : 0.040 0.295 3981 Planarity : 0.004 0.056 3455 Dihedral : 26.316 161.597 5699 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.65 % Allowed : 20.16 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.18), residues: 2186 helix: 0.84 (0.19), residues: 778 sheet: -0.67 (0.28), residues: 360 loop : -1.65 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP O 135 HIS 0.008 0.001 HIS M 292 PHE 0.022 0.001 PHE N 910 TYR 0.032 0.001 TYR Q 156 ARG 0.004 0.000 ARG E 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4372 Ramachandran restraints generated. 2186 Oldfield, 0 Emsley, 2186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 190 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 31 LYS cc_start: 0.7687 (mmpt) cc_final: 0.6936 (mmmt) REVERT: D 34 LYS cc_start: 0.8661 (tppt) cc_final: 0.8108 (mttm) REVERT: D 85 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8580 (mmtp) REVERT: G 99 ARG cc_start: 0.7961 (mmm-85) cc_final: 0.7755 (mmm160) REVERT: K 6 LYS cc_start: 0.8326 (ttmm) cc_final: 0.7585 (tptp) REVERT: K 34 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7256 (tp30) REVERT: K 41 GLN cc_start: 0.7191 (pp30) cc_final: 0.6943 (pp30) REVERT: K 72 ARG cc_start: 0.6355 (ttp-110) cc_final: 0.5940 (ttp-170) REVERT: M 145 PHE cc_start: 0.6361 (OUTLIER) cc_final: 0.5917 (p90) REVERT: M 206 CYS cc_start: 0.7011 (OUTLIER) cc_final: 0.6469 (m) REVERT: N 904 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7428 (ptp-110) REVERT: N 979 MET cc_start: 0.7582 (tpp) cc_final: 0.7301 (tpp) REVERT: O 381 LEU cc_start: 0.8372 (pt) cc_final: 0.7639 (tt) REVERT: O 391 TYR cc_start: 0.4040 (OUTLIER) cc_final: 0.3522 (m-10) REVERT: Q 156 TYR cc_start: 0.6127 (OUTLIER) cc_final: 0.5834 (p90) REVERT: R 214 LEU cc_start: 0.8186 (tp) cc_final: 0.7964 (pp) REVERT: R 327 GLU cc_start: 0.8203 (pp20) cc_final: 0.7848 (pp20) outliers start: 71 outliers final: 63 residues processed: 250 average time/residue: 0.3728 time to fit residues: 143.5469 Evaluate side-chains 261 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 192 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 104 PHE Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 256 VAL Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 145 PHE Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 178 THR Chi-restraints excluded: chain M residue 206 CYS Chi-restraints excluded: chain M residue 216 ASN Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 249 ASN Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 265 ASN Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain M residue 343 VAL Chi-restraints excluded: chain N residue 821 ASN Chi-restraints excluded: chain N residue 904 ARG Chi-restraints excluded: chain N residue 968 VAL Chi-restraints excluded: chain N residue 1011 ILE Chi-restraints excluded: chain N residue 1070 CYS Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain O residue 125 ASP Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 199 PHE Chi-restraints excluded: chain O residue 331 THR Chi-restraints excluded: chain O residue 352 ASP Chi-restraints excluded: chain O residue 391 TYR Chi-restraints excluded: chain O residue 440 ILE Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain Q residue 127 ASN Chi-restraints excluded: chain Q residue 156 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 318 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 60 optimal weight: 0.9990 chunk 180 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 196 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 201 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 821 ASN N 912 GLN ** O 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.125424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.082105 restraints weight = 56203.115| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.73 r_work: 0.2921 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25070 Z= 0.194 Angle : 0.570 10.414 35149 Z= 0.317 Chirality : 0.039 0.204 3981 Planarity : 0.004 0.056 3455 Dihedral : 26.101 161.384 5699 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.29 % Allowed : 20.42 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.18), residues: 2186 helix: 1.07 (0.19), residues: 769 sheet: -0.69 (0.27), residues: 368 loop : -1.54 (0.18), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP O 135 HIS 0.007 0.001 HIS M 292 PHE 0.023 0.001 PHE N 910 TYR 0.032 0.001 TYR Q 156 ARG 0.004 0.000 ARG D 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4694.06 seconds wall clock time: 86 minutes 6.84 seconds (5166.84 seconds total)