Starting phenix.real_space_refine on Sat Dec 9 05:18:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0t_32924/12_2023/7x0t_32924_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0t_32924/12_2023/7x0t_32924.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0t_32924/12_2023/7x0t_32924_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0t_32924/12_2023/7x0t_32924_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0t_32924/12_2023/7x0t_32924_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0t_32924/12_2023/7x0t_32924.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0t_32924/12_2023/7x0t_32924.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0t_32924/12_2023/7x0t_32924_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0t_32924/12_2023/7x0t_32924_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.030 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 49 5.16 5 C 6504 2.51 5 N 1796 2.21 5 O 1834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "A ARG 85": "NH1" <-> "NH2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ASP 115": "OD1" <-> "OD2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ASP 200": "OD1" <-> "OD2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 259": "NH1" <-> "NH2" Residue "A PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A ARG 324": "NH1" <-> "NH2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 363": "OE1" <-> "OE2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A GLU 380": "OE1" <-> "OE2" Residue "A PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A GLU 498": "OE1" <-> "OE2" Residue "A TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 555": "OD1" <-> "OD2" Residue "A ASP 561": "OD1" <-> "OD2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 575": "OD1" <-> "OD2" Residue "A GLU 577": "OE1" <-> "OE2" Residue "A ASP 581": "OD1" <-> "OD2" Residue "A ARG 622": "NH1" <-> "NH2" Residue "A ASP 629": "OD1" <-> "OD2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "B ARG 69": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ASP 115": "OD1" <-> "OD2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B ARG 120": "NH1" <-> "NH2" Residue "B ARG 124": "NH1" <-> "NH2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 152": "NH1" <-> "NH2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ASP 187": "OD1" <-> "OD2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B ASP 194": "OD1" <-> "OD2" Residue "B ARG 231": "NH1" <-> "NH2" Residue "B ARG 234": "NH1" <-> "NH2" Residue "B ARG 259": "NH1" <-> "NH2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "B ARG 285": "NH1" <-> "NH2" Residue "B ARG 324": "NH1" <-> "NH2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 397": "OD1" <-> "OD2" Residue "B TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 421": "OE1" <-> "OE2" Residue "B ARG 431": "NH1" <-> "NH2" Residue "B ARG 496": "NH1" <-> "NH2" Residue "B GLU 498": "OE1" <-> "OE2" Residue "B TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ASP 555": "OD1" <-> "OD2" Residue "B ASP 561": "OD1" <-> "OD2" Residue "B GLU 564": "OE1" <-> "OE2" Residue "B ARG 568": "NH1" <-> "NH2" Residue "B GLU 596": "OE1" <-> "OE2" Residue "B ASP 600": "OD1" <-> "OD2" Residue "B PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 622": "NH1" <-> "NH2" Residue "B ASP 629": "OD1" <-> "OD2" Residue "B GLU 640": "OE1" <-> "OE2" Residue "B ASP 685": "OD1" <-> "OD2" Residue "B ARG 712": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10189 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 5051 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 22, 'TRANS': 610} Chain breaks: 1 Chain: "B" Number of atoms: 5051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 5051 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 22, 'TRANS': 610} Chain breaks: 1 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 56 Unusual residues: {'CO8': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.82, per 1000 atoms: 0.57 Number of scatterers: 10189 At special positions: 0 Unit cell: (75.53, 113.71, 154.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 P 6 15.00 O 1834 8.00 N 1796 7.00 C 6504 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: 4.25 Conformation dependent library (CDL) restraints added in 1.8 seconds 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2372 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 0 sheets defined 40.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 70 through 79 removed outlier: 3.616A pdb=" N LEU A 75 " --> pdb=" O PHE A 71 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 107 removed outlier: 3.611A pdb=" N SER A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ARG A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 138 removed outlier: 3.986A pdb=" N GLN A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLN A 136 " --> pdb=" O TRP A 132 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP A 137 " --> pdb=" O GLN A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 149 removed outlier: 3.656A pdb=" N VAL A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 160 No H-bonds generated for 'chain 'A' and resid 157 through 160' Processing helix chain 'A' and resid 193 through 196 No H-bonds generated for 'chain 'A' and resid 193 through 196' Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.603A pdb=" N ALA A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N HIS A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 211 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ASN A 214 " --> pdb=" O HIS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 4.298A pdb=" N ALA A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 235 removed outlier: 3.627A pdb=" N ALA A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 275 Processing helix chain 'A' and resid 277 through 288 removed outlier: 3.539A pdb=" N TYR A 281 " --> pdb=" O GLY A 277 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 295 No H-bonds generated for 'chain 'A' and resid 292 through 295' Processing helix chain 'A' and resid 303 through 306 No H-bonds generated for 'chain 'A' and resid 303 through 306' Processing helix chain 'A' and resid 330 through 336 removed outlier: 3.945A pdb=" N MET A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 352 No H-bonds generated for 'chain 'A' and resid 349 through 352' Processing helix chain 'A' and resid 363 through 371 removed outlier: 3.596A pdb=" N ALA A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLU A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 377 No H-bonds generated for 'chain 'A' and resid 374 through 377' Processing helix chain 'A' and resid 383 through 397 removed outlier: 3.647A pdb=" N ALA A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 405 removed outlier: 3.784A pdb=" N SER A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 431 removed outlier: 3.648A pdb=" N GLY A 414 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET A 422 " --> pdb=" O ARG A 418 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN A 430 " --> pdb=" O PHE A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 511 No H-bonds generated for 'chain 'A' and resid 509 through 511' Processing helix chain 'A' and resid 514 through 521 removed outlier: 3.826A pdb=" N ARG A 518 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE A 519 " --> pdb=" O LEU A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 555 No H-bonds generated for 'chain 'A' and resid 553 through 555' Processing helix chain 'A' and resid 574 through 582 removed outlier: 3.755A pdb=" N ILE A 579 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A 582 " --> pdb=" O ILE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 590 No H-bonds generated for 'chain 'A' and resid 588 through 590' Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.780A pdb=" N GLN A 611 " --> pdb=" O GLY A 607 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ARG A 612 " --> pdb=" O GLY A 608 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET A 618 " --> pdb=" O GLY A 614 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N PHE A 619 " --> pdb=" O MET A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 650 Processing helix chain 'A' and resid 661 through 666 removed outlier: 3.881A pdb=" N TRP A 664 " --> pdb=" O PRO A 661 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS A 665 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 699 removed outlier: 4.186A pdb=" N LYS A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 720 removed outlier: 3.739A pdb=" N LEU A 720 " --> pdb=" O LEU A 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 73 Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 99 through 105 removed outlier: 3.565A pdb=" N SER B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 116 No H-bonds generated for 'chain 'B' and resid 113 through 116' Processing helix chain 'B' and resid 132 through 138 removed outlier: 3.868A pdb=" N GLN B 136 " --> pdb=" O TRP B 132 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TRP B 137 " --> pdb=" O GLN B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 149 removed outlier: 3.754A pdb=" N VAL B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 160 removed outlier: 3.799A pdb=" N LEU B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 166 No H-bonds generated for 'chain 'B' and resid 163 through 166' Processing helix chain 'B' and resid 202 through 216 removed outlier: 3.871A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR B 212 " --> pdb=" O VAL B 208 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN B 214 " --> pdb=" O HIS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 224 removed outlier: 3.999A pdb=" N ALA B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 251 through 254 No H-bonds generated for 'chain 'B' and resid 251 through 254' Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 268 through 275 Processing helix chain 'B' and resid 279 through 288 removed outlier: 3.588A pdb=" N VAL B 286 " --> pdb=" O MET B 282 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 287 " --> pdb=" O HIS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 295 No H-bonds generated for 'chain 'B' and resid 292 through 295' Processing helix chain 'B' and resid 301 through 304 No H-bonds generated for 'chain 'B' and resid 301 through 304' Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 318 through 323 Processing helix chain 'B' and resid 340 through 343 No H-bonds generated for 'chain 'B' and resid 340 through 343' Processing helix chain 'B' and resid 349 through 352 No H-bonds generated for 'chain 'B' and resid 349 through 352' Processing helix chain 'B' and resid 363 through 370 Processing helix chain 'B' and resid 374 through 393 removed outlier: 3.881A pdb=" N SER B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 420 removed outlier: 4.879A pdb=" N ARG B 418 " --> pdb=" O GLY B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 431 removed outlier: 4.052A pdb=" N GLU B 427 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN B 430 " --> pdb=" O PHE B 426 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG B 431 " --> pdb=" O GLU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 521 removed outlier: 3.602A pdb=" N ARG B 518 " --> pdb=" O SER B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 555 No H-bonds generated for 'chain 'B' and resid 553 through 555' Processing helix chain 'B' and resid 576 through 582 Processing helix chain 'B' and resid 589 through 591 No H-bonds generated for 'chain 'B' and resid 589 through 591' Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.649A pdb=" N ARG B 612 " --> pdb=" O GLY B 608 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET B 615 " --> pdb=" O GLN B 611 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET B 618 " --> pdb=" O GLY B 614 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE B 619 " --> pdb=" O MET B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 650 removed outlier: 4.881A pdb=" N ILE B 643 " --> pdb=" O VAL B 639 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE B 644 " --> pdb=" O GLU B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 664 Processing helix chain 'B' and resid 689 through 703 Processing helix chain 'B' and resid 706 through 720 removed outlier: 3.920A pdb=" N MET B 709 " --> pdb=" O ILE B 706 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 713 " --> pdb=" O GLN B 710 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN B 714 " --> pdb=" O ARG B 711 " (cutoff:3.500A) 192 hydrogen bonds defined for protein. 522 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.35 Time building geometry restraints manager: 4.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1630 1.31 - 1.44: 2801 1.44 - 1.57: 5879 1.57 - 1.70: 11 1.70 - 1.83: 82 Bond restraints: 10403 Sorted by residual: bond pdb=" C1B CO8 A 801 " pdb=" O4B CO8 A 801 " ideal model delta sigma weight residual 1.655 1.308 0.347 2.00e-02 2.50e+03 3.01e+02 bond pdb=" C4B CO8 A 801 " pdb=" O4B CO8 A 801 " ideal model delta sigma weight residual 1.294 1.603 -0.309 2.00e-02 2.50e+03 2.38e+02 bond pdb=" C3B CO8 A 801 " pdb=" C4B CO8 A 801 " ideal model delta sigma weight residual 1.593 1.307 0.286 2.00e-02 2.50e+03 2.05e+02 bond pdb=" C1B CO8 A 801 " pdb=" C2B CO8 A 801 " ideal model delta sigma weight residual 1.326 1.531 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C3B CO8 A 801 " pdb=" O3B CO8 A 801 " ideal model delta sigma weight residual 1.339 1.494 -0.155 2.00e-02 2.50e+03 6.04e+01 ... (remaining 10398 not shown) Histogram of bond angle deviations from ideal: 95.71 - 103.47: 108 103.47 - 111.23: 3423 111.23 - 118.99: 5063 118.99 - 126.74: 5337 126.74 - 134.50: 155 Bond angle restraints: 14086 Sorted by residual: angle pdb=" PB ATP B 801 " pdb=" O3B ATP B 801 " pdb=" PG ATP B 801 " ideal model delta sigma weight residual 139.87 122.64 17.23 1.00e+00 1.00e+00 2.97e+02 angle pdb=" N ILE B 317 " pdb=" CA ILE B 317 " pdb=" C ILE B 317 " ideal model delta sigma weight residual 111.45 100.41 11.04 9.30e-01 1.16e+00 1.41e+02 angle pdb=" N VAL A 167 " pdb=" CA VAL A 167 " pdb=" C VAL A 167 " ideal model delta sigma weight residual 111.91 104.73 7.18 8.90e-01 1.26e+00 6.51e+01 angle pdb=" PA ATP B 801 " pdb=" O3A ATP B 801 " pdb=" PB ATP B 801 " ideal model delta sigma weight residual 136.83 129.58 7.25 1.00e+00 1.00e+00 5.25e+01 angle pdb=" N ILE B 317 " pdb=" CA ILE B 317 " pdb=" CB ILE B 317 " ideal model delta sigma weight residual 110.31 120.81 -10.50 1.60e+00 3.91e-01 4.30e+01 ... (remaining 14081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 5466 17.24 - 34.47: 625 34.47 - 51.71: 131 51.71 - 68.94: 30 68.94 - 86.18: 12 Dihedral angle restraints: 6264 sinusoidal: 2580 harmonic: 3684 Sorted by residual: dihedral pdb=" CA GLN B 316 " pdb=" C GLN B 316 " pdb=" N ILE B 317 " pdb=" CA ILE B 317 " ideal model delta harmonic sigma weight residual 180.00 151.56 28.44 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" C TYR B 541 " pdb=" N TYR B 541 " pdb=" CA TYR B 541 " pdb=" CB TYR B 541 " ideal model delta harmonic sigma weight residual -122.60 -110.54 -12.06 0 2.50e+00 1.60e-01 2.33e+01 dihedral pdb=" C ILE A 652 " pdb=" N ILE A 652 " pdb=" CA ILE A 652 " pdb=" CB ILE A 652 " ideal model delta harmonic sigma weight residual -122.00 -133.38 11.38 0 2.50e+00 1.60e-01 2.07e+01 ... (remaining 6261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 1343 0.117 - 0.233: 204 0.233 - 0.350: 19 0.350 - 0.467: 2 0.467 - 0.583: 1 Chirality restraints: 1569 Sorted by residual: chirality pdb=" CB VAL A 102 " pdb=" CA VAL A 102 " pdb=" CG1 VAL A 102 " pdb=" CG2 VAL A 102 " both_signs ideal model delta sigma weight residual False -2.63 -2.05 -0.58 2.00e-01 2.50e+01 8.50e+00 chirality pdb=" CA THR B 632 " pdb=" N THR B 632 " pdb=" C THR B 632 " pdb=" CB THR B 632 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.43 2.00e-01 2.50e+01 4.60e+00 chirality pdb=" CA TYR A 559 " pdb=" N TYR A 559 " pdb=" C TYR A 559 " pdb=" CB TYR A 559 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.39 2.00e-01 2.50e+01 3.71e+00 ... (remaining 1566 not shown) Planarity restraints: 1779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 499 " 0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C GLU A 499 " -0.070 2.00e-02 2.50e+03 pdb=" O GLU A 499 " 0.027 2.00e-02 2.50e+03 pdb=" N GLY A 500 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 299 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C HIS B 299 " -0.064 2.00e-02 2.50e+03 pdb=" O HIS B 299 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU B 300 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 102 " 0.018 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C VAL A 102 " -0.060 2.00e-02 2.50e+03 pdb=" O VAL A 102 " 0.022 2.00e-02 2.50e+03 pdb=" N SER A 103 " 0.020 2.00e-02 2.50e+03 ... (remaining 1776 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1081 2.75 - 3.29: 9996 3.29 - 3.83: 15660 3.83 - 4.36: 21114 4.36 - 4.90: 34055 Nonbonded interactions: 81906 Sorted by model distance: nonbonded pdb=" O ASN B 318 " pdb=" ND2 ASN B 318 " model vdw 2.217 2.520 nonbonded pdb=" O VAL B 349 " pdb=" OG1 THR B 353 " model vdw 2.227 2.440 nonbonded pdb=" O ASP A 221 " pdb=" OG1 THR A 225 " model vdw 2.259 2.440 nonbonded pdb=" NH2 ARG B 554 " pdb=" O VAL B 563 " model vdw 2.369 2.520 nonbonded pdb=" O SER A 226 " pdb=" OG SER A 226 " model vdw 2.393 2.440 ... (remaining 81901 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 67 through 722) selection = (chain 'B' and resid 67 through 722) } 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: 2.720 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: 0.010 Extract box with map and model: 11.820 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 29.750 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 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 0.347 10403 Z= 0.623 Angle : 1.306 17.226 14086 Z= 0.882 Chirality : 0.085 0.583 1569 Planarity : 0.006 0.048 1779 Dihedral : 15.648 86.179 3892 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.94 % Favored : 89.83 % Rotamer: Outliers : 1.87 % Allowed : 6.18 % Favored : 91.95 % Cbeta Deviations : 0.25 % 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: -5.80 (0.18), residues: 1258 helix: -3.87 (0.13), residues: 788 sheet: -4.41 (0.88), residues: 22 loop : -3.38 (0.24), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 137 HIS 0.007 0.002 HIS B 659 PHE 0.013 0.003 PHE B 162 TYR 0.024 0.004 TYR B 541 ARG 0.008 0.001 ARG A 554 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 1.169 Fit side-chains outliers start: 20 outliers final: 12 residues processed: 154 average time/residue: 0.2692 time to fit residues: 56.6165 Evaluate side-chains 127 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 1.110 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 1 residues processed: 12 average time/residue: 0.1392 time to fit residues: 4.3794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN B 210 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10403 Z= 0.252 Angle : 0.652 9.991 14086 Z= 0.339 Chirality : 0.042 0.158 1569 Planarity : 0.004 0.043 1779 Dihedral : 8.427 85.844 1470 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 1.40 % Allowed : 10.11 % Favored : 88.48 % 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: -5.45 (0.18), residues: 1258 helix: -3.53 (0.14), residues: 805 sheet: -5.77 (0.76), residues: 10 loop : -3.38 (0.24), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 137 HIS 0.003 0.001 HIS B 97 PHE 0.011 0.001 PHE B 434 TYR 0.022 0.002 TYR B 174 ARG 0.003 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 113 time to evaluate : 1.261 Fit side-chains outliers start: 15 outliers final: 5 residues processed: 121 average time/residue: 0.2653 time to fit residues: 44.6117 Evaluate side-chains 101 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 1.273 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1015 time to fit residues: 2.6964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 91 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10403 Z= 0.352 Angle : 0.669 9.851 14086 Z= 0.342 Chirality : 0.044 0.152 1569 Planarity : 0.005 0.041 1779 Dihedral : 8.497 86.014 1470 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 1.03 % Allowed : 14.70 % Favored : 84.27 % 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: -5.29 (0.19), residues: 1258 helix: -3.36 (0.14), residues: 810 sheet: -5.78 (0.76), residues: 10 loop : -3.40 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 137 HIS 0.005 0.001 HIS B 210 PHE 0.012 0.001 PHE B 434 TYR 0.024 0.002 TYR B 174 ARG 0.003 0.000 ARG B 496 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 1.142 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 111 average time/residue: 0.2908 time to fit residues: 45.4079 Evaluate side-chains 100 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 1.334 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1252 time to fit residues: 3.1456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 76 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 109 optimal weight: 0.6980 chunk 32 optimal weight: 0.2980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 ASN B 586 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10403 Z= 0.217 Angle : 0.590 9.539 14086 Z= 0.303 Chirality : 0.041 0.158 1569 Planarity : 0.004 0.040 1779 Dihedral : 7.910 84.839 1470 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.84 % Allowed : 16.48 % Favored : 82.68 % 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: -5.03 (0.20), residues: 1258 helix: -3.15 (0.15), residues: 810 sheet: -5.37 (0.68), residues: 20 loop : -3.24 (0.25), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 137 HIS 0.003 0.001 HIS A 621 PHE 0.009 0.001 PHE A 106 TYR 0.019 0.001 TYR A 620 ARG 0.003 0.000 ARG B 496 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 1.129 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 111 average time/residue: 0.2574 time to fit residues: 39.8619 Evaluate side-chains 101 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 1.137 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1090 time to fit residues: 2.4925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.2980 chunk 69 optimal weight: 0.3980 chunk 1 optimal weight: 0.9980 chunk 90 optimal weight: 0.0770 chunk 50 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10403 Z= 0.194 Angle : 0.570 9.454 14086 Z= 0.290 Chirality : 0.040 0.159 1569 Planarity : 0.004 0.041 1779 Dihedral : 7.438 83.443 1470 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 1.22 % Allowed : 17.70 % Favored : 81.09 % 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: -4.82 (0.20), residues: 1258 helix: -2.94 (0.16), residues: 811 sheet: -5.13 (0.73), residues: 20 loop : -3.27 (0.25), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 664 HIS 0.004 0.001 HIS A 621 PHE 0.035 0.001 PHE A 71 TYR 0.020 0.001 TYR A 620 ARG 0.004 0.000 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 1.193 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 114 average time/residue: 0.2572 time to fit residues: 40.9355 Evaluate side-chains 105 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 1.218 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1048 time to fit residues: 2.4900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN ** B 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 10403 Z= 0.452 Angle : 0.704 10.673 14086 Z= 0.353 Chirality : 0.047 0.169 1569 Planarity : 0.005 0.049 1779 Dihedral : 7.953 83.086 1470 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 1.87 % Allowed : 17.60 % Favored : 80.52 % 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: -5.04 (0.19), residues: 1258 helix: -3.11 (0.15), residues: 809 sheet: -5.39 (0.70), residues: 20 loop : -3.35 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 137 HIS 0.006 0.001 HIS B 210 PHE 0.026 0.002 PHE A 71 TYR 0.024 0.002 TYR B 174 ARG 0.004 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 1.151 Fit side-chains outliers start: 20 outliers final: 13 residues processed: 122 average time/residue: 0.2379 time to fit residues: 41.1082 Evaluate side-chains 113 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 1.159 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0988 time to fit residues: 4.0673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10403 Z= 0.225 Angle : 0.594 9.475 14086 Z= 0.302 Chirality : 0.041 0.160 1569 Planarity : 0.004 0.045 1779 Dihedral : 7.445 82.997 1470 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 1.50 % Allowed : 17.88 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.78 (0.20), residues: 1258 helix: -2.91 (0.16), residues: 815 sheet: -5.15 (0.74), residues: 20 loop : -3.25 (0.25), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 326 HIS 0.006 0.001 HIS B 433 PHE 0.024 0.001 PHE A 71 TYR 0.022 0.001 TYR A 620 ARG 0.003 0.000 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 1.140 Fit side-chains outliers start: 16 outliers final: 6 residues processed: 121 average time/residue: 0.2576 time to fit residues: 44.2515 Evaluate side-chains 108 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 1.140 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0936 time to fit residues: 2.5726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 0.2980 chunk 77 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 110 optimal weight: 0.5980 chunk 116 optimal weight: 0.0370 chunk 106 optimal weight: 2.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN A 584 HIS ** A 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10403 Z= 0.174 Angle : 0.574 9.228 14086 Z= 0.288 Chirality : 0.040 0.158 1569 Planarity : 0.004 0.040 1779 Dihedral : 7.043 81.025 1470 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.47 % Allowed : 19.48 % Favored : 80.06 % 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: -4.46 (0.21), residues: 1258 helix: -2.67 (0.16), residues: 818 sheet: -4.92 (1.15), residues: 10 loop : -3.16 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 326 HIS 0.007 0.001 HIS B 433 PHE 0.022 0.001 PHE A 71 TYR 0.021 0.001 TYR A 620 ARG 0.004 0.000 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 1.377 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 106 average time/residue: 0.2900 time to fit residues: 44.1629 Evaluate side-chains 100 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 1.170 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1039 time to fit residues: 2.2188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN ** A 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10403 Z= 0.260 Angle : 0.617 12.026 14086 Z= 0.307 Chirality : 0.042 0.153 1569 Planarity : 0.004 0.039 1779 Dihedral : 7.224 80.930 1470 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.19 % Allowed : 19.94 % Favored : 79.87 % 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: -4.41 (0.21), residues: 1258 helix: -2.65 (0.16), residues: 814 sheet: -5.05 (1.12), residues: 10 loop : -3.11 (0.26), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 137 HIS 0.006 0.001 HIS A 621 PHE 0.021 0.001 PHE A 71 TYR 0.018 0.001 TYR A 620 ARG 0.004 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 1.439 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 108 average time/residue: 0.2542 time to fit residues: 39.6113 Evaluate side-chains 102 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.042 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 125 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 0.0570 chunk 79 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN ** A 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10403 Z= 0.230 Angle : 0.602 11.266 14086 Z= 0.299 Chirality : 0.041 0.155 1569 Planarity : 0.004 0.038 1779 Dihedral : 7.150 81.460 1470 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 0.56 % Allowed : 19.94 % Favored : 79.49 % 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: -4.38 (0.21), residues: 1258 helix: -2.57 (0.17), residues: 814 sheet: -3.59 (0.74), residues: 32 loop : -3.20 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 664 HIS 0.006 0.001 HIS B 433 PHE 0.020 0.001 PHE A 71 TYR 0.019 0.001 TYR A 620 ARG 0.004 0.000 ARG B 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 1.174 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 108 average time/residue: 0.2382 time to fit residues: 37.2038 Evaluate side-chains 104 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 1.209 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0998 time to fit residues: 2.3467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 102 optimal weight: 0.1980 chunk 12 optimal weight: 0.0970 chunk 18 optimal weight: 0.0470 chunk 87 optimal weight: 2.9990 chunk 5 optimal weight: 0.0670 overall best weight: 0.2814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN ** A 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.212585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.159801 restraints weight = 10477.358| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 1.75 r_work: 0.3757 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 10403 Z= 0.158 Angle : 0.577 10.519 14086 Z= 0.286 Chirality : 0.040 0.223 1569 Planarity : 0.004 0.038 1779 Dihedral : 6.819 80.028 1470 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.19 % Allowed : 20.13 % Favored : 79.68 % 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: -4.15 (0.21), residues: 1258 helix: -2.38 (0.17), residues: 817 sheet: -3.41 (0.73), residues: 32 loop : -3.14 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 326 HIS 0.014 0.001 HIS B 433 PHE 0.029 0.001 PHE A 295 TYR 0.018 0.001 TYR A 620 ARG 0.004 0.000 ARG B 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2486.89 seconds wall clock time: 45 minutes 46.93 seconds (2746.93 seconds total)