Starting phenix.real_space_refine on Wed Feb 14 17:55:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vwc_32152/02_2024/7vwc_32152_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vwc_32152/02_2024/7vwc_32152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vwc_32152/02_2024/7vwc_32152.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vwc_32152/02_2024/7vwc_32152.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vwc_32152/02_2024/7vwc_32152_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vwc_32152/02_2024/7vwc_32152_updated.pdb" } resolution = 3.53 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= 0.006 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 2 5.49 5 S 46 5.16 5 C 6340 2.51 5 N 1741 2.21 5 O 1763 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 85": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A GLU 271": "OE1" <-> "OE2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A GLU 380": "OE1" <-> "OE2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A GLU 421": "OE1" <-> "OE2" Residue "A ARG 431": "NH1" <-> "NH2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A GLU 487": "OE1" <-> "OE2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A ARG 568": "NH1" <-> "NH2" Residue "A GLU 573": "OE1" <-> "OE2" Residue "A ARG 591": "NH1" <-> "NH2" Residue "A ARG 622": "NH1" <-> "NH2" Residue "A GLU 682": "OE1" <-> "OE2" Residue "A ARG 689": "NH1" <-> "NH2" Residue "A GLU 694": "OE1" <-> "OE2" Residue "B ARG 69": "NH1" <-> "NH2" Residue "B PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B GLU 271": "OE1" <-> "OE2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "B GLU 323": "OE1" <-> "OE2" Residue "B GLU 374": "OE1" <-> "OE2" Residue "B ARG 389": "NH1" <-> "NH2" Residue "B GLU 411": "OE1" <-> "OE2" Residue "B GLU 427": "OE1" <-> "OE2" Residue "B ARG 431": "NH1" <-> "NH2" Residue "B ARG 496": "NH1" <-> "NH2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ARG 568": "NH1" <-> "NH2" Residue "B GLU 596": "OE1" <-> "OE2" Residue "B ARG 622": "NH1" <-> "NH2" Residue "B GLU 630": "OE1" <-> "OE2" Residue "B GLU 694": "OE1" <-> "OE2" Residue "B ARG 712": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9892 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4929 Classifications: {'peptide': 617} Link IDs: {'PTRANS': 21, 'TRANS': 595} Chain breaks: 2 Chain: "B" Number of atoms: 4899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4899 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 21, 'TRANS': 590} Chain breaks: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'82T': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'82T': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.43, per 1000 atoms: 0.55 Number of scatterers: 9892 At special positions: 0 Unit cell: (103.88, 147.34, 111.3, 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 46 16.00 P 2 15.00 O 1763 8.00 N 1741 7.00 C 6340 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: 3.67 Conformation dependent library (CDL) restraints added in 1.9 seconds 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 5 sheets defined 52.4% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 69 through 82 removed outlier: 3.853A pdb=" N LEU A 81 " --> pdb=" O TRP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 96 through 105 removed outlier: 3.753A pdb=" N VAL A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 123 removed outlier: 3.774A pdb=" N CYS A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 140 removed outlier: 3.705A pdb=" N GLN A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLN A 136 " --> pdb=" O TRP A 132 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 149 through 174 removed outlier: 3.508A pdb=" N GLY A 156 " --> pdb=" O ARG A 152 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER A 161 " --> pdb=" O GLN A 157 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 173 " --> pdb=" O HIS A 169 " (cutoff:3.500A) 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 234 removed outlier: 3.579A pdb=" N ALA A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Proline residue: A 218 - end of helix removed outlier: 3.762A pdb=" N ALA A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 225 " --> pdb=" O ASP A 221 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TYR A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 250 removed outlier: 4.077A pdb=" N ALA A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.838A pdb=" N GLU A 267 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 284 removed outlier: 3.681A pdb=" N ARG A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 279 " --> pdb=" O ARG A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 299 through 310 removed outlier: 3.952A pdb=" N ALA A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 325 through 336 removed outlier: 3.811A pdb=" N MET A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 342 No H-bonds generated for 'chain 'A' and resid 339 through 342' Processing helix chain 'A' and resid 345 through 353 Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 375 through 379 removed outlier: 3.744A pdb=" N SER A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 375 through 379' Processing helix chain 'A' and resid 386 through 389 No H-bonds generated for 'chain 'A' and resid 386 through 389' Processing helix chain 'A' and resid 399 through 402 No H-bonds generated for 'chain 'A' and resid 399 through 402' Processing helix chain 'A' and resid 407 through 429 removed outlier: 4.079A pdb=" N LEU A 412 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 415 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR A 416 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA A 417 " --> pdb=" O GLY A 414 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL A 419 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N HIS A 420 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 423 " --> pdb=" O HIS A 420 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN A 424 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE A 426 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL A 429 " --> pdb=" O PHE A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 521 removed outlier: 3.772A pdb=" N ARG A 518 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 538 No H-bonds generated for 'chain 'A' and resid 536 through 538' Processing helix chain 'A' and resid 553 through 557 removed outlier: 3.698A pdb=" N VAL A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 553 through 557' Processing helix chain 'A' and resid 563 through 569 removed outlier: 3.912A pdb=" N GLN A 567 " --> pdb=" O VAL A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 579 No H-bonds generated for 'chain 'A' and resid 576 through 579' Processing helix chain 'A' and resid 586 through 588 No H-bonds generated for 'chain 'A' and resid 586 through 588' Processing helix chain 'A' and resid 601 through 603 No H-bonds generated for 'chain 'A' and resid 601 through 603' Processing helix chain 'A' and resid 607 through 621 removed outlier: 3.723A pdb=" N ARG A 612 " --> pdb=" O GLY A 608 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET A 618 " --> pdb=" O GLY A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 650 removed outlier: 5.122A pdb=" N LYS A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 645 " --> pdb=" O GLY A 641 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 650 " --> pdb=" O ALA A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 665 removed outlier: 3.845A pdb=" N LYS A 665 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 699 removed outlier: 3.962A pdb=" N GLN A 697 " --> pdb=" O THR A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 710 Processing helix chain 'A' and resid 713 through 722 removed outlier: 4.888A pdb=" N GLN A 718 " --> pdb=" O GLU A 715 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU A 722 " --> pdb=" O ILE A 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 82 removed outlier: 3.684A pdb=" N LEU B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 81 " --> pdb=" O TRP B 77 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 96 through 102 Processing helix chain 'B' and resid 108 through 123 removed outlier: 4.068A pdb=" N CYS B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 147 removed outlier: 3.578A pdb=" N TRP B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN B 136 " --> pdb=" O TRP B 132 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP B 137 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA B 141 " --> pdb=" O TRP B 137 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Proline residue: B 143 - end of helix Processing helix chain 'B' and resid 152 through 167 removed outlier: 3.554A pdb=" N GLY B 156 " --> pdb=" O ARG B 152 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 174 No H-bonds generated for 'chain 'B' and resid 171 through 174' Processing helix chain 'B' and resid 181 through 184 No H-bonds generated for 'chain 'B' and resid 181 through 184' Processing helix chain 'B' and resid 195 through 198 No H-bonds generated for 'chain 'B' and resid 195 through 198' Processing helix chain 'B' and resid 205 through 208 No H-bonds generated for 'chain 'B' and resid 205 through 208' Processing helix chain 'B' and resid 213 through 216 No H-bonds generated for 'chain 'B' and resid 213 through 216' Processing helix chain 'B' and resid 218 through 233 removed outlier: 4.111A pdb=" N ALA B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 254 removed outlier: 4.058A pdb=" N ILE B 246 " --> pdb=" O TRP B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 269 Proline residue: B 263 - end of helix removed outlier: 4.015A pdb=" N VAL B 269 " --> pdb=" O GLY B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 282 No H-bonds generated for 'chain 'B' and resid 279 through 282' Processing helix chain 'B' and resid 284 through 288 Processing helix chain 'B' and resid 290 through 296 removed outlier: 3.618A pdb=" N PHE B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 311 removed outlier: 3.768A pdb=" N ALA B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 320 No H-bonds generated for 'chain 'B' and resid 317 through 320' Processing helix chain 'B' and resid 328 through 336 removed outlier: 3.864A pdb=" N PHE B 333 " --> pdb=" O MET B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 342 No H-bonds generated for 'chain 'B' and resid 339 through 342' 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 376 through 379 No H-bonds generated for 'chain 'B' and resid 376 through 379' Processing helix chain 'B' and resid 386 through 395 removed outlier: 4.075A pdb=" N LEU B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 393 " --> pdb=" O ARG B 389 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA B 394 " --> pdb=" O ASN B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing helix chain 'B' and resid 411 through 431 removed outlier: 3.609A pdb=" N TYR B 415 " --> pdb=" O GLU B 411 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N HIS B 420 " --> pdb=" O THR B 416 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET B 422 " --> pdb=" O ARG B 418 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE B 423 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU B 427 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN B 430 " --> pdb=" O PHE B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 520 removed outlier: 3.985A pdb=" N ARG B 518 " --> pdb=" O SER B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 538 No H-bonds generated for 'chain 'B' and resid 536 through 538' Processing helix chain 'B' and resid 553 through 556 No H-bonds generated for 'chain 'B' and resid 553 through 556' Processing helix chain 'B' and resid 563 through 569 Processing helix chain 'B' and resid 576 through 582 Processing helix chain 'B' and resid 586 through 589 No H-bonds generated for 'chain 'B' and resid 586 through 589' Processing helix chain 'B' and resid 601 through 603 No H-bonds generated for 'chain 'B' and resid 601 through 603' Processing helix chain 'B' and resid 607 through 621 removed outlier: 3.721A pdb=" N GLY B 614 " --> pdb=" O LYS B 610 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET B 618 " --> pdb=" O GLY B 614 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B 619 " --> pdb=" O MET B 615 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR B 620 " --> pdb=" O ALA B 616 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS B 621 " --> pdb=" O ARG B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 650 removed outlier: 3.778A pdb=" N GLY B 641 " --> pdb=" O ILE B 637 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYS B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 643 " --> pdb=" O VAL B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 663 No H-bonds generated for 'chain 'B' and resid 661 through 663' Processing helix chain 'B' and resid 686 through 689 No H-bonds generated for 'chain 'B' and resid 686 through 689' Processing helix chain 'B' and resid 694 through 701 removed outlier: 3.919A pdb=" N ARG B 698 " --> pdb=" O GLU B 694 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLU B 700 " --> pdb=" O LYS B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 715 removed outlier: 3.584A pdb=" N GLN B 714 " --> pdb=" O GLN B 710 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLU B 715 " --> pdb=" O ARG B 711 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 503 through 506 removed outlier: 6.459A pdb=" N HIS A 669 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N THR A 506 " --> pdb=" O HIS A 669 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU A 671 " --> pdb=" O THR A 506 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 539 through 542 removed outlier: 6.332A pdb=" N TYR A 625 " --> pdb=" O PHE A 540 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ILE A 542 " --> pdb=" O TYR A 625 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU A 627 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ALA A 653 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N LEU A 628 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU A 655 " --> pdb=" O LEU A 628 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 467 through 469 removed outlier: 6.516A pdb=" N LEU B 531 " --> pdb=" O VAL B 468 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 539 through 542 removed outlier: 6.095A pdb=" N TYR B 625 " --> pdb=" O PHE B 540 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ILE B 542 " --> pdb=" O TYR B 625 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU B 627 " --> pdb=" O ILE B 542 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA B 653 " --> pdb=" O ALA B 626 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU B 628 " --> pdb=" O ALA B 653 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU B 655 " --> pdb=" O LEU B 628 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 669 through 673 251 hydrogen bonds defined for protein. 672 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: 2.63 Time building geometry restraints manager: 3.98 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: 1578 1.31 - 1.43: 2725 1.43 - 1.56: 5711 1.56 - 1.69: 4 1.69 - 1.81: 76 Bond restraints: 10094 Sorted by residual: bond pdb=" C18 82T B 801 " pdb=" O20 82T B 801 " ideal model delta sigma weight residual 1.335 1.399 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C18 82T A 801 " pdb=" O20 82T A 801 " ideal model delta sigma weight residual 1.335 1.395 -0.060 2.00e-02 2.50e+03 9.11e+00 bond pdb=" N TYR B 406 " pdb=" CA TYR B 406 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.31e-02 5.83e+03 5.14e+00 bond pdb=" N GLU A 380 " pdb=" CA GLU A 380 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.33e-02 5.65e+03 5.03e+00 bond pdb=" N THR B 693 " pdb=" CA THR B 693 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.35e-02 5.49e+03 4.37e+00 ... (remaining 10089 not shown) Histogram of bond angle deviations from ideal: 99.07 - 106.07: 176 106.07 - 113.07: 5476 113.07 - 120.07: 3833 120.07 - 127.06: 4043 127.06 - 134.06: 117 Bond angle restraints: 13645 Sorted by residual: angle pdb=" N TYR B 406 " pdb=" CA TYR B 406 " pdb=" C TYR B 406 " ideal model delta sigma weight residual 114.31 105.53 8.78 1.29e+00 6.01e-01 4.63e+01 angle pdb=" N ILE B 399 " pdb=" CA ILE B 399 " pdb=" C ILE B 399 " ideal model delta sigma weight residual 112.96 106.89 6.07 1.00e+00 1.00e+00 3.68e+01 angle pdb=" CA GLU A 471 " pdb=" C GLU A 471 " pdb=" O GLU A 471 " ideal model delta sigma weight residual 121.54 116.16 5.38 1.16e+00 7.43e-01 2.15e+01 angle pdb=" N THR B 693 " pdb=" CA THR B 693 " pdb=" C THR B 693 " ideal model delta sigma weight residual 113.43 107.67 5.76 1.26e+00 6.30e-01 2.09e+01 angle pdb=" O24 82T A 801 " pdb=" P25 82T A 801 " pdb=" O28 82T A 801 " ideal model delta sigma weight residual 97.38 110.71 -13.33 3.00e+00 1.11e-01 1.97e+01 ... (remaining 13640 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.42: 5817 29.42 - 58.83: 239 58.83 - 88.25: 32 88.25 - 117.66: 2 117.66 - 147.08: 1 Dihedral angle restraints: 6091 sinusoidal: 2516 harmonic: 3575 Sorted by residual: dihedral pdb=" CA GLU A 682 " pdb=" C GLU A 682 " pdb=" N LYS A 683 " pdb=" CA LYS A 683 " ideal model delta harmonic sigma weight residual -180.00 -151.70 -28.30 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA GLU B 271 " pdb=" C GLU B 271 " pdb=" N GLU B 272 " pdb=" CA GLU B 272 " ideal model delta harmonic sigma weight residual 180.00 154.16 25.84 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA LEU B 690 " pdb=" C LEU B 690 " pdb=" N SER B 691 " pdb=" CA SER B 691 " ideal model delta harmonic sigma weight residual 180.00 157.69 22.31 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 6088 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 962 0.047 - 0.093: 453 0.093 - 0.140: 100 0.140 - 0.186: 5 0.186 - 0.233: 3 Chirality restraints: 1523 Sorted by residual: chirality pdb=" CA GLU A 471 " pdb=" N GLU A 471 " pdb=" C GLU A 471 " pdb=" CB GLU A 471 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB VAL B 347 " pdb=" CA VAL B 347 " pdb=" CG1 VAL B 347 " pdb=" CG2 VAL B 347 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE B 558 " pdb=" CA ILE B 558 " pdb=" CG1 ILE B 558 " pdb=" CG2 ILE B 558 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.41e-01 ... (remaining 1520 not shown) Planarity restraints: 1728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 236 " 0.030 2.00e-02 2.50e+03 6.28e-02 3.94e+01 pdb=" C ARG A 236 " -0.108 2.00e-02 2.50e+03 pdb=" O ARG A 236 " 0.042 2.00e-02 2.50e+03 pdb=" N GLY A 237 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 545 " -0.040 5.00e-02 4.00e+02 6.01e-02 5.77e+00 pdb=" N PRO B 546 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 546 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 546 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 242 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO B 243 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 243 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 243 " 0.024 5.00e-02 4.00e+02 ... (remaining 1725 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 264 2.68 - 3.24: 9875 3.24 - 3.79: 14342 3.79 - 4.35: 20514 4.35 - 4.90: 32324 Nonbonded interactions: 77319 Sorted by model distance: nonbonded pdb=" O ASN B 318 " pdb=" ND2 ASN B 318 " model vdw 2.127 2.520 nonbonded pdb=" OG SER B 562 " pdb=" OD1 ASP B 565 " model vdw 2.218 2.440 nonbonded pdb=" NH2 ARG A 189 " pdb=" OD2 ASP A 428 " model vdw 2.230 2.520 nonbonded pdb=" NE2 GLN B 611 " pdb=" O CYS B 631 " model vdw 2.246 2.520 nonbonded pdb=" O GLU B 471 " pdb=" NZ LYS B 624 " model vdw 2.257 2.520 ... (remaining 77314 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 68 through 720 or resid 801)) selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 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: 2.870 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.470 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 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 : 0.009 0.069 10094 Z= 0.558 Angle : 0.933 13.330 13645 Z= 0.502 Chirality : 0.052 0.233 1523 Planarity : 0.005 0.063 1728 Dihedral : 16.123 147.075 3787 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 0.38 % Allowed : 1.06 % Favored : 98.56 % 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 (0.21), residues: 1217 helix: -3.47 (0.14), residues: 795 sheet: -2.35 (0.74), residues: 47 loop : -1.96 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 326 HIS 0.006 0.002 HIS B 97 PHE 0.018 0.002 PHE B 162 TYR 0.018 0.002 TYR B 174 ARG 0.008 0.001 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 139 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: A 427 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7510 (mt-10) outliers start: 4 outliers final: 1 residues processed: 142 average time/residue: 0.2437 time to fit residues: 47.2166 Evaluate side-chains 121 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 693 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.0270 chunk 92 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 71 optimal weight: 0.3980 chunk 110 optimal weight: 8.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10094 Z= 0.159 Angle : 0.623 9.932 13645 Z= 0.311 Chirality : 0.041 0.180 1523 Planarity : 0.004 0.057 1728 Dihedral : 8.447 114.660 1438 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.29 % Allowed : 8.17 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.22), residues: 1217 helix: -2.83 (0.16), residues: 780 sheet: -2.29 (0.76), residues: 48 loop : -1.76 (0.34), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 77 HIS 0.004 0.001 HIS A 667 PHE 0.014 0.001 PHE A 673 TYR 0.011 0.001 TYR A 406 ARG 0.004 0.000 ARG B 234 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 154 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 320 ILE cc_start: 0.8732 (pt) cc_final: 0.8365 (mt) REVERT: A 427 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7575 (mt-10) outliers start: 3 outliers final: 3 residues processed: 156 average time/residue: 0.2280 time to fit residues: 49.2465 Evaluate side-chains 130 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 127 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 693 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10094 Z= 0.180 Angle : 0.564 9.916 13645 Z= 0.282 Chirality : 0.041 0.166 1523 Planarity : 0.003 0.054 1728 Dihedral : 7.628 95.036 1438 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.06 % Allowed : 11.54 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.23), residues: 1217 helix: -2.54 (0.16), residues: 778 sheet: -2.29 (0.72), residues: 58 loop : -1.71 (0.34), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 242 HIS 0.003 0.001 HIS A 97 PHE 0.013 0.001 PHE A 673 TYR 0.009 0.001 TYR A 620 ARG 0.004 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 137 time to evaluate : 1.129 Fit side-chains revert: symmetry clash REVERT: A 583 VAL cc_start: 0.8523 (t) cc_final: 0.8164 (m) outliers start: 11 outliers final: 7 residues processed: 143 average time/residue: 0.2535 time to fit residues: 49.2963 Evaluate side-chains 131 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 124 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 392 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 10094 Z= 0.370 Angle : 0.653 13.819 13645 Z= 0.323 Chirality : 0.046 0.155 1523 Planarity : 0.004 0.054 1728 Dihedral : 7.467 86.067 1437 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.02 % Allowed : 13.75 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.23), residues: 1217 helix: -2.53 (0.16), residues: 789 sheet: -2.17 (0.74), residues: 57 loop : -1.86 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 137 HIS 0.005 0.001 HIS A 97 PHE 0.014 0.002 PHE B 130 TYR 0.017 0.002 TYR A 620 ARG 0.008 0.001 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 1.553 Fit side-chains REVERT: A 192 ASN cc_start: 0.9005 (OUTLIER) cc_final: 0.8639 (p0) REVERT: B 225 THR cc_start: 0.8792 (m) cc_final: 0.8306 (p) outliers start: 21 outliers final: 15 residues processed: 145 average time/residue: 0.3127 time to fit residues: 65.1827 Evaluate side-chains 141 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 693 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 81 optimal weight: 0.0070 chunk 0 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 105 optimal weight: 0.0770 chunk 29 optimal weight: 0.3980 chunk 39 optimal weight: 5.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10094 Z= 0.147 Angle : 0.546 10.442 13645 Z= 0.271 Chirality : 0.041 0.338 1523 Planarity : 0.003 0.053 1728 Dihedral : 6.643 61.526 1437 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.67 % Allowed : 15.87 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.23), residues: 1217 helix: -2.24 (0.17), residues: 780 sheet: -2.24 (0.74), residues: 58 loop : -1.65 (0.34), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 77 HIS 0.002 0.000 HIS A 97 PHE 0.013 0.001 PHE A 673 TYR 0.033 0.001 TYR A 620 ARG 0.003 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 143 time to evaluate : 1.073 Fit side-chains REVERT: A 69 ARG cc_start: 0.6631 (ttt90) cc_final: 0.6217 (mmt90) REVERT: A 76 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7789 (tp) REVERT: A 418 ARG cc_start: 0.6953 (mtp-110) cc_final: 0.6488 (mtm-85) REVERT: A 583 VAL cc_start: 0.8462 (t) cc_final: 0.8042 (m) REVERT: A 615 MET cc_start: 0.7528 (mmm) cc_final: 0.7024 (tpp) REVERT: B 225 THR cc_start: 0.8691 (m) cc_final: 0.8402 (p) REVERT: B 422 MET cc_start: 0.8687 (ttp) cc_final: 0.8401 (ttp) REVERT: B 567 GLN cc_start: 0.8169 (mt0) cc_final: 0.7795 (mm-40) REVERT: B 615 MET cc_start: 0.8382 (mmm) cc_final: 0.7986 (mmt) outliers start: 7 outliers final: 4 residues processed: 148 average time/residue: 0.2488 time to fit residues: 50.3234 Evaluate side-chains 136 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 700 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 118 optimal weight: 8.9990 chunk 97 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 318 ASN ** B 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 10094 Z= 0.478 Angle : 0.707 9.251 13645 Z= 0.350 Chirality : 0.049 0.334 1523 Planarity : 0.005 0.054 1728 Dihedral : 7.272 75.106 1437 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 2.12 % Allowed : 17.79 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.23), residues: 1217 helix: -2.37 (0.17), residues: 790 sheet: -2.26 (0.74), residues: 58 loop : -1.89 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 77 HIS 0.005 0.001 HIS B 97 PHE 0.015 0.002 PHE B 130 TYR 0.019 0.002 TYR A 620 ARG 0.010 0.001 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 128 time to evaluate : 1.173 Fit side-chains REVERT: A 69 ARG cc_start: 0.6723 (ttt90) cc_final: 0.6245 (mmt90) REVERT: A 192 ASN cc_start: 0.8999 (OUTLIER) cc_final: 0.8633 (p0) REVERT: A 583 VAL cc_start: 0.8470 (t) cc_final: 0.8071 (m) REVERT: B 567 GLN cc_start: 0.8070 (mt0) cc_final: 0.7667 (mm-40) outliers start: 22 outliers final: 16 residues processed: 146 average time/residue: 0.2393 time to fit residues: 48.1465 Evaluate side-chains 138 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 700 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 72 optimal weight: 0.4980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 502 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10094 Z= 0.168 Angle : 0.558 10.432 13645 Z= 0.276 Chirality : 0.041 0.267 1523 Planarity : 0.003 0.052 1728 Dihedral : 6.625 56.299 1437 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.15 % Allowed : 19.13 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.23), residues: 1217 helix: -2.15 (0.17), residues: 782 sheet: -2.20 (0.74), residues: 58 loop : -1.67 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 77 HIS 0.002 0.001 HIS A 97 PHE 0.013 0.001 PHE A 673 TYR 0.015 0.001 TYR A 620 ARG 0.004 0.000 ARG A 660 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 133 time to evaluate : 1.132 Fit side-chains REVERT: A 69 ARG cc_start: 0.6768 (ttt90) cc_final: 0.6267 (mmt90) REVERT: A 76 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7648 (tp) REVERT: A 583 VAL cc_start: 0.8441 (t) cc_final: 0.8014 (m) REVERT: B 225 THR cc_start: 0.8682 (m) cc_final: 0.8453 (p) REVERT: B 567 GLN cc_start: 0.8071 (mt0) cc_final: 0.7722 (mm-40) outliers start: 12 outliers final: 8 residues processed: 144 average time/residue: 0.2367 time to fit residues: 47.1046 Evaluate side-chains 136 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 127 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 700 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 502 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10094 Z= 0.182 Angle : 0.558 10.184 13645 Z= 0.274 Chirality : 0.043 0.515 1523 Planarity : 0.003 0.052 1728 Dihedral : 6.421 50.237 1437 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.35 % Allowed : 19.23 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.24), residues: 1217 helix: -2.03 (0.17), residues: 786 sheet: -2.31 (0.68), residues: 68 loop : -1.69 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 77 HIS 0.003 0.001 HIS A 97 PHE 0.012 0.001 PHE A 71 TYR 0.021 0.001 TYR A 620 ARG 0.004 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 1.516 Fit side-chains REVERT: A 69 ARG cc_start: 0.6795 (ttt90) cc_final: 0.6265 (mmt90) REVERT: A 76 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7557 (tp) REVERT: A 583 VAL cc_start: 0.8388 (t) cc_final: 0.7944 (m) REVERT: B 225 THR cc_start: 0.8702 (m) cc_final: 0.8404 (p) REVERT: B 567 GLN cc_start: 0.8094 (mt0) cc_final: 0.7736 (mm-40) outliers start: 14 outliers final: 11 residues processed: 144 average time/residue: 0.2413 time to fit residues: 48.6739 Evaluate side-chains 139 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 700 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 103 optimal weight: 0.2980 chunk 71 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 502 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10094 Z= 0.220 Angle : 0.570 10.145 13645 Z= 0.280 Chirality : 0.044 0.515 1523 Planarity : 0.003 0.051 1728 Dihedral : 6.438 50.976 1437 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.44 % Allowed : 19.62 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.24), residues: 1217 helix: -1.97 (0.17), residues: 786 sheet: -2.23 (0.69), residues: 68 loop : -1.68 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP B 77 HIS 0.003 0.001 HIS A 97 PHE 0.012 0.001 PHE A 71 TYR 0.020 0.001 TYR A 620 ARG 0.007 0.000 ARG A 660 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 1.217 Fit side-chains REVERT: A 69 ARG cc_start: 0.6812 (ttt90) cc_final: 0.6272 (mmt90) REVERT: A 76 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7557 (tp) REVERT: A 583 VAL cc_start: 0.8428 (t) cc_final: 0.8018 (m) REVERT: B 225 THR cc_start: 0.8722 (m) cc_final: 0.8317 (p) REVERT: B 567 GLN cc_start: 0.8101 (mt0) cc_final: 0.7720 (mm-40) REVERT: B 588 ILE cc_start: 0.8317 (mm) cc_final: 0.8080 (mm) outliers start: 15 outliers final: 12 residues processed: 146 average time/residue: 0.2565 time to fit residues: 52.3356 Evaluate side-chains 142 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 700 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 121 optimal weight: 0.5980 chunk 111 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 76 optimal weight: 0.7980 chunk 103 optimal weight: 0.0670 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 502 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10094 Z= 0.138 Angle : 0.545 10.774 13645 Z= 0.265 Chirality : 0.042 0.473 1523 Planarity : 0.003 0.052 1728 Dihedral : 6.070 46.762 1437 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.25 % Allowed : 19.81 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.24), residues: 1217 helix: -1.75 (0.18), residues: 788 sheet: -2.10 (0.70), residues: 68 loop : -1.65 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP B 77 HIS 0.002 0.000 HIS A 621 PHE 0.013 0.001 PHE A 673 TYR 0.018 0.001 TYR A 620 ARG 0.005 0.000 ARG A 660 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 140 time to evaluate : 1.212 Fit side-chains REVERT: A 69 ARG cc_start: 0.6826 (ttt90) cc_final: 0.6265 (mmt90) REVERT: A 76 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7427 (tt) REVERT: A 583 VAL cc_start: 0.8386 (t) cc_final: 0.7977 (m) REVERT: A 590 GLN cc_start: 0.6396 (tm-30) cc_final: 0.6187 (tm-30) REVERT: B 225 THR cc_start: 0.8646 (m) cc_final: 0.8431 (p) REVERT: B 406 TYR cc_start: 0.6876 (t80) cc_final: 0.6462 (t80) REVERT: B 567 GLN cc_start: 0.8081 (mt0) cc_final: 0.7733 (mm-40) REVERT: B 615 MET cc_start: 0.8376 (mmm) cc_final: 0.8005 (mmt) REVERT: B 712 ARG cc_start: 0.7638 (ttp80) cc_final: 0.7429 (tpt90) outliers start: 13 outliers final: 10 residues processed: 151 average time/residue: 0.2311 time to fit residues: 48.6909 Evaluate side-chains 145 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 134 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 700 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 40 optimal weight: 0.0010 chunk 99 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.153936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.112332 restraints weight = 13310.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.109635 restraints weight = 11196.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.111029 restraints weight = 12886.779| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10094 Z= 0.164 Angle : 0.547 10.427 13645 Z= 0.266 Chirality : 0.043 0.494 1523 Planarity : 0.003 0.054 1728 Dihedral : 6.122 52.442 1437 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.54 % Allowed : 19.81 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.24), residues: 1217 helix: -1.66 (0.18), residues: 796 sheet: -2.03 (0.70), residues: 68 loop : -1.68 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP B 77 HIS 0.004 0.001 HIS A 667 PHE 0.011 0.001 PHE A 71 TYR 0.017 0.001 TYR A 620 ARG 0.005 0.000 ARG A 660 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1963.38 seconds wall clock time: 36 minutes 29.93 seconds (2189.93 seconds total)