Starting phenix.real_space_refine (version: dev) on Fri Feb 24 22:55:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ven_21157/02_2023/6ven_21157_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ven_21157/02_2023/6ven_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_2023/6ven_21157.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ven_21157/02_2023/6ven_21157.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ven_21157/02_2023/6ven_21157_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ven_21157/02_2023/6ven_21157_updated.pdb" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 13.39, per 1000 atoms: 0.56 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: 11.38 Conformation dependent library (CDL) restraints added in 2.8 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: 9.17 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: 11.22 Time building geometry restraints manager: 11.97 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: 12187 30.94 - 61.89: 1763 61.89 - 92.83: 70 92.83 - 123.78: 1 123.78 - 154.72: 2 Dihedral angle restraints: 14023 sinusoidal: 7418 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 14020 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 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. 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: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 16.410 Check model and map are aligned: 0.360 Process input model: 76.440 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.200 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 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 : 23.330 154.722 9745 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 % 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 *********************** 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 : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 293 average time/residue: 0.4435 time to fit residues: 189.7355 Evaluate side-chains 202 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 2.272 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2897 ------------------------------------------------------------------------------- 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: 9.9990 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 R 304 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.063 25070 Z= 0.511 Angle : 0.724 10.985 35149 Z= 0.399 Chirality : 0.046 0.254 3981 Planarity : 0.005 0.081 3455 Dihedral : 27.134 157.590 5411 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer Outliers : 3.03 % 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: 768 sheet: -1.82 (0.25), residues: 380 loop : -2.56 (0.17), residues: 1038 *********************** 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 256 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 197 time to evaluate : 2.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 36 residues processed: 243 average time/residue: 0.3866 time to fit residues: 145.6244 Evaluate side-chains 218 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 182 time to evaluate : 2.639 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.2821 time to fit residues: 21.5569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 124 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 186 optimal weight: 4.9990 chunk 152 optimal weight: 0.0270 chunk 61 optimal weight: 0.7980 chunk 224 optimal weight: 9.9990 chunk 242 optimal weight: 9.9990 chunk 200 optimal weight: 9.9990 chunk 222 optimal weight: 30.0000 chunk 76 optimal weight: 2.9990 chunk 180 optimal weight: 9.9990 overall best weight: 1.1040 ------------------------------------------------------------------------------- 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 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 319 ASN M 361 ASN Q 127 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1595 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= 0.221 Angle : 0.592 11.283 35149 Z= 0.333 Chirality : 0.040 0.167 3981 Planarity : 0.004 0.079 3455 Dihedral : 26.718 157.657 5411 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer Outliers : 2.16 % 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: -1.79 (0.17), residues: 2186 helix: 0.20 (0.18), residues: 780 sheet: -1.43 (0.26), residues: 375 loop : -2.20 (0.17), residues: 1031 *********************** 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 260 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 218 time to evaluate : 2.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 16 residues processed: 254 average time/residue: 0.3914 time to fit residues: 154.0978 Evaluate side-chains 204 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 188 time to evaluate : 2.473 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2128 time to fit residues: 9.4411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 222 optimal weight: 30.0000 chunk 168 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 150 optimal weight: 5.9990 chunk 225 optimal weight: 5.9990 chunk 238 optimal weight: 20.0000 chunk 117 optimal weight: 3.9990 chunk 213 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 238 HIS M 199 HIS ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 249 ASN N 821 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 25070 Z= 0.382 Angle : 0.644 10.035 35149 Z= 0.358 Chirality : 0.043 0.336 3981 Planarity : 0.005 0.067 3455 Dihedral : 26.884 158.408 5411 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer Outliers : 2.98 % 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: 0.25 (0.18), residues: 770 sheet: -1.32 (0.27), residues: 371 loop : -2.09 (0.17), residues: 1045 *********************** 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 256 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 198 time to evaluate : 2.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 31 residues processed: 246 average time/residue: 0.3888 time to fit residues: 148.5830 Evaluate side-chains 216 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 185 time to evaluate : 2.389 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2326 time to fit residues: 16.6086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 198 optimal weight: 0.7980 chunk 135 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 177 optimal weight: 20.0000 chunk 98 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 chunk 165 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 121 optimal weight: 0.9990 chunk 214 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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** M 216 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 25070 Z= 0.291 Angle : 0.610 10.924 35149 Z= 0.340 Chirality : 0.041 0.264 3981 Planarity : 0.004 0.062 3455 Dihedral : 26.784 159.331 5411 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer Outliers : 1.85 % 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: -1.41 (0.17), residues: 2186 helix: 0.47 (0.18), residues: 771 sheet: -1.13 (0.27), residues: 370 loop : -1.97 (0.18), residues: 1045 *********************** 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 233 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 197 time to evaluate : 2.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 21 residues processed: 228 average time/residue: 0.3903 time to fit residues: 137.4433 Evaluate side-chains 207 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 186 time to evaluate : 2.397 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 21 outliers final: 1 residues processed: 21 average time/residue: 0.2391 time to fit residues: 12.8582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 140 optimal weight: 0.0270 chunk 58 optimal weight: 0.8980 chunk 238 optimal weight: 20.0000 chunk 198 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 overall best weight: 1.3042 ------------------------------------------------------------------------------- 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 ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 821 ASN N 912 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 25070 Z= 0.245 Angle : 0.587 10.878 35149 Z= 0.328 Chirality : 0.040 0.215 3981 Planarity : 0.004 0.059 3455 Dihedral : 26.650 159.421 5411 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 1.13 % 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: -1.22 (0.18), residues: 2186 helix: 0.64 (0.19), residues: 773 sheet: -1.08 (0.27), residues: 378 loop : -1.84 (0.18), residues: 1035 *********************** 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 221 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 199 time to evaluate : 2.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 8 residues processed: 214 average time/residue: 0.4428 time to fit residues: 144.5566 Evaluate side-chains 197 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 189 time to evaluate : 2.392 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.3394 time to fit residues: 7.4677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 230 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 174 optimal weight: 0.0470 chunk 135 optimal weight: 10.0000 chunk 201 optimal weight: 9.9990 chunk 133 optimal weight: 0.9990 chunk 238 optimal weight: 20.0000 chunk 148 optimal weight: 0.3980 chunk 145 optimal weight: 0.6980 chunk 109 optimal weight: 9.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- 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 H 49 HIS ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8433 moved from start: 0.2549 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= 0.172 Angle : 0.557 10.887 35149 Z= 0.311 Chirality : 0.038 0.184 3981 Planarity : 0.004 0.061 3455 Dihedral : 26.377 159.152 5411 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer Outliers : 0.93 % 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: -0.88 (0.18), residues: 2186 helix: 0.98 (0.19), residues: 765 sheet: -0.78 (0.27), residues: 366 loop : -1.73 (0.18), residues: 1055 *********************** 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 238 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 220 time to evaluate : 2.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 236 average time/residue: 0.4117 time to fit residues: 147.5531 Evaluate side-chains 205 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 198 time to evaluate : 2.393 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.2170 time to fit residues: 5.9716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 147 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 187 optimal weight: 7.9990 chunk 216 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 ** 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: 0.8470 moved from start: 0.2589 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= 0.245 Angle : 0.583 10.728 35149 Z= 0.324 Chirality : 0.040 0.334 3981 Planarity : 0.004 0.058 3455 Dihedral : 26.505 159.386 5411 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer Outliers : 0.82 % 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: -0.89 (0.18), residues: 2186 helix: 0.90 (0.19), residues: 769 sheet: -0.80 (0.27), residues: 368 loop : -1.66 (0.18), residues: 1049 *********************** 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 219 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 203 time to evaluate : 2.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 210 average time/residue: 0.4078 time to fit residues: 131.1638 Evaluate side-chains 205 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 194 time to evaluate : 2.397 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.2234 time to fit residues: 7.9187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 228 optimal weight: 9.9990 chunk 208 optimal weight: 3.9990 chunk 221 optimal weight: 0.9990 chunk 133 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 200 optimal weight: 6.9990 chunk 209 optimal weight: 8.9990 chunk 145 optimal weight: 0.9990 chunk 234 optimal weight: 7.9990 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 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 292 HIS ** N 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2624 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= 0.260 Angle : 0.592 10.796 35149 Z= 0.328 Chirality : 0.040 0.340 3981 Planarity : 0.004 0.057 3455 Dihedral : 26.502 160.151 5411 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 0.41 % 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: -0.88 (0.18), residues: 2186 helix: 0.84 (0.19), residues: 774 sheet: -0.70 (0.28), residues: 360 loop : -1.66 (0.18), residues: 1052 *********************** 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 207 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 199 time to evaluate : 2.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 204 average time/residue: 0.4018 time to fit residues: 126.6494 Evaluate side-chains 197 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 191 time to evaluate : 2.513 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.2353 time to fit residues: 5.8095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 143 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 163 optimal weight: 2.9990 chunk 246 optimal weight: 9.9990 chunk 226 optimal weight: 0.6980 chunk 195 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 120 optimal weight: 0.0470 chunk 155 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 overall best weight: 1.5482 ------------------------------------------------------------------------------- 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 40 GLN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 912 GLN ** O 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 127 ASN ** 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: 0.8483 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 25070 Z= 0.276 Angle : 0.602 10.891 35149 Z= 0.333 Chirality : 0.040 0.337 3981 Planarity : 0.004 0.057 3455 Dihedral : 26.543 160.729 5411 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer Outliers : 0.21 % 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: -0.89 (0.18), residues: 2186 helix: 0.82 (0.19), residues: 774 sheet: -0.75 (0.28), residues: 361 loop : -1.63 (0.18), residues: 1051 ********************** 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 199 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 195 time to evaluate : 2.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 198 average time/residue: 0.4123 time to fit residues: 124.4194 Evaluate side-chains 190 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 189 time to evaluate : 2.504 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2179 time to fit residues: 3.6415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 60 optimal weight: 0.7980 chunk 180 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 196 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 201 optimal weight: 0.8980 chunk 24 optimal weight: 0.0050 chunk 36 optimal weight: 0.8980 chunk 172 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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** ** O 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.126439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.083322 restraints weight = 56194.308| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.54 r_work: 0.2970 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2863 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= 0.176 Angle : 0.565 11.061 35149 Z= 0.314 Chirality : 0.039 0.316 3981 Planarity : 0.004 0.056 3455 Dihedral : 26.307 160.699 5411 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer Outliers : 0.31 % 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: -0.70 (0.18), residues: 2186 helix: 1.04 (0.19), residues: 771 sheet: -0.73 (0.27), residues: 373 loop : -1.54 (0.18), residues: 1042 =============================================================================== Job complete usr+sys time: 4449.74 seconds wall clock time: 82 minutes 36.31 seconds (4956.31 seconds total)