Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 20 08:38:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr1_27668/10_2023/8dr1_27668_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr1_27668/10_2023/8dr1_27668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr1_27668/10_2023/8dr1_27668.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr1_27668/10_2023/8dr1_27668.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr1_27668/10_2023/8dr1_27668_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dr1_27668/10_2023/8dr1_27668_trim.pdb" } resolution = 2.14 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= 0.048 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: 7 Type Number sf(0) Gaussians P 77 5.49 5 Mg 4 5.21 5 S 101 5.16 5 C 13683 2.51 5 N 3753 2.21 5 O 4381 1.98 5 H 21631 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 397": "OD1" <-> "OD2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A GLU 730": "OE1" <-> "OE2" Residue "A GLU 740": "OE1" <-> "OE2" Residue "A TYR 784": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 229": "OD1" <-> "OD2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C GLU 26": "OE1" <-> "OE2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C ASP 229": "OD1" <-> "OD2" Residue "C ASP 230": "OD1" <-> "OD2" Residue "C ASP 254": "OD1" <-> "OD2" Residue "C TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 276": "OD1" <-> "OD2" Residue "C GLU 279": "OE1" <-> "OE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "D ASP 37": "OD1" <-> "OD2" Residue "D ASP 43": "OD1" <-> "OD2" Residue "D ASP 86": "OD1" <-> "OD2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D ASP 178": "OD1" <-> "OD2" Residue "D GLU 206": "OE1" <-> "OE2" Residue "D ASP 222": "OD1" <-> "OD2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "D ASP 281": "OD1" <-> "OD2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "D PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 306": "OE1" <-> "OE2" Residue "E GLU 21": "OE1" <-> "OE2" Residue "E GLU 58": "OE1" <-> "OE2" Residue "E GLU 115": "OE1" <-> "OE2" Residue "E GLU 142": "OE1" <-> "OE2" Residue "E ASP 195": "OD1" <-> "OD2" Residue "E GLU 281": "OE1" <-> "OE2" Residue "E ASP 288": "OD1" <-> "OD2" Residue "E GLU 311": "OE1" <-> "OE2" Residue "E GLU 323": "OE1" <-> "OE2" Residue "E GLU 330": "OE1" <-> "OE2" Residue "F ASP 33": "OD1" <-> "OD2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "F GLU 59": "OE1" <-> "OE2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F GLU 113": "OE1" <-> "OE2" Residue "G GLU 8": "OE1" <-> "OE2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "G PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 150": "OD1" <-> "OD2" Residue "G PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 71": "OD1" <-> "OD2" Residue "H ASP 156": "OD1" <-> "OD2" Residue "H GLU 198": "OE1" <-> "OE2" Residue "H ASP 240": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 43630 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 7844 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 19, 'TRANS': 473} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 5083 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain: "C" Number of atoms: 5263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5263 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "D" Number of atoms: 5457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 5457 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 330} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 5698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5698 Classifications: {'peptide': 354} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 339} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 4055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 4055 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 8, 'TRANS': 249} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 4047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 4047 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain: "H" Number of atoms: 4023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 4023 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "I" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 616 Classifications: {'DNA': 19} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 18} Chain: "J" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 553 Classifications: {'DNA': 18} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 17} Chain: "K" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 426 Classifications: {'DNA': 13} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 12} Chain: "L" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 397 Classifications: {'DNA': 13} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 17.49, per 1000 atoms: 0.40 Number of scatterers: 43630 At special positions: 0 Unit cell: (132.16, 119.77, 142.072, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 101 16.00 P 77 15.00 Mg 4 11.99 O 4381 8.00 N 3753 7.00 C 13683 6.00 H 21631 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 34.17 Conformation dependent library (CDL) restraints added in 3.2 seconds 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4960 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 14 sheets defined 55.6% alpha, 15.4% beta 17 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 19.00 Creating SS restraints... Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 342 through 346 removed outlier: 4.276A pdb=" N VAL A 345 " --> pdb=" O GLY A 342 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 346 " --> pdb=" O SER A 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 342 through 346' Processing helix chain 'A' and resid 358 through 370 Processing helix chain 'A' and resid 384 through 391 Processing helix chain 'A' and resid 392 through 396 Processing helix chain 'A' and resid 400 through 406 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.545A pdb=" N MET A 429 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 447 removed outlier: 3.684A pdb=" N ARG A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 467 Proline residue: A 465 - end of helix Processing helix chain 'A' and resid 483 through 495 Processing helix chain 'A' and resid 502 through 511 Processing helix chain 'A' and resid 513 through 526 removed outlier: 3.719A pdb=" N THR A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 544 Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 560 through 564 removed outlier: 3.667A pdb=" N ILE A 563 " --> pdb=" O ASP A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 573 through 584 removed outlier: 4.266A pdb=" N ASP A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 596 Processing helix chain 'A' and resid 609 through 632 Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 649 through 657 Processing helix chain 'A' and resid 668 through 691 Processing helix chain 'A' and resid 697 through 704 Processing helix chain 'A' and resid 704 through 714 removed outlier: 4.266A pdb=" N THR A 708 " --> pdb=" O ASP A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 721 removed outlier: 3.668A pdb=" N LEU A 718 " --> pdb=" O LEU A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 735 Processing helix chain 'A' and resid 738 through 749 removed outlier: 4.350A pdb=" N PHE A 749 " --> pdb=" O ILE A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 754 Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 763 through 776 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.647A pdb=" N ILE B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 85 through 99 removed outlier: 3.967A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 134 removed outlier: 3.674A pdb=" N ARG B 128 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 151 through 157 removed outlier: 3.528A pdb=" N ARG B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 217 Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 231 through 242 removed outlier: 3.744A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 256 Processing helix chain 'B' and resid 262 through 276 Processing helix chain 'B' and resid 281 through 301 Processing helix chain 'B' and resid 305 through 321 Processing helix chain 'C' and resid 9 through 13 Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 58 through 72 Processing helix chain 'C' and resid 74 through 77 Processing helix chain 'C' and resid 89 through 103 removed outlier: 4.067A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 123 through 137 removed outlier: 3.691A pdb=" N ARG C 131 " --> pdb=" O GLN C 127 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.535A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 160 Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.700A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.531A pdb=" N VAL C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 255 through 271 removed outlier: 4.074A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 288 removed outlier: 3.947A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR C 288 " --> pdb=" O ILE C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 312 removed outlier: 3.945A pdb=" N ARG C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS C 312 " --> pdb=" O TYR C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 332 Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'D' and resid 17 through 24 Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 35 through 39 Processing helix chain 'D' and resid 42 through 56 removed outlier: 4.582A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR D 52 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 84 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.920A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 141 through 145 Processing helix chain 'D' and resid 146 through 152 Processing helix chain 'D' and resid 153 through 160 removed outlier: 3.501A pdb=" N GLU D 158 " --> pdb=" O ARG D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'D' and resid 193 through 208 removed outlier: 5.551A pdb=" N ASP D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ARG D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 225 removed outlier: 3.528A pdb=" N ALA D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 252 through 260 Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 279 through 292 removed outlier: 3.866A pdb=" N LYS D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 310 Processing helix chain 'D' and resid 315 through 334 removed outlier: 3.589A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 12 through 16 Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.388A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 36 Processing helix chain 'E' and resid 48 through 62 Processing helix chain 'E' and resid 63 through 67 Processing helix chain 'E' and resid 97 through 103 removed outlier: 6.981A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 111 removed outlier: 3.717A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 118 Processing helix chain 'E' and resid 143 through 146 Processing helix chain 'E' and resid 147 through 161 removed outlier: 3.539A pdb=" N ARG E 155 " --> pdb=" O GLN E 151 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 184 Processing helix chain 'E' and resid 194 through 210 Processing helix chain 'E' and resid 216 through 227 removed outlier: 3.510A pdb=" N ASN E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 292 removed outlier: 3.556A pdb=" N HIS E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 309 Processing helix chain 'E' and resid 314 through 335 Processing helix chain 'E' and resid 337 through 354 removed outlier: 4.017A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 20 removed outlier: 4.138A pdb=" N PHE F 12 " --> pdb=" O GLU F 8 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 57 No H-bonds generated for 'chain 'F' and resid 55 through 57' Processing helix chain 'F' and resid 72 through 80 Processing helix chain 'F' and resid 141 through 153 removed outlier: 3.800A pdb=" N GLN F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 194 Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 217 through 221 removed outlier: 4.000A pdb=" N SER F 220 " --> pdb=" O LYS F 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 20 removed outlier: 4.514A pdb=" N PHE G 12 " --> pdb=" O GLU G 8 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 57 No H-bonds generated for 'chain 'G' and resid 55 through 57' Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 153 removed outlier: 3.587A pdb=" N GLN G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 194 Processing helix chain 'G' and resid 209 through 216 Processing helix chain 'G' and resid 217 through 221 removed outlier: 4.033A pdb=" N SER G 220 " --> pdb=" O LYS G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 19 removed outlier: 3.926A pdb=" N PHE H 19 " --> pdb=" O ILE H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 57 No H-bonds generated for 'chain 'H' and resid 55 through 57' Processing helix chain 'H' and resid 72 through 81 removed outlier: 3.803A pdb=" N CYS H 81 " --> pdb=" O LYS H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 155 removed outlier: 3.805A pdb=" N LEU H 154 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 216 Processing helix chain 'H' and resid 217 through 221 removed outlier: 3.944A pdb=" N SER H 220 " --> pdb=" O LYS H 217 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 373 through 377 removed outlier: 6.364A pdb=" N ALA A 349 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N CYS A 455 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU A 351 " --> pdb=" O CYS A 455 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ALA A 348 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE A 473 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N MET A 350 " --> pdb=" O ILE A 473 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 497 through 498 removed outlier: 6.571A pdb=" N LYS A 497 " --> pdb=" O ILE A 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 599 through 601 Processing sheet with id=AA4, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.326A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N MET B 45 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N CYS B 144 " --> pdb=" O MET B 45 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE B 47 " --> pdb=" O CYS B 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.496A pdb=" N LEU C 49 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ALA C 147 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE C 51 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.344A pdb=" N MET D 61 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N CYS D 170 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE D 63 " --> pdb=" O CYS D 170 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU D 62 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 69 through 76 removed outlier: 6.659A pdb=" N LEU E 94 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ASN E 141 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE E 96 " --> pdb=" O ASN E 141 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N CYS E 171 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU E 41 " --> pdb=" O CYS E 171 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU E 40 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 212 through 213 removed outlier: 6.340A pdb=" N GLN E 212 " --> pdb=" O LEU E 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 59 through 62 removed outlier: 3.962A pdb=" N GLU F 59 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE F 111 " --> pdb=" O ILE H 181 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ASP H 172 " --> pdb=" O SER H 157 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N SER H 157 " --> pdb=" O ASP H 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 66 through 71 removed outlier: 6.628A pdb=" N LEU F 25 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N VAL F 40 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ASN F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN F 38 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N SER F 230 " --> pdb=" O PRO F 234 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASP F 240 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ARG F 224 " --> pdb=" O ASP F 240 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 203 through 208 removed outlier: 6.009A pdb=" N SER F 157 " --> pdb=" O ASP F 172 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASP F 172 " --> pdb=" O SER F 157 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE G 111 " --> pdb=" O ILE F 181 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 66 through 71 removed outlier: 6.796A pdb=" N LEU G 25 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N VAL G 40 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASN G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN G 38 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ASP G 240 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ARG G 224 " --> pdb=" O ASP G 240 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 203 through 208 removed outlier: 6.021A pdb=" N SER G 157 " --> pdb=" O ASP G 172 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ASP G 172 " --> pdb=" O SER G 157 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU H 113 " --> pdb=" O SER G 179 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE G 181 " --> pdb=" O ILE H 111 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ILE H 111 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU H 101 " --> pdb=" O TYR H 114 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 66 through 71 removed outlier: 8.204A pdb=" N LEU H 25 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL H 40 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ASN H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN H 38 " --> pdb=" O ASN H 27 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP H 240 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG H 224 " --> pdb=" O ASP H 240 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR H 136 " --> pdb=" O GLU H 198 " (cutoff:3.500A) 1163 hydrogen bonds defined for protein. 3258 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 18.50 Time building geometry restraints manager: 35.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 21592 1.05 - 1.27: 3629 1.27 - 1.49: 8891 1.49 - 1.70: 9830 1.70 - 1.92: 159 Bond restraints: 44101 Sorted by residual: bond pdb=" C2' AGS A1001 " pdb=" C3' AGS A1001 " ideal model delta sigma weight residual 1.530 1.239 0.291 1.30e-02 5.92e+03 5.02e+02 bond pdb=" C2' AGS B 402 " pdb=" C3' AGS B 402 " ideal model delta sigma weight residual 1.530 1.239 0.291 1.30e-02 5.92e+03 5.00e+02 bond pdb=" C2' AGS D 402 " pdb=" C3' AGS D 402 " ideal model delta sigma weight residual 1.530 1.240 0.290 1.30e-02 5.92e+03 4.98e+02 bond pdb=" C2' AGS C 402 " pdb=" C3' AGS C 402 " ideal model delta sigma weight residual 1.530 1.240 0.290 1.30e-02 5.92e+03 4.97e+02 bond pdb=" C6 AGS D 402 " pdb=" N6 AGS D 402 " ideal model delta sigma weight residual 1.335 1.470 -0.135 1.00e-02 1.00e+04 1.82e+02 ... (remaining 44096 not shown) Histogram of bond angle deviations from ideal: 99.48 - 106.39: 826 106.39 - 113.29: 53082 113.29 - 120.19: 13552 120.19 - 127.09: 12260 127.09 - 133.99: 291 Bond angle restraints: 80011 Sorted by residual: angle pdb=" N1 AGS A1001 " pdb=" C2 AGS A1001 " pdb=" N3 AGS A1001 " ideal model delta sigma weight residual 128.80 120.08 8.72 8.41e-01 1.41e+00 1.07e+02 angle pdb=" N1 AGS B 402 " pdb=" C2 AGS B 402 " pdb=" N3 AGS B 402 " ideal model delta sigma weight residual 128.80 120.10 8.70 8.41e-01 1.41e+00 1.07e+02 angle pdb=" N1 AGS C 402 " pdb=" C2 AGS C 402 " pdb=" N3 AGS C 402 " ideal model delta sigma weight residual 128.80 120.14 8.66 8.41e-01 1.41e+00 1.06e+02 angle pdb=" N1 AGS D 402 " pdb=" C2 AGS D 402 " pdb=" N3 AGS D 402 " ideal model delta sigma weight residual 128.80 120.16 8.64 8.41e-01 1.41e+00 1.06e+02 angle pdb=" C5 AGS A1001 " pdb=" N7 AGS A1001 " pdb=" C8 AGS A1001 " ideal model delta sigma weight residual 103.67 107.99 -4.32 4.26e-01 5.51e+00 1.03e+02 ... (remaining 80006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 16813 35.40 - 70.80: 553 70.80 - 106.20: 42 106.20 - 141.60: 2 141.60 - 177.00: 4 Dihedral angle restraints: 17414 sinusoidal: 8779 harmonic: 8635 Sorted by residual: dihedral pdb=" O2B GDP E 401 " pdb=" O3A GDP E 401 " pdb=" PB GDP E 401 " pdb=" PA GDP E 401 " ideal model delta sinusoidal sigma weight residual 180.00 9.81 170.19 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' GDP E 401 " pdb=" O5' GDP E 401 " pdb=" PA GDP E 401 " pdb=" O3A GDP E 401 " ideal model delta sinusoidal sigma weight residual 179.98 -70.23 -109.79 1 2.00e+01 2.50e-03 3.21e+01 dihedral pdb=" O1A AGS D 402 " pdb=" O3A AGS D 402 " pdb=" PA AGS D 402 " pdb=" PB AGS D 402 " ideal model delta sinusoidal sigma weight residual -67.73 75.46 -143.19 1 3.00e+01 1.11e-03 1.92e+01 ... (remaining 17411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3118 0.060 - 0.119: 398 0.119 - 0.179: 45 0.179 - 0.238: 4 0.238 - 0.298: 4 Chirality restraints: 3569 Sorted by residual: chirality pdb=" C2' AGS C 402 " pdb=" C1' AGS C 402 " pdb=" C3' AGS C 402 " pdb=" O2' AGS C 402 " both_signs ideal model delta sigma weight residual False -2.67 -2.38 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C2' AGS B 402 " pdb=" C1' AGS B 402 " pdb=" C3' AGS B 402 " pdb=" O2' AGS B 402 " both_signs ideal model delta sigma weight residual False -2.67 -2.38 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C2' AGS D 402 " pdb=" C1' AGS D 402 " pdb=" C3' AGS D 402 " pdb=" O2' AGS D 402 " both_signs ideal model delta sigma weight residual False -2.67 -2.38 -0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 3566 not shown) Planarity restraints: 6236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 460 " -0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO A 461 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 461 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 461 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 32 " 0.140 9.50e-02 1.11e+02 4.68e-02 2.58e+00 pdb=" NE ARG B 32 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 32 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 32 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 32 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG B 32 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG B 32 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG B 32 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 32 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 183 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO F 184 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO F 184 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 184 " 0.022 5.00e-02 4.00e+02 ... (remaining 6233 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 1328 2.15 - 2.76: 82972 2.76 - 3.38: 125911 3.38 - 3.99: 165886 3.99 - 4.60: 255377 Nonbonded interactions: 631474 Sorted by model distance: nonbonded pdb=" OE1 GLU G 8 " pdb=" H GLU G 8 " model vdw 1.538 1.850 nonbonded pdb=" OE1 GLU F 55 " pdb=" H GLU F 55 " model vdw 1.538 1.850 nonbonded pdb=" O SER F 0 " pdb="HH12 ARG F 61 " model vdw 1.557 1.850 nonbonded pdb=" HG SER H 142 " pdb=" OE1 GLU H 143 " model vdw 1.608 1.850 nonbonded pdb=" OE1 GLU F 8 " pdb=" H GLU F 8 " model vdw 1.611 1.850 ... (remaining 631469 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 'F' and resid 0 through 254) selection = (chain 'G' and ((resid 0 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 1 through 254)) selection = (chain 'H' and ((resid 0 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 1 through 254)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.660 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: 0.670 Extract box with map and model: 14.300 Check model and map are aligned: 0.620 Set scattering table: 0.370 Process input model: 143.040 Find NCS groups from input model: 1.230 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: 0.010 Load rotamer database and sin/cos tables:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 175.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 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 : 0.008 0.291 22470 Z= 0.363 Angle : 0.572 8.836 30651 Z= 0.392 Chirality : 0.041 0.298 3569 Planarity : 0.003 0.061 3672 Dihedral : 17.933 176.996 8571 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.74 % Allowed : 16.88 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.17), residues: 2590 helix: 1.84 (0.15), residues: 1228 sheet: 0.80 (0.22), residues: 523 loop : 0.65 (0.23), residues: 839 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 56 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 348 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 331 time to evaluate : 3.518 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 outliers start: 17 outliers final: 5 residues processed: 346 average time/residue: 3.5620 time to fit residues: 1378.5144 Evaluate side-chains 206 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 201 time to evaluate : 3.611 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 4.1728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 220 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 67 optimal weight: 0.0980 chunk 133 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 237 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 389 ASN A 439 GLN A 571 ASN A 775 ASN B 244 ASN C 180 ASN C 184 HIS C 221 ASN C 264 ASN D 171 ASN E 32 GLN E 45 ASN E 93 HIS G 201 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22470 Z= 0.242 Angle : 0.525 7.010 30651 Z= 0.286 Chirality : 0.041 0.160 3569 Planarity : 0.003 0.040 3672 Dihedral : 15.240 177.165 3455 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.99 % Allowed : 16.57 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.17), residues: 2590 helix: 1.83 (0.15), residues: 1246 sheet: 0.78 (0.22), residues: 532 loop : 0.53 (0.23), residues: 812 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 56 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 256 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 210 time to evaluate : 3.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 17 residues processed: 248 average time/residue: 3.3989 time to fit residues: 951.0330 Evaluate side-chains 212 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 195 time to evaluate : 3.427 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 2 average time/residue: 1.2127 time to fit residues: 7.5354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 131 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 197 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 237 optimal weight: 0.7980 chunk 256 optimal weight: 0.9980 chunk 211 optimal weight: 3.9990 chunk 235 optimal weight: 7.9990 chunk 80 optimal weight: 0.3980 chunk 190 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN E 45 ASN F 153 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22470 Z= 0.177 Angle : 0.492 7.193 30651 Z= 0.266 Chirality : 0.039 0.145 3569 Planarity : 0.003 0.037 3672 Dihedral : 15.115 177.436 3455 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.47 % Allowed : 16.75 % Favored : 81.78 % 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: 1.88 (0.17), residues: 2590 helix: 1.93 (0.15), residues: 1248 sheet: 0.93 (0.22), residues: 527 loop : 0.54 (0.23), residues: 815 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 56 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 234 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 200 time to evaluate : 3.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 19 residues processed: 227 average time/residue: 3.5030 time to fit residues: 895.1781 Evaluate side-chains 205 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 186 time to evaluate : 3.386 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 19 residues processed: 1 average time/residue: 0.6190 time to fit residues: 5.2473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 234 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 159 optimal weight: 20.0000 chunk 238 optimal weight: 0.0050 chunk 252 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 225 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN E 45 ASN G 201 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22470 Z= 0.241 Angle : 0.512 6.661 30651 Z= 0.276 Chirality : 0.040 0.147 3569 Planarity : 0.003 0.037 3672 Dihedral : 15.066 177.399 3455 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.60 % Allowed : 16.44 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.17), residues: 2590 helix: 1.89 (0.15), residues: 1246 sheet: 0.88 (0.22), residues: 542 loop : 0.54 (0.23), residues: 802 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 56 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 234 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 197 time to evaluate : 3.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 23 residues processed: 228 average time/residue: 3.5526 time to fit residues: 910.6497 Evaluate side-chains 214 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 191 time to evaluate : 3.488 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 21 residues processed: 2 average time/residue: 0.5872 time to fit residues: 6.3198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 210 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 226 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 45 ASN G 201 GLN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22470 Z= 0.243 Angle : 0.510 6.613 30651 Z= 0.275 Chirality : 0.040 0.146 3569 Planarity : 0.003 0.057 3672 Dihedral : 15.071 177.294 3455 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.73 % Allowed : 16.66 % Favored : 81.61 % 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: 1.81 (0.17), residues: 2590 helix: 1.86 (0.15), residues: 1246 sheet: 0.90 (0.22), residues: 542 loop : 0.52 (0.23), residues: 802 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 56 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 236 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 196 time to evaluate : 3.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 26 residues processed: 226 average time/residue: 3.5265 time to fit residues: 902.9688 Evaluate side-chains 213 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 187 time to evaluate : 3.731 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 22 residues processed: 5 average time/residue: 0.8668 time to fit residues: 10.8816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 84 optimal weight: 0.7980 chunk 227 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 252 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 24 GLN E 45 ASN E 224 GLN G 201 GLN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22470 Z= 0.200 Angle : 0.501 6.340 30651 Z= 0.270 Chirality : 0.040 0.147 3569 Planarity : 0.003 0.082 3672 Dihedral : 15.063 177.478 3455 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.51 % Allowed : 16.57 % Favored : 81.91 % 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: 1.88 (0.17), residues: 2590 helix: 1.92 (0.15), residues: 1247 sheet: 0.97 (0.22), residues: 531 loop : 0.51 (0.23), residues: 812 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 56 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 194 time to evaluate : 3.773 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 24 residues processed: 220 average time/residue: 3.5299 time to fit residues: 873.4165 Evaluate side-chains 214 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 190 time to evaluate : 3.375 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 22 residues processed: 2 average time/residue: 0.6306 time to fit residues: 6.2993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 243 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 143 optimal weight: 0.4980 chunk 184 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 212 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 251 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 45 ASN F 201 GLN G 201 GLN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22470 Z= 0.226 Angle : 0.504 6.462 30651 Z= 0.272 Chirality : 0.040 0.149 3569 Planarity : 0.004 0.139 3672 Dihedral : 15.078 177.386 3455 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.34 % Allowed : 16.53 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.17), residues: 2590 helix: 1.93 (0.15), residues: 1247 sheet: 1.06 (0.22), residues: 533 loop : 0.47 (0.23), residues: 810 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 56 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 190 time to evaluate : 3.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 25 residues processed: 215 average time/residue: 3.4053 time to fit residues: 826.7833 Evaluate side-chains 213 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 188 time to evaluate : 3.637 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 21 residues processed: 4 average time/residue: 0.9275 time to fit residues: 9.5714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 155 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 159 optimal weight: 10.0000 chunk 171 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 197 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 45 ASN G 201 GLN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2716 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: