Starting phenix.real_space_refine on Wed Jul 30 08:22:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gi0_40056/07_2025/8gi0_40056.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gi0_40056/07_2025/8gi0_40056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gi0_40056/07_2025/8gi0_40056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gi0_40056/07_2025/8gi0_40056.map" model { file = "/net/cci-nas-00/data/ceres_data/8gi0_40056/07_2025/8gi0_40056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gi0_40056/07_2025/8gi0_40056.cif" } resolution = 3.5 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= 0.040 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: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 7734 2.51 5 N 2124 2.21 5 O 2266 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12189 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2333 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 293} Chain breaks: 1 Chain: "B" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2333 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 293} Chain breaks: 1 Chain: "C" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2333 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 293} Chain breaks: 1 Chain: "D" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2333 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 293} Chain breaks: 1 Chain: "E" Number of atoms: 2402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2402 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 15, 'TRANS': 287} Chain breaks: 1 Time building chain proxies: 8.77, per 1000 atoms: 0.72 Number of scatterers: 12189 At special positions: 0 Unit cell: (104.06, 124.7, 133.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 2266 8.00 N 2124 7.00 C 7734 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 - 3.00 Amino acid : True - 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: 3.09 Conformation dependent library (CDL) restraints added in 1.7 seconds 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2990 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 12 sheets defined 57.4% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'F' and resid 25 through 38 removed outlier: 3.521A pdb=" N ARG F 29 " --> pdb=" O GLU F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 44 removed outlier: 4.416A pdb=" N ILE F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 56 removed outlier: 3.610A pdb=" N LYS F 50 " --> pdb=" O PRO F 46 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER F 56 " --> pdb=" O GLN F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 71 Processing helix chain 'F' and resid 76 through 82 Processing helix chain 'A' and resid 11 through 23 removed outlier: 4.173A pdb=" N SER A 16 " --> pdb=" O GLY A 12 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 47 Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 99 through 116 removed outlier: 4.290A pdb=" N GLY A 105 " --> pdb=" O ASN A 101 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 145 Proline residue: A 135 - end of helix removed outlier: 3.659A pdb=" N ILE A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 169 removed outlier: 4.213A pdb=" N GLY A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 194 through 197 removed outlier: 3.633A pdb=" N ILE A 197 " --> pdb=" O TYR A 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 197' Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.895A pdb=" N GLN A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 225 removed outlier: 3.679A pdb=" N GLU A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 222 " --> pdb=" O GLY A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 252 removed outlier: 3.562A pdb=" N HIS A 245 " --> pdb=" O ARG A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 317 removed outlier: 3.828A pdb=" N GLY A 306 " --> pdb=" O GLU A 302 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 25 removed outlier: 4.234A pdb=" N SER B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU B 24 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 47 removed outlier: 3.502A pdb=" N VAL B 42 " --> pdb=" O GLY B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 76 Processing helix chain 'B' and resid 98 through 116 removed outlier: 3.764A pdb=" N GLY B 105 " --> pdb=" O ASN B 101 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP B 109 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 145 Proline residue: B 135 - end of helix removed outlier: 3.512A pdb=" N ILE B 144 " --> pdb=" O THR B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 171 removed outlier: 4.200A pdb=" N GLY B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 188 No H-bonds generated for 'chain 'B' and resid 186 through 188' Processing helix chain 'B' and resid 194 through 197 removed outlier: 3.556A pdb=" N ILE B 197 " --> pdb=" O TYR B 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 194 through 197' Processing helix chain 'B' and resid 203 through 225 removed outlier: 3.579A pdb=" N GLU B 209 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLY B 218 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N THR B 219 " --> pdb=" O GLN B 215 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU B 220 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 252 Processing helix chain 'B' and resid 294 through 323 removed outlier: 3.878A pdb=" N GLY B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS B 310 " --> pdb=" O GLY B 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 25 removed outlier: 4.234A pdb=" N SER C 16 " --> pdb=" O GLY C 12 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU C 24 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 47 removed outlier: 3.582A pdb=" N ASP C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 76 Processing helix chain 'C' and resid 98 through 116 removed outlier: 3.790A pdb=" N GLY C 105 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE C 106 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 145 Proline residue: C 135 - end of helix Processing helix chain 'C' and resid 156 through 171 removed outlier: 4.498A pdb=" N GLY C 160 " --> pdb=" O SER C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 188 No H-bonds generated for 'chain 'C' and resid 186 through 188' Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 203 through 225 removed outlier: 3.660A pdb=" N GLU C 209 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N GLY C 218 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR C 219 " --> pdb=" O GLN C 215 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU C 220 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL C 221 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL C 222 " --> pdb=" O GLY C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 252 Processing helix chain 'C' and resid 294 through 321 removed outlier: 3.622A pdb=" N GLU C 303 " --> pdb=" O GLU C 299 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS C 310 " --> pdb=" O GLY C 306 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER C 321 " --> pdb=" O THR C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 25 removed outlier: 4.215A pdb=" N SER D 16 " --> pdb=" O GLY D 12 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 47 Processing helix chain 'D' and resid 69 through 76 Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.703A pdb=" N ILE D 106 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 145 Proline residue: D 135 - end of helix removed outlier: 3.520A pdb=" N ILE D 144 " --> pdb=" O THR D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 172 removed outlier: 4.255A pdb=" N GLY D 160 " --> pdb=" O SER D 156 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA D 170 " --> pdb=" O PHE D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 194 through 197 removed outlier: 3.606A pdb=" N ILE D 197 " --> pdb=" O TYR D 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 194 through 197' Processing helix chain 'D' and resid 203 through 225 removed outlier: 3.959A pdb=" N GLU D 209 " --> pdb=" O SER D 205 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N GLY D 218 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N THR D 219 " --> pdb=" O GLN D 215 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL D 221 " --> pdb=" O ALA D 217 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL D 222 " --> pdb=" O GLY D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 252 Processing helix chain 'D' and resid 294 through 320 removed outlier: 3.840A pdb=" N GLU D 303 " --> pdb=" O GLU D 299 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS D 310 " --> pdb=" O GLY D 306 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N PHE D 318 " --> pdb=" O LYS D 314 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA D 319 " --> pdb=" O GLY D 315 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 344 removed outlier: 3.533A pdb=" N GLU E 334 " --> pdb=" O ARG E 330 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN E 340 " --> pdb=" O GLN E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 359 removed outlier: 4.302A pdb=" N TYR E 358 " --> pdb=" O PRO E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 373 removed outlier: 3.685A pdb=" N GLU E 365 " --> pdb=" O LYS E 361 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA E 368 " --> pdb=" O GLU E 364 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN E 371 " --> pdb=" O ILE E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 377 removed outlier: 3.597A pdb=" N GLU E 377 " --> pdb=" O ASN E 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 374 through 377' Processing helix chain 'E' and resid 378 through 389 removed outlier: 3.733A pdb=" N CYS E 386 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN E 387 " --> pdb=" O GLU E 383 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS E 388 " --> pdb=" O ALA E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 406 removed outlier: 3.778A pdb=" N TRP E 396 " --> pdb=" O ASN E 392 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA E 404 " --> pdb=" O GLY E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 423 removed outlier: 4.410A pdb=" N ILE E 414 " --> pdb=" O CYS E 410 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ALA E 415 " --> pdb=" O LEU E 411 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS E 418 " --> pdb=" O ILE E 414 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP E 423 " --> pdb=" O ALA E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 439 removed outlier: 3.750A pdb=" N HIS E 430 " --> pdb=" O ASP E 426 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA E 431 " --> pdb=" O ILE E 427 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA E 432 " --> pdb=" O ALA E 428 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN E 439 " --> pdb=" O VAL E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 456 removed outlier: 3.711A pdb=" N LEU E 454 " --> pdb=" O LEU E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 493 through 501 removed outlier: 4.400A pdb=" N LEU E 499 " --> pdb=" O ASP E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 524 removed outlier: 3.979A pdb=" N HIS E 514 " --> pdb=" O ASP E 510 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 526 through 541 removed outlier: 3.801A pdb=" N ALA E 531 " --> pdb=" O PHE E 527 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LYS E 532 " --> pdb=" O ASP E 528 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN E 533 " --> pdb=" O GLU E 529 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 558 removed outlier: 4.102A pdb=" N TRP E 548 " --> pdb=" O ASP E 544 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS E 550 " --> pdb=" O HIS E 546 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 575 removed outlier: 3.908A pdb=" N LEU E 565 " --> pdb=" O PRO E 561 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLU E 566 " --> pdb=" O GLN E 562 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA E 567 " --> pdb=" O GLU E 563 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP E 573 " --> pdb=" O ASN E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 592 removed outlier: 3.709A pdb=" N MET E 582 " --> pdb=" O TYR E 578 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN E 591 " --> pdb=" O VAL E 587 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 609 removed outlier: 4.202A pdb=" N LYS E 600 " --> pdb=" O PRO E 596 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG E 604 " --> pdb=" O LYS E 600 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU E 608 " --> pdb=" O ARG E 604 " (cutoff:3.500A) Processing helix chain 'E' and resid 620 through 625 removed outlier: 4.108A pdb=" N THR E 624 " --> pdb=" O SER E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 636 removed outlier: 3.674A pdb=" N LEU E 631 " --> pdb=" O LEU E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 643 through 648 Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 60 removed outlier: 6.737A pdb=" N SER A 29 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N LYS A 57 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU A 31 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ALA A 59 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU A 33 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL A 4 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N TYR A 34 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL A 6 " --> pdb=" O TYR A 34 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASN A 3 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N VAL A 83 " --> pdb=" O ASN A 3 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA A 5 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE A 123 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA3, first strand: chain 'A' and resid 257 through 263 removed outlier: 5.197A pdb=" N ARG A 287 " --> pdb=" O PRO A 276 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL A 278 " --> pdb=" O GLU A 285 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY A 283 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 54 through 60 removed outlier: 6.833A pdb=" N SER B 29 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N LYS B 57 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU B 31 " --> pdb=" O LYS B 57 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ALA B 59 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU B 33 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASN B 3 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N VAL B 83 " --> pdb=" O ASN B 3 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA B 5 " --> pdb=" O VAL B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AA6, first strand: chain 'B' and resid 257 through 263 removed outlier: 5.245A pdb=" N ARG B 287 " --> pdb=" O PRO B 276 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B 278 " --> pdb=" O GLU B 285 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 55 through 60 removed outlier: 6.444A pdb=" N LEU C 31 " --> pdb=" O LYS C 57 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ALA C 59 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU C 33 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL C 4 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N TYR C 34 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL C 6 " --> pdb=" O TYR C 34 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE C 123 " --> pdb=" O LEU C 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AA9, first strand: chain 'C' and resid 257 through 263 removed outlier: 5.067A pdb=" N ARG C 287 " --> pdb=" O PRO C 276 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL C 278 " --> pdb=" O GLU C 285 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 55 through 60 removed outlier: 3.715A pdb=" N ASP D 35 " --> pdb=" O ALA D 59 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AB3, first strand: chain 'D' and resid 257 through 263 removed outlier: 5.223A pdb=" N ARG D 287 " --> pdb=" O PRO D 276 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL D 278 " --> pdb=" O GLU D 285 " (cutoff:3.500A) 611 hydrogen bonds defined for protein. 1815 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: 3.77 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2882 1.33 - 1.45: 2141 1.45 - 1.57: 7275 1.57 - 1.69: 0 1.69 - 1.81: 109 Bond restraints: 12407 Sorted by residual: bond pdb=" CA GLU F 66 " pdb=" C GLU F 66 " ideal model delta sigma weight residual 1.522 1.488 0.034 1.39e-02 5.18e+03 5.92e+00 bond pdb=" CA LYS F 26 " pdb=" C LYS F 26 " ideal model delta sigma weight residual 1.522 1.489 0.033 1.39e-02 5.18e+03 5.77e+00 bond pdb=" CA SER E 647 " pdb=" C SER E 647 " ideal model delta sigma weight residual 1.522 1.491 0.031 1.36e-02 5.41e+03 5.22e+00 bond pdb=" CA CYS F 65 " pdb=" C CYS F 65 " ideal model delta sigma weight residual 1.524 1.496 0.028 1.27e-02 6.20e+03 4.76e+00 bond pdb=" CA ALA E 646 " pdb=" C ALA E 646 " ideal model delta sigma weight residual 1.523 1.493 0.030 1.37e-02 5.33e+03 4.76e+00 ... (remaining 12402 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 16486 1.97 - 3.94: 361 3.94 - 5.92: 33 5.92 - 7.89: 3 7.89 - 9.86: 1 Bond angle restraints: 16884 Sorted by residual: angle pdb=" C TRP E 648 " pdb=" N GLN E 649 " pdb=" CA GLN E 649 " ideal model delta sigma weight residual 121.54 111.68 9.86 1.91e+00 2.74e-01 2.66e+01 angle pdb=" N SER E 647 " pdb=" CA SER E 647 " pdb=" C SER E 647 " ideal model delta sigma weight residual 111.71 106.88 4.83 1.15e+00 7.56e-01 1.76e+01 angle pdb=" N SER A 321 " pdb=" CA SER A 321 " pdb=" C SER A 321 " ideal model delta sigma weight residual 108.96 115.51 -6.55 1.59e+00 3.96e-01 1.70e+01 angle pdb=" N LYS A 322 " pdb=" CA LYS A 322 " pdb=" C LYS A 322 " ideal model delta sigma weight residual 109.15 114.78 -5.63 1.44e+00 4.82e-01 1.53e+01 angle pdb=" C LYS F 26 " pdb=" N ARG F 27 " pdb=" CA ARG F 27 " ideal model delta sigma weight residual 120.28 114.89 5.39 1.44e+00 4.82e-01 1.40e+01 ... (remaining 16879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 6813 16.88 - 33.76: 529 33.76 - 50.64: 177 50.64 - 67.52: 41 67.52 - 84.39: 14 Dihedral angle restraints: 7574 sinusoidal: 2934 harmonic: 4640 Sorted by residual: dihedral pdb=" CA ASN E 636 " pdb=" C ASN E 636 " pdb=" N LEU E 637 " pdb=" CA LEU E 637 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ASP E 651 " pdb=" C ASP E 651 " pdb=" N LEU E 652 " pdb=" CA LEU E 652 " ideal model delta harmonic sigma weight residual 180.00 154.14 25.86 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA THR B 127 " pdb=" C THR B 127 " pdb=" N ASN B 128 " pdb=" CA ASN B 128 " ideal model delta harmonic sigma weight residual -180.00 -155.03 -24.97 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 7571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1218 0.036 - 0.071: 549 0.071 - 0.107: 167 0.107 - 0.142: 82 0.142 - 0.178: 5 Chirality restraints: 2021 Sorted by residual: chirality pdb=" CG LEU E 523 " pdb=" CB LEU E 523 " pdb=" CD1 LEU E 523 " pdb=" CD2 LEU E 523 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 7.93e-01 chirality pdb=" CA ASP E 651 " pdb=" N ASP E 651 " pdb=" C ASP E 651 " pdb=" CB ASP E 651 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.58e-01 chirality pdb=" CA GLU F 63 " pdb=" N GLU F 63 " pdb=" C GLU F 63 " pdb=" CB GLU F 63 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.13e-01 ... (remaining 2018 not shown) Planarity restraints: 2190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP E 510 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.23e+00 pdb=" CG ASP E 510 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASP E 510 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP E 510 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 176 " 0.029 5.00e-02 4.00e+02 4.40e-02 3.09e+00 pdb=" N PRO D 177 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO D 177 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 177 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 134 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO B 135 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 135 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 135 " -0.024 5.00e-02 4.00e+02 ... (remaining 2187 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 431 2.72 - 3.26: 12075 3.26 - 3.81: 17816 3.81 - 4.35: 22853 4.35 - 4.90: 39237 Nonbonded interactions: 92412 Sorted by model distance: nonbonded pdb=" O ARG D 320 " pdb=" OG SER D 321 " model vdw 2.170 3.040 nonbonded pdb=" O ASP E 510 " pdb=" OD1 ASP E 510 " model vdw 2.221 3.040 nonbonded pdb=" O GLN E 649 " pdb=" NE2 GLN E 650 " model vdw 2.273 3.120 nonbonded pdb=" OD1 ASP E 426 " pdb=" N ALA E 428 " model vdw 2.274 3.120 nonbonded pdb=" O ARG A 165 " pdb=" OD1 ASN A 169 " model vdw 2.304 3.040 ... (remaining 92407 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 47.070 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: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.020 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12407 Z= 0.211 Angle : 0.701 9.859 16884 Z= 0.393 Chirality : 0.047 0.178 2021 Planarity : 0.006 0.044 2190 Dihedral : 14.688 84.395 4584 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.14 % Allowed : 11.99 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.20), residues: 1603 helix: 0.39 (0.18), residues: 788 sheet: -0.32 (0.36), residues: 181 loop : -1.22 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 328 HIS 0.006 0.002 HIS E 601 PHE 0.020 0.002 PHE A 27 TYR 0.014 0.002 TYR E 568 ARG 0.006 0.001 ARG E 621 Details of bonding type rmsd hydrogen bonds : bond 0.19924 ( 611) hydrogen bonds : angle 6.00056 ( 1815) covalent geometry : bond 0.00437 (12407) covalent geometry : angle 0.70134 (16884) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 1.444 Fit side-chains REVERT: A 317 THR cc_start: 0.8109 (t) cc_final: 0.7869 (p) REVERT: C 143 LYS cc_start: 0.6822 (ttpp) cc_final: 0.6451 (tttt) REVERT: C 212 LYS cc_start: 0.7951 (tttp) cc_final: 0.7513 (tptp) REVERT: E 633 MET cc_start: 0.8231 (ttp) cc_final: 0.7790 (ttp) REVERT: E 645 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7256 (mm-30) outliers start: 15 outliers final: 8 residues processed: 163 average time/residue: 0.2501 time to fit residues: 59.2136 Evaluate side-chains 143 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 LYS Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 645 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 0.0570 chunk 64 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 48 optimal weight: 0.4980 chunk 75 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN D 139 GLN E 546 HIS E 601 HIS E 614 ASN E 650 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.134215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.107778 restraints weight = 139751.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.109310 restraints weight = 99203.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.109008 restraints weight = 85360.250| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12407 Z= 0.127 Angle : 0.575 6.648 16884 Z= 0.303 Chirality : 0.046 0.191 2021 Planarity : 0.005 0.048 2190 Dihedral : 6.093 65.308 1750 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.26 % Allowed : 12.06 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.21), residues: 1603 helix: 1.02 (0.18), residues: 820 sheet: 0.09 (0.35), residues: 192 loop : -1.14 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 328 HIS 0.003 0.001 HIS D 245 PHE 0.012 0.001 PHE D 27 TYR 0.008 0.001 TYR E 460 ARG 0.003 0.000 ARG E 398 Details of bonding type rmsd hydrogen bonds : bond 0.04825 ( 611) hydrogen bonds : angle 4.05835 ( 1815) covalent geometry : bond 0.00270 (12407) covalent geometry : angle 0.57468 (16884) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 142 time to evaluate : 1.879 Fit side-chains REVERT: A 157 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8093 (tt) REVERT: A 169 ASN cc_start: 0.8070 (p0) cc_final: 0.7822 (p0) REVERT: C 1 MET cc_start: 0.6074 (ttp) cc_final: 0.5842 (ttp) REVERT: C 143 LYS cc_start: 0.7333 (ttpp) cc_final: 0.6986 (tttt) REVERT: C 212 LYS cc_start: 0.8136 (tttp) cc_final: 0.7926 (tptp) REVERT: D 77 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6445 (mt-10) REVERT: D 285 GLU cc_start: 0.6465 (OUTLIER) cc_final: 0.6239 (tp30) REVERT: E 555 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7923 (mt) REVERT: E 633 MET cc_start: 0.7992 (ttp) cc_final: 0.7583 (ttt) REVERT: E 645 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7324 (mp0) outliers start: 43 outliers final: 21 residues processed: 166 average time/residue: 0.2615 time to fit residues: 64.4046 Evaluate side-chains 155 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain E residue 345 GLU Chi-restraints excluded: chain E residue 367 ILE Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 641 SER Chi-restraints excluded: chain E residue 645 GLU Chi-restraints excluded: chain E residue 651 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 98 optimal weight: 0.0870 chunk 39 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 143 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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 = 0.3341 r_free = 0.3341 target = 0.133616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.107257 restraints weight = 138714.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.108444 restraints weight = 99658.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.108362 restraints weight = 86820.496| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12407 Z= 0.126 Angle : 0.552 7.901 16884 Z= 0.287 Chirality : 0.045 0.183 2021 Planarity : 0.005 0.047 2190 Dihedral : 5.315 65.492 1738 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.34 % Allowed : 12.52 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.21), residues: 1603 helix: 1.40 (0.18), residues: 820 sheet: 0.00 (0.35), residues: 192 loop : -1.07 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 328 HIS 0.003 0.001 HIS D 245 PHE 0.014 0.001 PHE A 27 TYR 0.007 0.001 TYR E 358 ARG 0.003 0.000 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.04944 ( 611) hydrogen bonds : angle 3.84394 ( 1815) covalent geometry : bond 0.00273 (12407) covalent geometry : angle 0.55202 (16884) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 138 time to evaluate : 1.419 Fit side-chains REVERT: A 157 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8125 (tt) REVERT: B 74 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6915 (tp30) REVERT: B 232 THR cc_start: 0.8275 (OUTLIER) cc_final: 0.7891 (p) REVERT: C 1 MET cc_start: 0.6065 (ttp) cc_final: 0.5860 (ttp) REVERT: C 143 LYS cc_start: 0.7350 (ttpp) cc_final: 0.7004 (tttt) REVERT: C 212 LYS cc_start: 0.8134 (tttp) cc_final: 0.7895 (tptp) REVERT: D 77 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6438 (mt-10) REVERT: D 285 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.6330 (tp30) REVERT: E 555 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8068 (mt) REVERT: E 633 MET cc_start: 0.8119 (ttp) cc_final: 0.7796 (ttt) REVERT: E 645 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7035 (mm-30) outliers start: 44 outliers final: 23 residues processed: 167 average time/residue: 0.2412 time to fit residues: 59.1621 Evaluate side-chains 150 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 29 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 641 SER Chi-restraints excluded: chain E residue 645 GLU Chi-restraints excluded: chain E residue 651 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 145 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3309 r_free = 0.3309 target = 0.130802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.104225 restraints weight = 140466.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.105368 restraints weight = 99711.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.105590 restraints weight = 88349.490| |-----------------------------------------------------------------------------| r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12407 Z= 0.156 Angle : 0.597 9.559 16884 Z= 0.311 Chirality : 0.046 0.178 2021 Planarity : 0.006 0.054 2190 Dihedral : 5.432 65.345 1738 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.49 % Allowed : 13.05 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.21), residues: 1603 helix: 1.39 (0.18), residues: 823 sheet: -0.17 (0.35), residues: 192 loop : -1.22 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 328 HIS 0.003 0.001 HIS D 245 PHE 0.017 0.002 PHE A 27 TYR 0.007 0.001 TYR A 259 ARG 0.004 0.000 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.05869 ( 611) hydrogen bonds : angle 3.91718 ( 1815) covalent geometry : bond 0.00359 (12407) covalent geometry : angle 0.59710 (16884) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 125 time to evaluate : 1.502 Fit side-chains REVERT: A 157 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8238 (tt) REVERT: A 265 ASP cc_start: 0.7940 (t0) cc_final: 0.7677 (t0) REVERT: B 20 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7788 (mp) REVERT: B 74 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7058 (tp30) REVERT: B 232 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.7931 (p) REVERT: C 143 LYS cc_start: 0.7396 (ttpp) cc_final: 0.7006 (tttt) REVERT: C 212 LYS cc_start: 0.8243 (tttp) cc_final: 0.8003 (tptp) REVERT: D 77 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6422 (mt-10) REVERT: D 285 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.6312 (tp30) REVERT: E 433 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8399 (mm) REVERT: E 457 GLN cc_start: 0.8242 (mt0) cc_final: 0.7942 (mt0) REVERT: E 555 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8104 (mt) REVERT: E 633 MET cc_start: 0.7866 (ttp) cc_final: 0.7597 (ttt) REVERT: E 645 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7073 (mm-30) outliers start: 46 outliers final: 27 residues processed: 159 average time/residue: 0.3026 time to fit residues: 71.7544 Evaluate side-chains 161 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 641 SER Chi-restraints excluded: chain E residue 645 GLU Chi-restraints excluded: chain E residue 651 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 114 optimal weight: 0.0970 chunk 63 optimal weight: 0.5980 chunk 131 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 78 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.3341 r_free = 0.3341 target = 0.133570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.106827 restraints weight = 139654.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.108414 restraints weight = 98350.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.108100 restraints weight = 84011.849| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12407 Z= 0.120 Angle : 0.533 7.660 16884 Z= 0.278 Chirality : 0.044 0.173 2021 Planarity : 0.005 0.050 2190 Dihedral : 5.189 65.293 1738 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.19 % Allowed : 13.35 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.21), residues: 1603 helix: 1.53 (0.18), residues: 834 sheet: -0.14 (0.35), residues: 192 loop : -1.24 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 328 HIS 0.003 0.001 HIS A 245 PHE 0.013 0.001 PHE A 27 TYR 0.006 0.001 TYR E 358 ARG 0.003 0.000 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.04600 ( 611) hydrogen bonds : angle 3.70619 ( 1815) covalent geometry : bond 0.00261 (12407) covalent geometry : angle 0.53280 (16884) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 122 time to evaluate : 1.872 Fit side-chains REVERT: A 157 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8097 (tt) REVERT: A 265 ASP cc_start: 0.7955 (t0) cc_final: 0.7748 (t0) REVERT: B 74 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7081 (tp30) REVERT: B 157 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7601 (tt) REVERT: C 212 LYS cc_start: 0.8214 (tttp) cc_final: 0.7891 (tptp) REVERT: D 74 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6642 (tp30) REVERT: D 77 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6356 (mt-10) REVERT: D 223 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7134 (ttmt) REVERT: D 285 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.6297 (tp30) REVERT: E 457 GLN cc_start: 0.8284 (mt0) cc_final: 0.8047 (mt0) REVERT: E 523 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8043 (tt) REVERT: E 555 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7999 (mt) REVERT: E 633 MET cc_start: 0.7864 (ttp) cc_final: 0.7641 (ttt) REVERT: E 645 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7021 (mm-30) outliers start: 42 outliers final: 26 residues processed: 151 average time/residue: 0.2424 time to fit residues: 54.1578 Evaluate side-chains 153 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 641 SER Chi-restraints excluded: chain E residue 645 GLU Chi-restraints excluded: chain E residue 651 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 0.0980 chunk 37 optimal weight: 0.6980 chunk 153 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 430 HIS E 636 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.131750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.105083 restraints weight = 138655.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.106061 restraints weight = 99692.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.105936 restraints weight = 88711.353| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12407 Z= 0.141 Angle : 0.565 7.990 16884 Z= 0.294 Chirality : 0.045 0.175 2021 Planarity : 0.005 0.052 2190 Dihedral : 5.235 65.530 1738 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.49 % Allowed : 13.35 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.21), residues: 1603 helix: 1.56 (0.18), residues: 828 sheet: -0.22 (0.35), residues: 192 loop : -1.18 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 328 HIS 0.003 0.001 HIS D 245 PHE 0.015 0.002 PHE A 27 TYR 0.006 0.001 TYR E 358 ARG 0.003 0.000 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.05356 ( 611) hydrogen bonds : angle 3.78955 ( 1815) covalent geometry : bond 0.00321 (12407) covalent geometry : angle 0.56474 (16884) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 117 time to evaluate : 1.329 Fit side-chains REVERT: A 157 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8252 (tt) REVERT: A 265 ASP cc_start: 0.7922 (t0) cc_final: 0.7688 (t0) REVERT: B 74 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7046 (tp30) REVERT: C 212 LYS cc_start: 0.8162 (tttp) cc_final: 0.7959 (tptp) REVERT: D 77 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6519 (mt-10) REVERT: D 223 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7146 (ttmt) REVERT: D 285 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.6287 (tp30) REVERT: E 523 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8095 (tt) REVERT: E 555 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8175 (mt) REVERT: E 633 MET cc_start: 0.7915 (ttp) cc_final: 0.7673 (ttt) REVERT: E 645 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7003 (mm-30) outliers start: 46 outliers final: 29 residues processed: 149 average time/residue: 0.2206 time to fit residues: 49.0008 Evaluate side-chains 153 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 579 VAL Chi-restraints excluded: chain E residue 636 ASN Chi-restraints excluded: chain E residue 641 SER Chi-restraints excluded: chain E residue 645 GLU Chi-restraints excluded: chain E residue 651 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 1.9990 chunk 87 optimal weight: 0.0980 chunk 112 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 153 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 457 GLN E 636 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.132501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.105920 restraints weight = 140785.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.107153 restraints weight = 104463.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.107410 restraints weight = 87266.386| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12407 Z= 0.127 Angle : 0.544 7.208 16884 Z= 0.283 Chirality : 0.045 0.173 2021 Planarity : 0.005 0.062 2190 Dihedral : 5.155 65.247 1738 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.57 % Allowed : 13.35 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.21), residues: 1603 helix: 1.56 (0.18), residues: 841 sheet: -0.21 (0.35), residues: 192 loop : -1.26 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 328 HIS 0.003 0.001 HIS D 245 PHE 0.013 0.001 PHE A 27 TYR 0.006 0.001 TYR E 358 ARG 0.003 0.000 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.04864 ( 611) hydrogen bonds : angle 3.72829 ( 1815) covalent geometry : bond 0.00284 (12407) covalent geometry : angle 0.54361 (16884) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 118 time to evaluate : 1.457 Fit side-chains REVERT: A 157 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8195 (tt) REVERT: A 265 ASP cc_start: 0.7920 (t0) cc_final: 0.7652 (t0) REVERT: B 74 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6992 (tp30) REVERT: B 176 VAL cc_start: 0.7799 (OUTLIER) cc_final: 0.7482 (m) REVERT: C 212 LYS cc_start: 0.8157 (tttp) cc_final: 0.7937 (tptp) REVERT: D 74 GLU cc_start: 0.7363 (tp30) cc_final: 0.6657 (mp0) REVERT: D 77 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6260 (mt-10) REVERT: D 101 ASN cc_start: 0.7768 (OUTLIER) cc_final: 0.7475 (m-40) REVERT: D 223 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7198 (ttmt) REVERT: D 285 GLU cc_start: 0.6566 (OUTLIER) cc_final: 0.6319 (tp30) REVERT: E 523 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8102 (tt) REVERT: E 555 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8153 (mt) REVERT: E 633 MET cc_start: 0.7906 (ttp) cc_final: 0.7693 (ttt) REVERT: E 645 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.6946 (mm-30) outliers start: 47 outliers final: 31 residues processed: 152 average time/residue: 0.2285 time to fit residues: 51.5754 Evaluate side-chains 159 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 118 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 579 VAL Chi-restraints excluded: chain E residue 636 ASN Chi-restraints excluded: chain E residue 641 SER Chi-restraints excluded: chain E residue 645 GLU Chi-restraints excluded: chain E residue 651 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 0.0070 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 104 optimal weight: 0.0670 chunk 75 optimal weight: 3.9990 chunk 14 optimal weight: 0.0870 chunk 120 optimal weight: 5.9990 chunk 139 optimal weight: 0.6980 chunk 146 optimal weight: 0.0470 overall best weight: 0.1812 ------------------------------------------------------------------------------- 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 = 0.3411 r_free = 0.3411 target = 0.139442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.113225 restraints weight = 139978.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.114603 restraints weight = 98447.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.114701 restraints weight = 85053.685| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 12407 Z= 0.092 Angle : 0.483 8.131 16884 Z= 0.250 Chirality : 0.042 0.186 2021 Planarity : 0.005 0.044 2190 Dihedral : 4.721 65.678 1738 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.05 % Allowed : 14.87 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.22), residues: 1603 helix: 1.93 (0.18), residues: 837 sheet: 0.19 (0.41), residues: 156 loop : -1.08 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 548 HIS 0.002 0.000 HIS D 58 PHE 0.007 0.001 PHE F 36 TYR 0.005 0.001 TYR E 358 ARG 0.002 0.000 ARG B 51 Details of bonding type rmsd hydrogen bonds : bond 0.02758 ( 611) hydrogen bonds : angle 3.43461 ( 1815) covalent geometry : bond 0.00192 (12407) covalent geometry : angle 0.48328 (16884) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 1.422 Fit side-chains REVERT: A 62 LYS cc_start: 0.7846 (tppt) cc_final: 0.7386 (mmtm) REVERT: A 157 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7951 (tt) REVERT: A 302 GLU cc_start: 0.6953 (mt-10) cc_final: 0.6220 (mm-30) REVERT: B 74 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6924 (tp30) REVERT: B 176 VAL cc_start: 0.7653 (OUTLIER) cc_final: 0.7384 (m) REVERT: C 212 LYS cc_start: 0.7948 (tttp) cc_final: 0.7607 (tptt) REVERT: C 223 LYS cc_start: 0.7311 (mttt) cc_final: 0.6893 (ttmm) REVERT: D 74 GLU cc_start: 0.7099 (tp30) cc_final: 0.6434 (mp0) REVERT: D 77 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6199 (mt-10) REVERT: D 101 ASN cc_start: 0.7776 (OUTLIER) cc_final: 0.7508 (m-40) REVERT: D 176 VAL cc_start: 0.8214 (OUTLIER) cc_final: 0.7882 (m) REVERT: D 223 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7144 (ttmt) REVERT: D 285 GLU cc_start: 0.6442 (OUTLIER) cc_final: 0.6240 (tp30) REVERT: E 451 ARG cc_start: 0.6753 (ttt180) cc_final: 0.6535 (tpt-90) REVERT: E 555 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7838 (mt) REVERT: E 633 MET cc_start: 0.7921 (ttp) cc_final: 0.7426 (ttm) REVERT: E 645 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.6817 (mm-30) outliers start: 27 outliers final: 11 residues processed: 166 average time/residue: 0.2607 time to fit residues: 62.1060 Evaluate side-chains 154 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 645 GLU Chi-restraints excluded: chain E residue 651 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 5.9990 chunk 142 optimal weight: 0.0870 chunk 146 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 0.0470 chunk 129 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 93 optimal weight: 0.2980 chunk 151 optimal weight: 0.0060 overall best weight: 0.2072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 575 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.139482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.113223 restraints weight = 139566.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.114413 restraints weight = 99119.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.114671 restraints weight = 85990.072| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12407 Z= 0.096 Angle : 0.497 8.163 16884 Z= 0.255 Chirality : 0.042 0.165 2021 Planarity : 0.005 0.045 2190 Dihedral : 4.396 65.984 1736 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.67 % Allowed : 15.02 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.22), residues: 1603 helix: 2.04 (0.18), residues: 843 sheet: 0.29 (0.41), residues: 156 loop : -0.96 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 328 HIS 0.003 0.000 HIS A 172 PHE 0.008 0.001 PHE F 36 TYR 0.004 0.001 TYR A 261 ARG 0.002 0.000 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.03002 ( 611) hydrogen bonds : angle 3.34442 ( 1815) covalent geometry : bond 0.00198 (12407) covalent geometry : angle 0.49690 (16884) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 1.367 Fit side-chains REVERT: A 62 LYS cc_start: 0.7851 (tppt) cc_final: 0.7450 (mmtm) REVERT: A 157 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8106 (tt) REVERT: A 302 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6264 (mm-30) REVERT: B 74 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6885 (tp30) REVERT: B 176 VAL cc_start: 0.7655 (OUTLIER) cc_final: 0.7362 (m) REVERT: B 208 LYS cc_start: 0.6937 (ptmm) cc_final: 0.6500 (mtpp) REVERT: C 212 LYS cc_start: 0.7936 (tttp) cc_final: 0.7635 (tptt) REVERT: C 223 LYS cc_start: 0.7462 (mttt) cc_final: 0.6976 (ttmm) REVERT: D 74 GLU cc_start: 0.7144 (tp30) cc_final: 0.6501 (mp0) REVERT: D 77 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6244 (mt-10) REVERT: D 101 ASN cc_start: 0.7895 (OUTLIER) cc_final: 0.7587 (m-40) REVERT: D 176 VAL cc_start: 0.8234 (OUTLIER) cc_final: 0.7881 (m) REVERT: D 223 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7059 (ttmt) REVERT: E 555 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7861 (mt) REVERT: E 633 MET cc_start: 0.7921 (ttp) cc_final: 0.7437 (ttm) REVERT: E 645 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.6802 (mm-30) outliers start: 22 outliers final: 11 residues processed: 154 average time/residue: 0.2682 time to fit residues: 60.9553 Evaluate side-chains 152 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 645 GLU Chi-restraints excluded: chain E residue 651 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3334 r_free = 0.3334 target = 0.132964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.106553 restraints weight = 140310.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.108315 restraints weight = 100619.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.107929 restraints weight = 83209.907| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12407 Z= 0.139 Angle : 0.574 8.663 16884 Z= 0.296 Chirality : 0.045 0.170 2021 Planarity : 0.005 0.047 2190 Dihedral : 4.772 65.878 1736 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.75 % Allowed : 15.02 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.22), residues: 1603 helix: 1.84 (0.18), residues: 833 sheet: -0.08 (0.35), residues: 192 loop : -1.07 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 628 HIS 0.004 0.001 HIS A 172 PHE 0.014 0.002 PHE A 27 TYR 0.005 0.001 TYR A 259 ARG 0.003 0.000 ARG C 287 Details of bonding type rmsd hydrogen bonds : bond 0.05088 ( 611) hydrogen bonds : angle 3.68852 ( 1815) covalent geometry : bond 0.00318 (12407) covalent geometry : angle 0.57411 (16884) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 1.302 Fit side-chains REVERT: A 157 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8224 (tt) REVERT: A 300 MET cc_start: 0.7885 (mtp) cc_final: 0.7553 (mtp) REVERT: B 74 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6941 (tp30) REVERT: B 176 VAL cc_start: 0.7917 (OUTLIER) cc_final: 0.7654 (m) REVERT: B 208 LYS cc_start: 0.7224 (ptmm) cc_final: 0.6982 (ptpp) REVERT: C 212 LYS cc_start: 0.8161 (tttp) cc_final: 0.7777 (tptt) REVERT: D 74 GLU cc_start: 0.7209 (tp30) cc_final: 0.6569 (mp0) REVERT: D 77 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6328 (mt-10) REVERT: D 176 VAL cc_start: 0.8313 (OUTLIER) cc_final: 0.8007 (m) REVERT: D 223 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7216 (ttmt) REVERT: E 523 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8143 (tt) REVERT: E 555 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8111 (mt) REVERT: E 621 ARG cc_start: 0.7459 (ptm160) cc_final: 0.7199 (ptm-80) REVERT: E 633 MET cc_start: 0.7887 (ttp) cc_final: 0.7648 (ttt) REVERT: E 645 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7014 (mm-30) outliers start: 23 outliers final: 12 residues processed: 142 average time/residue: 0.2681 time to fit residues: 55.6084 Evaluate side-chains 152 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 645 GLU Chi-restraints excluded: chain E residue 651 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 0.0070 chunk 116 optimal weight: 0.2980 chunk 18 optimal weight: 0.0270 chunk 35 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 110 optimal weight: 0.0970 chunk 7 optimal weight: 1.9990 overall best weight: 0.2654 ------------------------------------------------------------------------------- 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 = 0.3399 r_free = 0.3399 target = 0.138572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.112203 restraints weight = 139498.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.113817 restraints weight = 98000.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.113671 restraints weight = 83277.361| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 12407 Z= 0.097 Angle : 0.509 8.439 16884 Z= 0.260 Chirality : 0.042 0.170 2021 Planarity : 0.005 0.046 2190 Dihedral : 4.448 65.800 1736 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.52 % Allowed : 15.40 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.22), residues: 1603 helix: 1.98 (0.18), residues: 847 sheet: 0.24 (0.41), residues: 156 loop : -1.03 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 328 HIS 0.003 0.000 HIS A 172 PHE 0.008 0.001 PHE A 27 TYR 0.004 0.001 TYR E 578 ARG 0.002 0.000 ARG E 580 Details of bonding type rmsd hydrogen bonds : bond 0.03087 ( 611) hydrogen bonds : angle 3.41962 ( 1815) covalent geometry : bond 0.00204 (12407) covalent geometry : angle 0.50891 (16884) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4067.91 seconds wall clock time: 73 minutes 14.18 seconds (4394.18 seconds total)