Starting phenix.real_space_refine on Tue Nov 21 14:29:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ltj_0974/11_2023/6ltj_0974.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ltj_0974/11_2023/6ltj_0974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ltj_0974/11_2023/6ltj_0974.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ltj_0974/11_2023/6ltj_0974.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ltj_0974/11_2023/6ltj_0974.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ltj_0974/11_2023/6ltj_0974.pdb" } resolution = 3.7 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= 0.107 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 238 5.49 5 S 150 5.16 5 C 20942 2.51 5 N 6119 2.21 5 O 6833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 47": "OE1" <-> "OE2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "F ARG 35": "NH1" <-> "NH2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "I ARG 370": "NH1" <-> "NH2" Residue "I ARG 408": "NH1" <-> "NH2" Residue "I GLU 449": "OE1" <-> "OE2" Residue "I GLU 861": "OE1" <-> "OE2" Residue "I ARG 1308": "NH1" <-> "NH2" Residue "J TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 80": "OE1" <-> "OE2" Residue "J GLU 114": "OE1" <-> "OE2" Residue "K GLU 83": "OE1" <-> "OE2" Residue "K GLU 167": "OE1" <-> "OE2" Residue "K GLU 205": "OE1" <-> "OE2" Residue "K PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 1718": "OE1" <-> "OE2" Residue "L ARG 1721": "NH1" <-> "NH2" Residue "L GLU 1956": "OE1" <-> "OE2" Residue "L GLU 2120": "OE1" <-> "OE2" Residue "L ARG 2232": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M ARG 190": "NH1" <-> "NH2" Residue "M ARG 201": "NH1" <-> "NH2" Residue "M PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 246": "OE1" <-> "OE2" Residue "M ARG 261": "NH1" <-> "NH2" Residue "M GLU 360": "OE1" <-> "OE2" Residue "N ARG 443": "NH1" <-> "NH2" Residue "N ARG 487": "NH1" <-> "NH2" Residue "N ARG 630": "NH1" <-> "NH2" Residue "N GLU 893": "OE1" <-> "OE2" Residue "N ARG 917": "NH1" <-> "NH2" Residue "N GLU 937": "OE1" <-> "OE2" Residue "O ARG 466": "NH1" <-> "NH2" Residue "O ARG 599": "NH1" <-> "NH2" Residue "O GLU 600": "OE1" <-> "OE2" Residue "O GLU 611": "OE1" <-> "OE2" Residue "O ARG 630": "NH1" <-> "NH2" Residue "O ARG 882": "NH1" <-> "NH2" Residue "P GLU 429": "OE1" <-> "OE2" Residue "P ARG 446": "NH1" <-> "NH2" Residue "P GLU 480": "OE1" <-> "OE2" Residue "P GLU 489": "OE1" <-> "OE2" Residue "P ARG 503": "NH1" <-> "NH2" Residue "Q ARG 201": "NH1" <-> "NH2" Residue "Q GLU 209": "OE1" <-> "OE2" Residue "Q ARG 223": "NH1" <-> "NH2" Residue "R GLU 58": "OE1" <-> "OE2" Residue "R ARG 62": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 34283 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 739 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 726 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "D" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 682 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "E" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 739 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "F" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "G" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 727 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "H" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 700 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "I" Number of atoms: 4606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4606 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 14, 'TRANS': 536} Chain breaks: 11 Chain: "J" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2612 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 15, 'TRANS': 318} Chain breaks: 4 Chain: "K" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2482 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain breaks: 3 Chain: "L" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3670 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 25, 'TRANS': 440} Chain breaks: 4 Chain: "M" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2277 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 13, 'TRANS': 269} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "N" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2120 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 6, 'TRANS': 254} Chain breaks: 3 Chain: "O" Number of atoms: 2632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2632 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 19, 'TRANS': 305} Chain breaks: 3 Chain: "P" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 2015 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 14, 'TRANS': 224} Chain breaks: 2 Chain: "Q" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 860 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "R" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 580 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "X" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2424 Classifications: {'DNA': 119} Link IDs: {'rna3p': 118} Chain: "Y" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2455 Classifications: {'DNA': 119} Link IDs: {'rna3p': 118} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17569 SG CYS L2094 67.231 67.353 64.589 1.00 48.48 S Time building chain proxies: 17.94, per 1000 atoms: 0.52 Number of scatterers: 34283 At special positions: 0 Unit cell: (223.6, 175.76, 183.04, 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 150 16.00 P 238 15.00 O 6833 8.00 N 6119 7.00 C 20942 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: 16.63 Conformation dependent library (CDL) restraints added in 5.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L2301 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L2019 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L2021 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L2090 " pdb="ZN ZN L2301 " - pdb=" SG CYS L2094 " Number of angles added : 3 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6972 Finding SS restraints... Secondary structure from input PDB file: 166 helices and 27 sheets defined 63.5% alpha, 5.3% beta 100 base pairs and 205 stacking pairs defined. Time for finding SS restraints: 14.26 Creating SS restraints... Processing helix chain 'A' and resid 42 through 54 Processing helix chain 'A' and resid 60 through 76 Processing helix chain 'A' and resid 82 through 111 Processing helix chain 'A' and resid 117 through 128 removed outlier: 3.876A pdb=" N ILE A 121 " --> pdb=" O MET A 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.808A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.985A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.640A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.690A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.885A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.569A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 119 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.875A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 50 through 76 removed outlier: 4.368A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.648A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.370A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.521A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 35 through 43 removed outlier: 3.865A pdb=" N VAL H 41 " --> pdb=" O TYR H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.520A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.633A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 387 removed outlier: 3.565A pdb=" N ASN I 387 " --> pdb=" O GLN I 383 " (cutoff:3.500A) Processing helix chain 'I' and resid 397 through 409 Processing helix chain 'I' and resid 409 through 428 removed outlier: 3.552A pdb=" N GLN I 415 " --> pdb=" O ASN I 411 " (cutoff:3.500A) Processing helix chain 'I' and resid 430 through 434 Processing helix chain 'I' and resid 446 through 517 removed outlier: 3.882A pdb=" N ALA I 450 " --> pdb=" O SER I 446 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN I 477 " --> pdb=" O GLN I 473 " (cutoff:3.500A) Processing helix chain 'I' and resid 757 through 768 Processing helix chain 'I' and resid 784 through 795 removed outlier: 4.023A pdb=" N TYR I 795 " --> pdb=" O ALA I 791 " (cutoff:3.500A) Processing helix chain 'I' and resid 812 through 826 removed outlier: 3.501A pdb=" N ASN I 817 " --> pdb=" O SER I 813 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N TRP I 818 " --> pdb=" O THR I 814 " (cutoff:3.500A) Processing helix chain 'I' and resid 839 through 844 Processing helix chain 'I' and resid 845 through 849 removed outlier: 3.794A pdb=" N LEU I 848 " --> pdb=" O VAL I 845 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG I 849 " --> pdb=" O PRO I 846 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 845 through 849' Processing helix chain 'I' and resid 893 through 898 removed outlier: 4.253A pdb=" N ASN I 898 " --> pdb=" O THR I 894 " (cutoff:3.500A) Processing helix chain 'I' and resid 899 through 901 No H-bonds generated for 'chain 'I' and resid 899 through 901' Processing helix chain 'I' and resid 917 through 925 Processing helix chain 'I' and resid 931 through 939 removed outlier: 3.712A pdb=" N SER I 935 " --> pdb=" O THR I 931 " (cutoff:3.500A) Processing helix chain 'I' and resid 972 through 976 removed outlier: 3.924A pdb=" N PHE I 975 " --> pdb=" O LEU I 972 " (cutoff:3.500A) Processing helix chain 'I' and resid 1001 through 1013 Processing helix chain 'I' and resid 1039 through 1048 Processing helix chain 'I' and resid 1055 through 1059 Processing helix chain 'I' and resid 1079 through 1089 Processing helix chain 'I' and resid 1107 through 1120 Processing helix chain 'I' and resid 1179 through 1182 removed outlier: 4.069A pdb=" N GLN I1182 " --> pdb=" O ASN I1179 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1179 through 1182' Processing helix chain 'I' and resid 1183 through 1192 removed outlier: 4.986A pdb=" N ALA I1190 " --> pdb=" O ALA I1186 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG I1192 " --> pdb=" O ASP I1188 " (cutoff:3.500A) Processing helix chain 'I' and resid 1300 through 1306 Processing helix chain 'I' and resid 1311 through 1323 removed outlier: 4.561A pdb=" N ARG I1323 " --> pdb=" O MET I1319 " (cutoff:3.500A) Processing helix chain 'I' and resid 1352 through 1362 Processing helix chain 'J' and resid 70 through 77 Processing helix chain 'J' and resid 95 through 110 Processing helix chain 'J' and resid 129 through 143 removed outlier: 3.709A pdb=" N HIS J 143 " --> pdb=" O LEU J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 154 through 162 Processing helix chain 'J' and resid 198 through 213 removed outlier: 3.555A pdb=" N MET J 213 " --> pdb=" O LEU J 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 248 through 266 Processing helix chain 'J' and resid 304 through 310 removed outlier: 3.549A pdb=" N GLY J 307 " --> pdb=" O ILE J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 324 through 335 Processing helix chain 'J' and resid 340 through 347 Processing helix chain 'J' and resid 359 through 371 removed outlier: 4.058A pdb=" N ARG J 363 " --> pdb=" O SER J 359 " (cutoff:3.500A) Processing helix chain 'J' and resid 391 through 399 Processing helix chain 'J' and resid 404 through 409 Processing helix chain 'K' and resid 80 through 91 Processing helix chain 'K' and resid 112 through 125 Processing helix chain 'K' and resid 137 through 146 Processing helix chain 'K' and resid 181 through 196 removed outlier: 4.067A pdb=" N ARG K 196 " --> pdb=" O ILE K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 204 through 216 removed outlier: 4.961A pdb=" N ARG K 210 " --> pdb=" O ARG K 206 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ASP K 211 " --> pdb=" O GLU K 207 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 231 Processing helix chain 'K' and resid 252 through 257 Processing helix chain 'K' and resid 258 through 261 Processing helix chain 'K' and resid 263 through 268 Processing helix chain 'K' and resid 273 through 284 Processing helix chain 'K' and resid 289 through 296 Processing helix chain 'K' and resid 301 through 305 Processing helix chain 'K' and resid 308 through 321 Processing helix chain 'K' and resid 337 through 345 removed outlier: 3.581A pdb=" N ILE K 345 " --> pdb=" O ILE K 341 " (cutoff:3.500A) Processing helix chain 'K' and resid 346 through 353 removed outlier: 5.799A pdb=" N SER K 350 " --> pdb=" O ALA K 347 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N THR K 351 " --> pdb=" O SER K 348 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN K 353 " --> pdb=" O SER K 350 " (cutoff:3.500A) Processing helix chain 'K' and resid 359 through 366 Processing helix chain 'K' and resid 367 through 372 removed outlier: 3.577A pdb=" N ARG K 372 " --> pdb=" O ILE K 369 " (cutoff:3.500A) Processing helix chain 'L' and resid 1645 through 1649 Processing helix chain 'L' and resid 1668 through 1679 removed outlier: 4.055A pdb=" N GLY L1679 " --> pdb=" O SER L1675 " (cutoff:3.500A) Processing helix chain 'L' and resid 1680 through 1697 Processing helix chain 'L' and resid 1698 through 1701 removed outlier: 3.727A pdb=" N ILE L1701 " --> pdb=" O ASP L1698 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1698 through 1701' Processing helix chain 'L' and resid 1705 through 1709 Processing helix chain 'L' and resid 1711 through 1729 Processing helix chain 'L' and resid 1740 through 1745 Processing helix chain 'L' and resid 1840 through 1846 removed outlier: 3.578A pdb=" N TRP L1844 " --> pdb=" O GLY L1840 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE L1846 " --> pdb=" O LEU L1842 " (cutoff:3.500A) Processing helix chain 'L' and resid 1971 through 1992 Processing helix chain 'L' and resid 1996 through 2002 removed outlier: 4.201A pdb=" N GLU L2000 " --> pdb=" O GLY L1996 " (cutoff:3.500A) Processing helix chain 'L' and resid 2004 through 2016 removed outlier: 4.406A pdb=" N LEU L2016 " --> pdb=" O GLY L2012 " (cutoff:3.500A) Processing helix chain 'L' and resid 2049 through 2068 removed outlier: 3.644A pdb=" N MET L2055 " --> pdb=" O ASP L2051 " (cutoff:3.500A) Processing helix chain 'L' and resid 2069 through 2071 No H-bonds generated for 'chain 'L' and resid 2069 through 2071' Processing helix chain 'L' and resid 2077 through 2094 Proline residue: L2083 - end of helix Processing helix chain 'L' and resid 2113 through 2127 Processing helix chain 'L' and resid 2128 through 2137 Processing helix chain 'L' and resid 2140 through 2158 removed outlier: 3.723A pdb=" N LEU L2144 " --> pdb=" O PRO L2140 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ARG L2158 " --> pdb=" O PHE L2154 " (cutoff:3.500A) Processing helix chain 'L' and resid 2160 through 2178 Processing helix chain 'L' and resid 2178 through 2187 removed outlier: 3.654A pdb=" N ALA L2182 " --> pdb=" O ASP L2178 " (cutoff:3.500A) Processing helix chain 'L' and resid 2190 through 2209 removed outlier: 3.703A pdb=" N GLN L2209 " --> pdb=" O ALA L2205 " (cutoff:3.500A) Processing helix chain 'L' and resid 2228 through 2243 Processing helix chain 'L' and resid 2247 through 2252 removed outlier: 3.552A pdb=" N PHE L2251 " --> pdb=" O ASN L2247 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR L2252 " --> pdb=" O HIS L2248 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 2247 through 2252' Processing helix chain 'L' and resid 2254 through 2264 Processing helix chain 'L' and resid 2268 through 2284 Processing helix chain 'M' and resid 29 through 36 Processing helix chain 'M' and resid 41 through 47 Processing helix chain 'M' and resid 56 through 66 Processing helix chain 'M' and resid 80 through 84 Processing helix chain 'M' and resid 93 through 98 Processing helix chain 'M' and resid 173 through 181 Processing helix chain 'M' and resid 214 through 226 Processing helix chain 'M' and resid 229 through 248 Proline residue: M 235 - end of helix Processing helix chain 'M' and resid 289 through 302 Processing helix chain 'M' and resid 305 through 324 removed outlier: 4.135A pdb=" N THR M 309 " --> pdb=" O GLY M 305 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA M 312 " --> pdb=" O VAL M 308 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS M 324 " --> pdb=" O SER M 320 " (cutoff:3.500A) Processing helix chain 'M' and resid 342 through 348 Processing helix chain 'M' and resid 357 through 381 removed outlier: 3.741A pdb=" N THR M 381 " --> pdb=" O ARG M 377 " (cutoff:3.500A) Processing helix chain 'N' and resid 427 through 431 Processing helix chain 'N' and resid 440 through 446 Processing helix chain 'N' and resid 447 through 452 removed outlier: 4.692A pdb=" N GLY N 452 " --> pdb=" O GLU N 448 " (cutoff:3.500A) Processing helix chain 'N' and resid 458 through 475 removed outlier: 3.532A pdb=" N LEU N 475 " --> pdb=" O ASP N 471 " (cutoff:3.500A) Processing helix chain 'N' and resid 482 through 490 removed outlier: 3.677A pdb=" N ASN N 489 " --> pdb=" O ALA N 485 " (cutoff:3.500A) Processing helix chain 'N' and resid 493 through 507 Processing helix chain 'N' and resid 603 through 616 Processing helix chain 'N' and resid 620 through 628 removed outlier: 3.553A pdb=" N SER N 624 " --> pdb=" O TRP N 620 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY N 628 " --> pdb=" O SER N 624 " (cutoff:3.500A) Processing helix chain 'N' and resid 631 through 641 Processing helix chain 'N' and resid 672 through 682 Processing helix chain 'N' and resid 685 through 702 Processing helix chain 'N' and resid 859 through 949 Processing helix chain 'O' and resid 439 through 446 removed outlier: 3.599A pdb=" N ARG O 443 " --> pdb=" O HIS O 439 " (cutoff:3.500A) Processing helix chain 'O' and resid 447 through 450 Processing helix chain 'O' and resid 458 through 475 Processing helix chain 'O' and resid 482 through 490 removed outlier: 3.824A pdb=" N CYS O 486 " --> pdb=" O THR O 482 " (cutoff:3.500A) Processing helix chain 'O' and resid 493 through 507 Processing helix chain 'O' and resid 602 through 616 Processing helix chain 'O' and resid 619 through 628 Processing helix chain 'O' and resid 631 through 641 Processing helix chain 'O' and resid 645 through 650 Processing helix chain 'O' and resid 657 through 661 removed outlier: 4.133A pdb=" N TYR O 661 " --> pdb=" O PRO O 658 " (cutoff:3.500A) Processing helix chain 'O' and resid 671 through 684 removed outlier: 3.740A pdb=" N THR O 676 " --> pdb=" O PRO O 672 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE O 679 " --> pdb=" O SER O 675 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL O 684 " --> pdb=" O LEU O 680 " (cutoff:3.500A) Processing helix chain 'O' and resid 685 through 705 removed outlier: 3.535A pdb=" N GLU O 705 " --> pdb=" O SER O 701 " (cutoff:3.500A) Processing helix chain 'O' and resid 711 through 716 Processing helix chain 'O' and resid 868 through 952 removed outlier: 4.276A pdb=" N LYS O 872 " --> pdb=" O ALA O 868 " (cutoff:3.500A) Processing helix chain 'P' and resid 128 through 132 removed outlier: 3.688A pdb=" N LYS P 131 " --> pdb=" O MET P 128 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE P 132 " --> pdb=" O ALA P 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 128 through 132' Processing helix chain 'P' and resid 134 through 141 Processing helix chain 'P' and resid 143 through 173 removed outlier: 3.606A pdb=" N TYR P 147 " --> pdb=" O GLU P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 298 through 306 Processing helix chain 'P' and resid 312 through 327 Processing helix chain 'P' and resid 353 through 355 No H-bonds generated for 'chain 'P' and resid 353 through 355' Processing helix chain 'P' and resid 356 through 361 Processing helix chain 'P' and resid 400 through 411 Processing helix chain 'P' and resid 414 through 447 removed outlier: 3.830A pdb=" N ASP P 447 " --> pdb=" O SER P 443 " (cutoff:3.500A) Processing helix chain 'P' and resid 447 through 468 Processing helix chain 'P' and resid 478 through 484 removed outlier: 3.701A pdb=" N PHE P 483 " --> pdb=" O GLU P 480 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN P 484 " --> pdb=" O PHE P 481 " (cutoff:3.500A) Processing helix chain 'P' and resid 486 through 505 Processing helix chain 'Q' and resid 186 through 207 Processing helix chain 'Q' and resid 220 through 276 Processing helix chain 'R' and resid 14 through 38 Processing helix chain 'R' and resid 58 through 62 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 removed outlier: 7.224A pdb=" N ARG A 80 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 116 removed outlier: 3.589A pdb=" N ILE A 116 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.194A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.768A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.133A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.470A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'I' and resid 991 through 992 Processing sheet with id=AB3, first strand: chain 'I' and resid 991 through 992 removed outlier: 5.702A pdb=" N LEU I1100 " --> pdb=" O ILE I1172 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 35 through 38 removed outlier: 6.529A pdb=" N LEU J 14 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N SER J 123 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N PHE J 16 " --> pdb=" O SER J 123 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 41 through 43 Processing sheet with id=AB6, first strand: chain 'J' and resid 88 through 89 Processing sheet with id=AB7, first strand: chain 'J' and resid 186 through 187 Processing sheet with id=AB8, first strand: chain 'J' and resid 186 through 187 removed outlier: 6.166A pdb=" N LEU J 168 " --> pdb=" O ILE J 349 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ALA J 351 " --> pdb=" O LEU J 168 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU J 170 " --> pdb=" O ALA J 351 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 18 through 21 removed outlier: 6.498A pdb=" N LEU K 8 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N THR K 106 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL K 10 " --> pdb=" O THR K 106 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 176 through 178 Processing sheet with id=AC2, first strand: chain 'L' and resid 1814 through 1816 removed outlier: 6.197A pdb=" N LYS L1815 " --> pdb=" O ILE O 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'M' and resid 26 through 28 Processing sheet with id=AC4, first strand: chain 'M' and resid 186 through 195 Processing sheet with id=AC5, first strand: chain 'M' and resid 261 through 270 Processing sheet with id=AC6, first strand: chain 'N' and resid 424 through 426 removed outlier: 7.442A pdb=" N ILE N 424 " --> pdb=" O LEU O 534 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'N' and resid 437 through 439 removed outlier: 6.782A pdb=" N VAL N 438 " --> pdb=" O LEU R 71 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 523 through 524 Processing sheet with id=AC9, first strand: chain 'P' and resid 309 through 311 removed outlier: 3.549A pdb=" N MET P 366 " --> pdb=" O LYS P 296 " (cutoff:3.500A) 1703 hydrogen bonds defined for protein. 4950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 256 hydrogen bonds 508 hydrogen bond angles 0 basepair planarities 100 basepair parallelities 205 stacking parallelities Total time for adding SS restraints: 18.78 Time building geometry restraints manager: 17.56 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: 8601 1.33 - 1.46: 9240 1.46 - 1.58: 16840 1.58 - 1.71: 469 1.71 - 1.83: 252 Bond restraints: 35402 Sorted by residual: bond pdb=" C HIS H 46 " pdb=" N PRO H 47 " ideal model delta sigma weight residual 1.334 1.297 0.037 8.40e-03 1.42e+04 1.93e+01 bond pdb=" N VAL I 832 " pdb=" CA VAL I 832 " ideal model delta sigma weight residual 1.456 1.502 -0.046 1.11e-02 8.12e+03 1.74e+01 bond pdb=" CA SER I 478 " pdb=" CB SER I 478 " ideal model delta sigma weight residual 1.528 1.472 0.057 1.56e-02 4.11e+03 1.33e+01 bond pdb=" C THR I 494 " pdb=" O THR I 494 " ideal model delta sigma weight residual 1.237 1.278 -0.041 1.17e-02 7.31e+03 1.23e+01 bond pdb=" N LEU I 928 " pdb=" CA LEU I 928 " ideal model delta sigma weight residual 1.453 1.493 -0.040 1.18e-02 7.18e+03 1.15e+01 ... (remaining 35397 not shown) Histogram of bond angle deviations from ideal: 96.51 - 104.46: 1380 104.46 - 112.42: 18610 112.42 - 120.38: 16352 120.38 - 128.34: 11964 128.34 - 136.29: 505 Bond angle restraints: 48811 Sorted by residual: angle pdb=" N GLN I 515 " pdb=" CA GLN I 515 " pdb=" C GLN I 515 " ideal model delta sigma weight residual 111.36 97.71 13.65 1.09e+00 8.42e-01 1.57e+02 angle pdb=" N GLU I 514 " pdb=" CA GLU I 514 " pdb=" C GLU I 514 " ideal model delta sigma weight residual 113.23 102.27 10.96 1.24e+00 6.50e-01 7.81e+01 angle pdb=" O3' DC X 122 " pdb=" C3' DC X 122 " pdb=" C2' DC X 122 " ideal model delta sigma weight residual 111.50 98.46 13.04 1.50e+00 4.44e-01 7.56e+01 angle pdb=" N PRO I 913 " pdb=" CA PRO I 913 " pdb=" C PRO I 913 " ideal model delta sigma weight residual 111.41 99.48 11.93 1.50e+00 4.44e-01 6.33e+01 angle pdb=" O3' DC X 56 " pdb=" C3' DC X 56 " pdb=" C2' DC X 56 " ideal model delta sigma weight residual 111.50 99.95 11.55 1.50e+00 4.44e-01 5.93e+01 ... (remaining 48806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.23: 18926 34.23 - 68.46: 1686 68.46 - 102.69: 91 102.69 - 136.92: 4 136.92 - 171.16: 8 Dihedral angle restraints: 20715 sinusoidal: 10017 harmonic: 10698 Sorted by residual: dihedral pdb=" C ASP J 339 " pdb=" N ASP J 339 " pdb=" CA ASP J 339 " pdb=" CB ASP J 339 " ideal model delta harmonic sigma weight residual -122.60 -141.57 18.97 0 2.50e+00 1.60e-01 5.76e+01 dihedral pdb=" C ASP J 71 " pdb=" N ASP J 71 " pdb=" CA ASP J 71 " pdb=" CB ASP J 71 " ideal model delta harmonic sigma weight residual -122.60 -140.47 17.87 0 2.50e+00 1.60e-01 5.11e+01 dihedral pdb=" C ASP K 288 " pdb=" N ASP K 288 " pdb=" CA ASP K 288 " pdb=" CB ASP K 288 " ideal model delta harmonic sigma weight residual -122.60 -140.43 17.83 0 2.50e+00 1.60e-01 5.09e+01 ... (remaining 20712 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 5243 0.138 - 0.276: 211 0.276 - 0.414: 31 0.414 - 0.552: 3 0.552 - 0.689: 3 Chirality restraints: 5491 Sorted by residual: chirality pdb=" CA ASP J 339 " pdb=" N ASP J 339 " pdb=" C ASP J 339 " pdb=" CB ASP J 339 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" CA ASP J 71 " pdb=" N ASP J 71 " pdb=" C ASP J 71 " pdb=" CB ASP J 71 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" CA ASP K 288 " pdb=" N ASP K 288 " pdb=" C ASP K 288 " pdb=" CB ASP K 288 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.89e+00 ... (remaining 5488 not shown) Planarity restraints: 5406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR M 355 " 0.027 2.00e-02 2.50e+03 5.35e-02 2.86e+01 pdb=" C THR M 355 " -0.093 2.00e-02 2.50e+03 pdb=" O THR M 355 " 0.035 2.00e-02 2.50e+03 pdb=" N LEU M 356 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS I 487 " -0.023 2.00e-02 2.50e+03 4.72e-02 2.23e+01 pdb=" C LYS I 487 " 0.082 2.00e-02 2.50e+03 pdb=" O LYS I 487 " -0.031 2.00e-02 2.50e+03 pdb=" N GLU I 488 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU I 768 " 0.023 2.00e-02 2.50e+03 4.64e-02 2.16e+01 pdb=" C LEU I 768 " -0.080 2.00e-02 2.50e+03 pdb=" O LEU I 768 " 0.030 2.00e-02 2.50e+03 pdb=" N TYR I 769 " 0.027 2.00e-02 2.50e+03 ... (remaining 5403 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 2847 2.72 - 3.26: 34746 3.26 - 3.81: 61067 3.81 - 4.35: 75387 4.35 - 4.90: 116660 Nonbonded interactions: 290707 Sorted by model distance: nonbonded pdb=" OD1 ASP L2157 " pdb=" N ARG L2158 " model vdw 2.173 2.520 nonbonded pdb=" OG SER L1645 " pdb=" OG SER O 669 " model vdw 2.202 2.440 nonbonded pdb=" O SER P 410 " pdb=" OG SER P 413 " model vdw 2.212 2.440 nonbonded pdb=" OG SER L2096 " pdb=" OE1 GLU L2098 " model vdw 2.214 2.440 nonbonded pdb=" O LEU L2017 " pdb=" NH2 ARG L2057 " model vdw 2.214 2.520 ... (remaining 290702 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 25 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 16 through 109) selection = (chain 'G' and resid 16 through 109) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 33 through 120) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.21 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 30.830 Check model and map are aligned: 0.560 Set scattering table: 0.300 Process input model: 112.450 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 158.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0836 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 : 0.010 0.102 35402 Z= 0.628 Angle : 1.078 13.650 48811 Z= 0.657 Chirality : 0.069 0.689 5491 Planarity : 0.007 0.073 5406 Dihedral : 22.081 171.156 13743 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.45 % Favored : 93.27 % Rotamer: Outliers : 2.63 % Allowed : 9.75 % Favored : 87.61 % Cbeta Deviations : 0.34 % 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: -3.67 (0.12), residues: 3552 helix: -2.03 (0.09), residues: 2151 sheet: -2.61 (0.37), residues: 152 loop : -2.90 (0.15), residues: 1249 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 489 time to evaluate : 3.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 6 residues processed: 569 average time/residue: 0.5822 time to fit residues: 500.7243 Evaluate side-chains 267 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 261 time to evaluate : 3.404 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4118 time to fit residues: 8.8719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 320 optimal weight: 8.9990 chunk 288 optimal weight: 0.9990 chunk 159 optimal weight: 30.0000 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 297 optimal weight: 0.0980 chunk 115 optimal weight: 9.9990 chunk 181 optimal weight: 20.0000 chunk 221 optimal weight: 0.7980 chunk 345 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 90 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN D 44 GLN D 81 ASN D 92 GLN D 106 HIS E 93 GLN F 25 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS ** I 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 473 GLN I 477 ASN I 854 ASN ** I 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1054 HIS ** I1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1191 HIS I1195 GLN J 183 HIS J 205 GLN J 251 HIS J 294 ASN ** J 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1997 ASN L2248 HIS L2268 ASN ** N 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 604 GLN N 638 HIS O 439 HIS ** O 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 935 HIS ** P 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 321 GLN ** P 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 432 ASN P 457 GLN Q 232 GLN ** Q 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 267 ASN ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 HIS R 70 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1282 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 35402 Z= 0.249 Angle : 0.751 10.113 48811 Z= 0.401 Chirality : 0.045 0.329 5491 Planarity : 0.005 0.066 5406 Dihedral : 24.352 173.473 6370 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.67 % Favored : 95.30 % Rotamer: Outliers : 2.60 % Allowed : 15.65 % Favored : 81.75 % 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: -1.61 (0.13), residues: 3552 helix: -0.32 (0.10), residues: 2214 sheet: -1.78 (0.40), residues: 154 loop : -2.29 (0.17), residues: 1184 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 289 time to evaluate : 3.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 21 residues processed: 357 average time/residue: 0.5434 time to fit residues: 310.7822 Evaluate side-chains 257 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 236 time to evaluate : 3.375 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.3343 time to fit residues: 17.6704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 191 optimal weight: 0.8980 chunk 107 optimal weight: 20.0000 chunk 287 optimal weight: 10.0000 chunk 234 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 345 optimal weight: 10.0000 chunk 373 optimal weight: 10.0000 chunk 307 optimal weight: 7.9990 chunk 342 optimal weight: 7.9990 chunk 117 optimal weight: 0.6980 chunk 277 optimal weight: 20.0000 overall best weight: 3.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS D 92 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 445 GLN ** I 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1182 GLN ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1858 HIS L1986 ASN ** L2090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L2176 GLN ** L2194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 260 GLN M 278 GLN ** N 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 638 HIS O 925 GLN P 344 GLN P 425 HIS P 500 GLN ** Q 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1839 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.156 35402 Z= 0.344 Angle : 0.849 15.334 48811 Z= 0.448 Chirality : 0.047 0.251 5491 Planarity : 0.007 0.066 5406 Dihedral : 24.169 172.284 6370 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 23.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.23 % Allowed : 17.65 % Favored : 79.12 % 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: -1.62 (0.13), residues: 3552 helix: -0.35 (0.10), residues: 2195 sheet: -1.58 (0.39), residues: 161 loop : -2.24 (0.17), residues: 1196 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 269 time to evaluate : 3.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 39 residues processed: 355 average time/residue: 0.5277 time to fit residues: 299.3064 Evaluate side-chains 269 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 230 time to evaluate : 3.467 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.3226 time to fit residues: 28.5558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 341 optimal weight: 3.9990 chunk 259 optimal weight: 10.0000 chunk 179 optimal weight: 50.0000 chunk 38 optimal weight: 7.9990 chunk 164 optimal weight: 8.9990 chunk 232 optimal weight: 0.1980 chunk 346 optimal weight: 8.9990 chunk 367 optimal weight: 7.9990 chunk 181 optimal weight: 20.0000 chunk 328 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN F 25 ASN H 64 ASN ** I 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 ASN ** K 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1705 ASN ** L1854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 513 GLN N 925 GLN ** O 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 513 GLN O 530 HIS ** O 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 432 ASN ** Q 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1916 moved from start: 0.5805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 35402 Z= 0.264 Angle : 0.726 16.747 48811 Z= 0.384 Chirality : 0.043 0.287 5491 Planarity : 0.005 0.060 5406 Dihedral : 24.104 174.279 6370 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.79 % Allowed : 18.78 % Favored : 78.43 % 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: -1.15 (0.13), residues: 3552 helix: 0.03 (0.10), residues: 2204 sheet: -1.19 (0.41), residues: 166 loop : -2.12 (0.17), residues: 1182 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 250 time to evaluate : 3.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 32 residues processed: 322 average time/residue: 0.5142 time to fit residues: 267.1761 Evaluate side-chains 251 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 219 time to evaluate : 3.422 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.4277 time to fit residues: 28.4607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 305 optimal weight: 9.9990 chunk 208 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 chunk 273 optimal weight: 6.9990 chunk 151 optimal weight: 40.0000 chunk 313 optimal weight: 4.9990 chunk 253 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 187 optimal weight: 40.0000 chunk 329 optimal weight: 1.9990 chunk 92 optimal weight: 20.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 327 HIS ** J 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L2268 ASN ** M 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 278 GLN ** M 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 423 HIS ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 359 GLN ** Q 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2136 moved from start: 0.6770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.139 35402 Z= 0.289 Angle : 0.765 18.389 48811 Z= 0.401 Chirality : 0.044 0.271 5491 Planarity : 0.005 0.066 5406 Dihedral : 24.055 174.088 6370 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 24.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.70 % Allowed : 20.23 % Favored : 77.08 % 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: -1.21 (0.13), residues: 3552 helix: -0.04 (0.11), residues: 2203 sheet: -1.18 (0.41), residues: 167 loop : -2.10 (0.17), residues: 1182 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 256 time to evaluate : 3.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 35 residues processed: 325 average time/residue: 0.5180 time to fit residues: 268.9193 Evaluate side-chains 262 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 227 time to evaluate : 3.425 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.3323 time to fit residues: 26.6653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 123 optimal weight: 10.0000 chunk 330 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 215 optimal weight: 0.3980 chunk 90 optimal weight: 9.9990 chunk 367 optimal weight: 7.9990 chunk 305 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 121 optimal weight: 9.9990 chunk 193 optimal weight: 0.4980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 356 GLN I 472 HIS ** I 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1304 GLN ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L2070 GLN ** L2173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 HIS ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2069 moved from start: 0.7183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 35402 Z= 0.215 Angle : 0.688 15.109 48811 Z= 0.360 Chirality : 0.042 0.253 5491 Planarity : 0.005 0.054 5406 Dihedral : 23.932 174.610 6370 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.72 % Allowed : 21.95 % Favored : 76.32 % 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: -0.81 (0.14), residues: 3552 helix: 0.32 (0.11), residues: 2211 sheet: -1.11 (0.41), residues: 172 loop : -2.05 (0.17), residues: 1169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 261 time to evaluate : 3.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 19 residues processed: 305 average time/residue: 0.5221 time to fit residues: 250.6977 Evaluate side-chains 258 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 239 time to evaluate : 3.414 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.3225 time to fit residues: 16.1094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 354 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 chunk 268 optimal weight: 0.7980 chunk 208 optimal weight: 5.9990 chunk 309 optimal weight: 9.9990 chunk 205 optimal weight: 1.9990 chunk 366 optimal weight: 10.0000 chunk 229 optimal weight: 6.9990 chunk 223 optimal weight: 0.8980 chunk 169 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 481 GLN ** I 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 432 ASN ** Q 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2095 moved from start: 0.7507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 35402 Z= 0.210 Angle : 0.676 14.228 48811 Z= 0.353 Chirality : 0.041 0.259 5491 Planarity : 0.005 0.075 5406 Dihedral : 23.785 175.064 6370 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.94 % Allowed : 23.27 % Favored : 75.79 % 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: -0.57 (0.14), residues: 3552 helix: 0.50 (0.11), residues: 2203 sheet: -1.04 (0.41), residues: 172 loop : -1.91 (0.17), residues: 1177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 247 time to evaluate : 4.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 12 residues processed: 269 average time/residue: 0.5225 time to fit residues: 223.8501 Evaluate side-chains 240 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 228 time to evaluate : 3.644 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3371 time to fit residues: 12.6860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 226 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 218 optimal weight: 3.9990 chunk 110 optimal weight: 20.0000 chunk 71 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 232 optimal weight: 6.9990 chunk 249 optimal weight: 6.9990 chunk 181 optimal weight: 0.7980 chunk 34 optimal weight: 0.0010 chunk 287 optimal weight: 9.9990 overall best weight: 1.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 470 GLN ** I 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 277 GLN ** J 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 229 ASN ** N 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 489 ASN ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 530 HIS ** O 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 350 GLN Q 199 ASN ** Q 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2186 moved from start: 0.7992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 35402 Z= 0.228 Angle : 0.711 15.050 48811 Z= 0.368 Chirality : 0.042 0.264 5491 Planarity : 0.005 0.061 5406 Dihedral : 23.722 176.238 6370 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 21.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.69 % Allowed : 23.96 % Favored : 75.35 % 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: -0.59 (0.14), residues: 3552 helix: 0.48 (0.11), residues: 2209 sheet: -0.99 (0.41), residues: 172 loop : -1.92 (0.17), residues: 1171 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 242 time to evaluate : 3.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 9 residues processed: 261 average time/residue: 0.5256 time to fit residues: 216.1909 Evaluate side-chains 233 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 224 time to evaluate : 3.501 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3263 time to fit residues: 10.4204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 333 optimal weight: 10.0000 chunk 350 optimal weight: 10.0000 chunk 320 optimal weight: 0.9980 chunk 341 optimal weight: 10.0000 chunk 205 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 268 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 308 optimal weight: 2.9990 chunk 322 optimal weight: 0.7980 chunk 340 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 470 GLN I 889 HIS ** I1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L2173 ASN ** L2194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 177 HIS ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 350 GLN Q 199 ASN Q 237 HIS ** Q 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2186 moved from start: 0.8313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 35402 Z= 0.209 Angle : 0.694 14.403 48811 Z= 0.359 Chirality : 0.042 0.265 5491 Planarity : 0.005 0.067 5406 Dihedral : 23.602 177.939 6370 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.82 % Allowed : 23.68 % Favored : 75.51 % 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: -0.40 (0.14), residues: 3552 helix: 0.62 (0.11), residues: 2197 sheet: -0.97 (0.41), residues: 175 loop : -1.81 (0.18), residues: 1180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 240 time to evaluate : 3.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 12 residues processed: 261 average time/residue: 0.5246 time to fit residues: 220.2576 Evaluate side-chains 236 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 224 time to evaluate : 3.545 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3394 time to fit residues: 12.4354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 224 optimal weight: 0.7980 chunk 360 optimal weight: 8.9990 chunk 220 optimal weight: 3.9990 chunk 171 optimal weight: 0.0470 chunk 250 optimal weight: 0.9980 chunk 378 optimal weight: 6.9990 chunk 348 optimal weight: 0.9990 chunk 301 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 232 optimal weight: 0.8980 chunk 184 optimal weight: 8.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 HIS ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 935 HIS ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 935 HIS P 504 GLN ** Q 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2104 moved from start: 0.8441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 35402 Z= 0.183 Angle : 0.686 18.945 48811 Z= 0.351 Chirality : 0.041 0.269 5491 Planarity : 0.004 0.052 5406 Dihedral : 23.484 179.242 6370 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.16 % Allowed : 24.33 % Favored : 75.51 % 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: -0.20 (0.14), residues: 3552 helix: 0.80 (0.11), residues: 2200 sheet: -0.84 (0.41), residues: 175 loop : -1.76 (0.18), residues: 1177 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 236 time to evaluate : 3.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 239 average time/residue: 0.5430 time to fit residues: 206.9025 Evaluate side-chains 229 residues out of total 3191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 227 time to evaluate : 3.646 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.6473 time to fit residues: 6.8734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 239 optimal weight: 4.9990 chunk 321 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 277 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 301 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 310 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 464 GLN I 470 GLN ** I1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 384 ASN ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L2273 GLN ** N 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 432 ASN Q 199 ASN Q 237 HIS ** Q 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.129180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.105555 restraints weight = 174540.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.107918 restraints weight = 86150.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.109327 restraints weight = 51532.472| |-----------------------------------------------------------------------------| r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4220 r_free = 0.4220 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4220 r_free = 0.4220 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2980 moved from start: 0.9327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.171 35402 Z= 0.315 Angle : 0.826 20.062 48811 Z= 0.425 Chirality : 0.046 0.284 5491 Planarity : 0.006 0.079 5406 Dihedral : 23.589 177.226 6370 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 27.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.60 % Allowed : 24.18 % Favored : 75.23 % 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: -0.80 (0.14), residues: 3552 helix: 0.28 (0.11), residues: 2197 sheet: -0.84 (0.41), residues: 168 loop : -1.93 (0.17), residues: 1187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7032.47 seconds wall clock time: 129 minutes 37.88 seconds (7777.88 seconds total)