Starting phenix.real_space_refine on Sat Feb 17 15:56:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z6f_11092/02_2024/6z6f_11092.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z6f_11092/02_2024/6z6f_11092.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z6f_11092/02_2024/6z6f_11092.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z6f_11092/02_2024/6z6f_11092.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z6f_11092/02_2024/6z6f_11092.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z6f_11092/02_2024/6z6f_11092.pdb" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 88 5.16 5 C 12208 2.51 5 N 3255 2.21 5 O 3664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 105": "OD1" <-> "OD2" Residue "A ASP 113": "OD1" <-> "OD2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A GLU 138": "OE1" <-> "OE2" Residue "A GLU 157": "OE1" <-> "OE2" Residue "A TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 169": "OD1" <-> "OD2" Residue "A ARG 201": "NH1" <-> "NH2" Residue "A TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 343": "OD1" <-> "OD2" Residue "A ASP 404": "OD1" <-> "OD2" Residue "A ASP 448": "OD1" <-> "OD2" Residue "A GLU 498": "OE1" <-> "OE2" Residue "A ASP 524": "OD1" <-> "OD2" Residue "A ASP 597": "OD1" <-> "OD2" Residue "A PHE 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 635": "OD1" <-> "OD2" Residue "A GLU 636": "OE1" <-> "OE2" Residue "A PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 685": "OE1" <-> "OE2" Residue "A PHE 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 689": "OE1" <-> "OE2" Residue "A PHE 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 81": "OD1" <-> "OD2" Residue "B ASP 105": "OD1" <-> "OD2" Residue "B GLU 129": "OE1" <-> "OE2" Residue "B GLU 152": "OE1" <-> "OE2" Residue "B TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B GLU 310": "OE1" <-> "OE2" Residue "B TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 381": "OD1" <-> "OD2" Residue "B GLU 397": "OE1" <-> "OE2" Residue "B ASP 404": "OD1" <-> "OD2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "B PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 487": "OD1" <-> "OD2" Residue "B ASP 511": "OD1" <-> "OD2" Residue "B ASP 543": "OD1" <-> "OD2" Residue "B PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 687": "NH1" <-> "NH2" Residue "B PHE 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 43": "OE1" <-> "OE2" Residue "D TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 68": "OD1" <-> "OD2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "D ASP 161": "OD1" <-> "OD2" Residue "D TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 261": "OE1" <-> "OE2" Residue "D TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 321": "OD1" <-> "OD2" Residue "D ASP 431": "OD1" <-> "OD2" Residue "D ASP 441": "OD1" <-> "OD2" Residue "D ASP 447": "OD1" <-> "OD2" Residue "D ASP 451": "OD1" <-> "OD2" Residue "D ASP 460": "OD1" <-> "OD2" Residue "D GLU 466": "OE1" <-> "OE2" Residue "D ASP 501": "OD1" <-> "OD2" Residue "D ASP 521": "OD1" <-> "OD2" Residue "D GLU 534": "OE1" <-> "OE2" Residue "D ARG 543": "NH1" <-> "NH2" Residue "D ASP 544": "OD1" <-> "OD2" Residue "D GLU 546": "OE1" <-> "OE2" Residue "D ASP 559": "OD1" <-> "OD2" Residue "D GLU 563": "OE1" <-> "OE2" Residue "D GLU 566": "OE1" <-> "OE2" Residue "D GLU 587": "OE1" <-> "OE2" Residue "D GLU 590": "OE1" <-> "OE2" Residue "C ASP 78": "OD1" <-> "OD2" Residue "C ASP 93": "OD1" <-> "OD2" Residue "C GLU 107": "OE1" <-> "OE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 257": "OD1" <-> "OD2" Residue "C PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 269": "OE1" <-> "OE2" Residue "C ASP 303": "OD1" <-> "OD2" Residue "C GLU 350": "OE1" <-> "OE2" Residue "C TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 362": "OE1" <-> "OE2" Residue "C PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 420": "OE1" <-> "OE2" Residue "C ASP 431": "OD1" <-> "OD2" Residue "C GLU 435": "OE1" <-> "OE2" Residue "C GLU 450": "OE1" <-> "OE2" Residue "C ASP 458": "OD1" <-> "OD2" Residue "C GLU 510": "OE1" <-> "OE2" Residue "C TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 552": "OE1" <-> "OE2" Residue "C GLU 559": "OE1" <-> "OE2" Residue "C GLU 580": "OE1" <-> "OE2" Residue "C GLU 609": "OE1" <-> "OE2" Residue "C PHE 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19217 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5178 Classifications: {'peptide': 651} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 615} Chain breaks: 2 Chain: "B" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5245 Classifications: {'peptide': 661} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 626} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 4376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4376 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 16, 'TRANS': 517} Chain breaks: 3 Chain: "C" Number of atoms: 4416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4416 Classifications: {'peptide': 541} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 520} Chain breaks: 6 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.71, per 1000 atoms: 0.51 Number of scatterers: 19217 At special positions: 0 Unit cell: (126.367, 142.901, 218.485, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 88 16.00 O 3664 8.00 N 3255 7.00 C 12208 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 359 " - pdb=" SG CYS C 366 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.95 Conformation dependent library (CDL) restraints added in 3.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" ND1 HIS A 247 " pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" ND1 HIS B 247 " 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4544 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 8 sheets defined 52.6% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 75 through 81 removed outlier: 3.863A pdb=" N ASP A 81 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 99 Processing helix chain 'A' and resid 127 through 133 removed outlier: 3.542A pdb=" N ILE A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 147 removed outlier: 3.810A pdb=" N GLU A 141 " --> pdb=" O LYS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 171 through 190 Proline residue: A 177 - end of helix Processing helix chain 'A' and resid 220 through 232 Processing helix chain 'A' and resid 249 through 256 Processing helix chain 'A' and resid 289 through 293 removed outlier: 3.773A pdb=" N GLY A 292 " --> pdb=" O GLU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 318 removed outlier: 3.811A pdb=" N TYR A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 327 removed outlier: 3.590A pdb=" N MET A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 366 removed outlier: 3.935A pdb=" N TYR A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY A 356 " --> pdb=" O PRO A 352 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 396 removed outlier: 3.505A pdb=" N GLY A 396 " --> pdb=" O LYS A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 428 removed outlier: 3.887A pdb=" N ILE A 414 " --> pdb=" O LYS A 410 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 423 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 474 Processing helix chain 'A' and resid 495 through 499 removed outlier: 3.881A pdb=" N GLU A 498 " --> pdb=" O ASN A 495 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER A 499 " --> pdb=" O ILE A 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 495 through 499' Processing helix chain 'A' and resid 535 through 543 Processing helix chain 'A' and resid 562 through 580 removed outlier: 3.501A pdb=" N TYR A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 584 removed outlier: 3.590A pdb=" N PHE A 584 " --> pdb=" O ILE A 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 581 through 584' Processing helix chain 'A' and resid 599 through 608 Processing helix chain 'A' and resid 636 through 645 Processing helix chain 'A' and resid 666 through 670 Processing helix chain 'A' and resid 679 through 699 removed outlier: 5.861A pdb=" N GLU A 689 " --> pdb=" O GLU A 685 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLU A 690 " --> pdb=" O GLU A 686 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 699 " --> pdb=" O ILE A 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 68 Processing helix chain 'B' and resid 87 through 100 removed outlier: 4.173A pdb=" N TYR B 91 " --> pdb=" O PRO B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 133 removed outlier: 3.673A pdb=" N ILE B 131 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 147 removed outlier: 3.533A pdb=" N LEU B 140 " --> pdb=" O THR B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 161 removed outlier: 3.777A pdb=" N GLY B 161 " --> pdb=" O GLU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 191 Proline residue: B 177 - end of helix Processing helix chain 'B' and resid 219 through 232 Processing helix chain 'B' and resid 249 through 256 removed outlier: 3.975A pdb=" N PHE B 256 " --> pdb=" O THR B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 274 removed outlier: 3.891A pdb=" N LYS B 274 " --> pdb=" O GLU B 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 271 through 274' Processing helix chain 'B' and resid 279 through 283 Processing helix chain 'B' and resid 307 through 318 removed outlier: 3.727A pdb=" N TYR B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 327 Processing helix chain 'B' and resid 351 through 366 removed outlier: 3.826A pdb=" N TYR B 355 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY B 356 " --> pdb=" O PRO B 352 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA B 366 " --> pdb=" O LEU B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 396 Processing helix chain 'B' and resid 410 through 428 removed outlier: 3.509A pdb=" N ILE B 414 " --> pdb=" O LYS B 410 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 423 " --> pdb=" O LYS B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 474 Processing helix chain 'B' and resid 486 through 489 removed outlier: 3.773A pdb=" N THR B 489 " --> pdb=" O PRO B 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 486 through 489' Processing helix chain 'B' and resid 495 through 499 removed outlier: 3.510A pdb=" N SER B 499 " --> pdb=" O ILE B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 534 No H-bonds generated for 'chain 'B' and resid 532 through 534' Processing helix chain 'B' and resid 535 through 544 removed outlier: 3.799A pdb=" N ASP B 543 " --> pdb=" O LYS B 539 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG B 544 " --> pdb=" O TRP B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 579 Processing helix chain 'B' and resid 580 through 584 Processing helix chain 'B' and resid 599 through 607 removed outlier: 3.539A pdb=" N LEU B 605 " --> pdb=" O GLY B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 645 removed outlier: 4.335A pdb=" N GLU B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 687 Processing helix chain 'B' and resid 687 through 700 Processing helix chain 'D' and resid 38 through 52 removed outlier: 3.792A pdb=" N HIS D 52 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 61 Processing helix chain 'D' and resid 70 through 87 removed outlier: 3.762A pdb=" N MET D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 96 removed outlier: 3.861A pdb=" N TYR D 95 " --> pdb=" O ILE D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 113 removed outlier: 3.994A pdb=" N ASN D 112 " --> pdb=" O HIS D 108 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 124 Processing helix chain 'D' and resid 140 through 151 removed outlier: 3.689A pdb=" N ASP D 144 " --> pdb=" O GLY D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 154 No H-bonds generated for 'chain 'D' and resid 152 through 154' Processing helix chain 'D' and resid 214 through 221 Processing helix chain 'D' and resid 243 through 252 Processing helix chain 'D' and resid 259 through 275 removed outlier: 3.627A pdb=" N LEU D 263 " --> pdb=" O SER D 259 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL D 271 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE D 272 " --> pdb=" O ALA D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 290 Processing helix chain 'D' and resid 292 through 294 No H-bonds generated for 'chain 'D' and resid 292 through 294' Processing helix chain 'D' and resid 295 through 301 Processing helix chain 'D' and resid 318 through 328 removed outlier: 3.514A pdb=" N VAL D 322 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR D 328 " --> pdb=" O ARG D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 443 removed outlier: 4.092A pdb=" N SER D 443 " --> pdb=" O LEU D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 515 Processing helix chain 'D' and resid 522 through 633 removed outlier: 4.542A pdb=" N ASN D 528 " --> pdb=" O VAL D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 633 through 639 removed outlier: 3.898A pdb=" N GLN D 639 " --> pdb=" O ARG D 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 42 removed outlier: 5.652A pdb=" N LYS C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER C 36 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE C 37 " --> pdb=" O HIS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 86 Processing helix chain 'C' and resid 87 through 92 removed outlier: 4.022A pdb=" N VAL C 92 " --> pdb=" O SER C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 104 removed outlier: 3.526A pdb=" N ARG C 102 " --> pdb=" O GLN C 99 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU C 104 " --> pdb=" O LEU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 111 Processing helix chain 'C' and resid 114 through 128 Processing helix chain 'C' and resid 147 through 158 removed outlier: 3.682A pdb=" N LEU C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 227 Processing helix chain 'C' and resid 243 through 249 removed outlier: 3.565A pdb=" N ASP C 249 " --> pdb=" O HIS C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 282 removed outlier: 4.268A pdb=" N LEU C 278 " --> pdb=" O ALA C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 307 Processing helix chain 'C' and resid 326 through 341 Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 413 through 437 Processing helix chain 'C' and resid 439 through 511 removed outlier: 3.970A pdb=" N LEU C 443 " --> pdb=" O GLY C 439 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LYS C 476 " --> pdb=" O GLN C 472 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASN C 511 " --> pdb=" O GLN C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 601 removed outlier: 3.936A pdb=" N SER C 561 " --> pdb=" O ASN C 557 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS C 562 " --> pdb=" O ALA C 558 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYS C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY C 601 " --> pdb=" O ASN C 597 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 120 removed outlier: 3.630A pdb=" N LEU A 374 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL A 331 " --> pdb=" O CYS A 371 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL A 373 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE A 333 " --> pdb=" O VAL A 373 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N MET A 240 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N SER A 334 " --> pdb=" O MET A 240 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU A 242 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE A 239 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N VAL A 265 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE A 241 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N LEU A 267 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP A 243 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N ARG A 269 " --> pdb=" O ASP A 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 476 through 477 removed outlier: 6.168A pdb=" N ILE A 503 " --> pdb=" O ILE A 549 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL A 551 " --> pdb=" O ILE A 503 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL A 505 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE A 590 " --> pdb=" O THR A 615 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR A 617 " --> pdb=" O ILE A 590 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N LEU A 647 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 618 " --> pdb=" O LEU A 647 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N PHE A 649 " --> pdb=" O VAL A 618 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN A 620 " --> pdb=" O PHE A 649 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 511 through 516 removed outlier: 3.634A pdb=" N ASP A 511 " --> pdb=" O ILE A 531 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS A 515 " --> pdb=" O SER A 527 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N SER A 527 " --> pdb=" O LYS A 515 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 118 through 121 removed outlier: 6.104A pdb=" N THR B 58 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE B 121 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU B 60 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLY B 59 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE B 239 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL B 265 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE B 241 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU B 267 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP B 243 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ARG B 269 " --> pdb=" O ASP B 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 476 through 478 removed outlier: 4.697A pdb=" N VAL B 490 " --> pdb=" O LEU B 478 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE B 503 " --> pdb=" O ILE B 549 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL B 551 " --> pdb=" O ILE B 503 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL B 505 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE B 502 " --> pdb=" O ALA B 591 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ILE B 593 " --> pdb=" O ILE B 502 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE B 504 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE B 595 " --> pdb=" O ILE B 504 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL B 506 " --> pdb=" O ILE B 595 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ILE B 619 " --> pdb=" O ILE B 590 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N PHE B 592 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N PHE B 621 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLY B 594 " --> pdb=" O PHE B 621 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL B 618 " --> pdb=" O LEU B 647 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N PHE B 649 " --> pdb=" O VAL B 618 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASN B 620 " --> pdb=" O PHE B 649 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU B 673 " --> pdb=" O SER B 646 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE B 648 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 512 through 513 Processing sheet with id=AA7, first strand: chain 'D' and resid 30 through 35 removed outlier: 3.504A pdb=" N ARG D 237 " --> pdb=" O TYR D 31 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL D 239 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR D 35 " --> pdb=" O VAL D 239 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE D 203 " --> pdb=" O ALA D 134 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 11 through 16 removed outlier: 3.716A pdb=" N LEU C 291 " --> pdb=" O SER C 263 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LYS C 140 " --> pdb=" O MET C 260 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N ILE C 262 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA C 142 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N CYS C 141 " --> pdb=" O PHE C 239 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ALA C 241 " --> pdb=" O CYS C 141 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE C 143 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ARG C 164 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N LEU C 240 " --> pdb=" O ARG C 164 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LYS C 166 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N THR C 242 " --> pdb=" O LYS C 166 " (cutoff:3.500A) 930 hydrogen bonds defined for protein. 2721 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: 5.29 Time building geometry restraints manager: 7.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5587 1.34 - 1.46: 3846 1.46 - 1.58: 10033 1.58 - 1.70: 0 1.70 - 1.82: 136 Bond restraints: 19602 Sorted by residual: bond pdb=" CG LEU A 573 " pdb=" CD2 LEU A 573 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.11e+00 bond pdb=" C VAL D 105 " pdb=" N PRO D 106 " ideal model delta sigma weight residual 1.335 1.364 -0.029 1.36e-02 5.41e+03 4.57e+00 bond pdb=" CB VAL A 200 " pdb=" CG1 VAL A 200 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.25e+00 bond pdb=" C GLU B 559 " pdb=" N PRO B 560 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.80e+00 bond pdb=" C VAL C 441 " pdb=" N PRO C 442 " ideal model delta sigma weight residual 1.335 1.359 -0.025 1.28e-02 6.10e+03 3.72e+00 ... (remaining 19597 not shown) Histogram of bond angle deviations from ideal: 97.35 - 104.75: 319 104.75 - 112.14: 9211 112.14 - 119.53: 7275 119.53 - 126.92: 9442 126.92 - 134.32: 253 Bond angle restraints: 26500 Sorted by residual: angle pdb=" C PRO A 456 " pdb=" N LEU A 457 " pdb=" CA LEU A 457 " ideal model delta sigma weight residual 121.54 130.16 -8.62 1.91e+00 2.74e-01 2.04e+01 angle pdb=" C LEU B 555 " pdb=" N THR B 556 " pdb=" CA THR B 556 " ideal model delta sigma weight residual 121.54 130.01 -8.47 1.91e+00 2.74e-01 1.97e+01 angle pdb=" CA THR B 493 " pdb=" CB THR B 493 " pdb=" CG2 THR B 493 " ideal model delta sigma weight residual 110.50 117.83 -7.33 1.70e+00 3.46e-01 1.86e+01 angle pdb=" CA GLU C 350 " pdb=" CB GLU C 350 " pdb=" CG GLU C 350 " ideal model delta sigma weight residual 114.10 122.47 -8.37 2.00e+00 2.50e-01 1.75e+01 angle pdb=" N ILE B 450 " pdb=" CA ILE B 450 " pdb=" C ILE B 450 " ideal model delta sigma weight residual 112.29 108.37 3.92 9.40e-01 1.13e+00 1.74e+01 ... (remaining 26495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 10512 18.04 - 36.08: 1088 36.08 - 54.12: 281 54.12 - 72.16: 46 72.16 - 90.19: 33 Dihedral angle restraints: 11960 sinusoidal: 4947 harmonic: 7013 Sorted by residual: dihedral pdb=" CA SER B 54 " pdb=" C SER B 54 " pdb=" N PRO B 55 " pdb=" CA PRO B 55 " ideal model delta harmonic sigma weight residual 180.00 135.87 44.13 0 5.00e+00 4.00e-02 7.79e+01 dihedral pdb=" CA SER A 54 " pdb=" C SER A 54 " pdb=" N PRO A 55 " pdb=" CA PRO A 55 " ideal model delta harmonic sigma weight residual 180.00 137.35 42.65 0 5.00e+00 4.00e-02 7.28e+01 dihedral pdb=" CA LEU B 32 " pdb=" C LEU B 32 " pdb=" N SER B 33 " pdb=" CA SER B 33 " ideal model delta harmonic sigma weight residual 180.00 145.70 34.30 0 5.00e+00 4.00e-02 4.71e+01 ... (remaining 11957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2403 0.072 - 0.145: 477 0.145 - 0.217: 70 0.217 - 0.290: 8 0.290 - 0.362: 3 Chirality restraints: 2961 Sorted by residual: chirality pdb=" CG LEU C 536 " pdb=" CB LEU C 536 " pdb=" CD1 LEU C 536 " pdb=" CD2 LEU C 536 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CB ILE B 530 " pdb=" CA ILE B 530 " pdb=" CG1 ILE B 530 " pdb=" CG2 ILE B 530 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA PHE C 512 " pdb=" N PHE C 512 " pdb=" C PHE C 512 " pdb=" CB PHE C 512 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 2958 not shown) Planarity restraints: 3405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 457 " 0.021 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C LEU A 457 " -0.073 2.00e-02 2.50e+03 pdb=" O LEU A 457 " 0.027 2.00e-02 2.50e+03 pdb=" N GLN A 458 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 54 " 0.060 5.00e-02 4.00e+02 8.97e-02 1.29e+01 pdb=" N PRO B 55 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO B 55 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 55 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 54 " -0.057 5.00e-02 4.00e+02 8.57e-02 1.17e+01 pdb=" N PRO A 55 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 55 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 55 " -0.048 5.00e-02 4.00e+02 ... (remaining 3402 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 657 2.71 - 3.26: 18654 3.26 - 3.80: 28959 3.80 - 4.35: 35765 4.35 - 4.90: 61035 Nonbonded interactions: 145070 Sorted by model distance: nonbonded pdb=" OD2 ASP A 338 " pdb="ZN ZN A 801 " model vdw 2.160 2.230 nonbonded pdb=" O GLU D 565 " pdb=" OG1 THR D 568 " model vdw 2.227 2.440 nonbonded pdb=" OH TYR A 468 " pdb=" OD2 ASP A 532 " model vdw 2.229 2.440 nonbonded pdb=" OD2 ASP B 338 " pdb="ZN ZN B 801 " model vdw 2.248 2.230 nonbonded pdb=" O VAL B 481 " pdb=" OH TYR B 575 " model vdw 2.262 2.440 ... (remaining 145065 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 40 through 515 or (resid 516 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ )) or resid \ 517 through 656 or resid 667 through 678 or resid 680 through 700 or resid 801) \ ) selection = (chain 'B' and (resid 40 through 439 or resid 445 through 700 or resid 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.94 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 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: 7.770 Check model and map are aligned: 0.280 Set scattering table: 0.150 Process input model: 49.750 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 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 : 0.006 0.082 19602 Z= 0.386 Angle : 1.018 12.508 26500 Z= 0.572 Chirality : 0.060 0.362 2961 Planarity : 0.007 0.090 3405 Dihedral : 16.346 90.195 7413 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.14 % Favored : 92.82 % Rotamer: Outliers : 3.55 % Allowed : 19.18 % Favored : 77.27 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.96 % Cis-general : 0.04 % Twisted Proline : 1.98 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.15), residues: 2353 helix: -0.42 (0.14), residues: 1164 sheet: -2.09 (0.31), residues: 228 loop : -3.86 (0.16), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 391 HIS 0.020 0.002 HIS C 487 PHE 0.029 0.002 PHE A 643 TYR 0.039 0.003 TYR A 468 ARG 0.005 0.001 ARG A 462 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 162 time to evaluate : 2.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 PHE cc_start: 0.9467 (OUTLIER) cc_final: 0.8637 (t80) REVERT: A 404 ASP cc_start: 0.8751 (t0) cc_final: 0.8543 (t0) REVERT: B 289 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8123 (tm-30) REVERT: B 374 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8847 (tt) REVERT: B 416 MET cc_start: 0.8513 (tmm) cc_final: 0.8302 (tmm) REVERT: B 566 MET cc_start: 0.8731 (tpp) cc_final: 0.8402 (tpp) REVERT: B 599 TYR cc_start: 0.8130 (t80) cc_final: 0.7916 (t80) REVERT: D 201 MET cc_start: 0.8286 (ptm) cc_final: 0.7861 (ppp) REVERT: D 327 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9051 (mm) REVERT: D 419 HIS cc_start: 0.7171 (t-90) cc_final: 0.6920 (t-90) REVERT: D 425 MET cc_start: 0.7881 (mmt) cc_final: 0.7631 (mmt) REVERT: D 429 TYR cc_start: 0.8348 (t80) cc_final: 0.8051 (t80) REVERT: D 455 PHE cc_start: 0.8741 (m-10) cc_final: 0.8528 (m-80) REVERT: C 155 GLU cc_start: 0.8761 (tt0) cc_final: 0.8522 (tt0) REVERT: C 552 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7843 (tm-30) REVERT: C 630 LYS cc_start: 0.7099 (OUTLIER) cc_final: 0.6753 (mtmm) outliers start: 77 outliers final: 41 residues processed: 239 average time/residue: 0.3403 time to fit residues: 120.8904 Evaluate side-chains 156 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 110 time to evaluate : 2.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 407 ASN Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 94 HIS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 360 CYS Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 552 GLU Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 630 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 4.9990 chunk 180 optimal weight: 5.9990 chunk 100 optimal weight: 0.0980 chunk 61 optimal weight: 0.2980 chunk 121 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 216 optimal weight: 0.4980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS A 167 ASN A 268 HIS A 286 GLN A 379 ASN A 465 GLN A 467 HIS A 517 ASN A 651 ASN B 83 HIS B 454 ASN B 500 ASN B 681 ASN D 153 ASN D 156 HIS D 404 ASN D 419 HIS D 479 ASN D 512 GLN D 530 GLN D 564 ASN C 87 HIS C 295 ASN C 308 ASN C 497 ASN C 543 ASN C 623 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 19602 Z= 0.156 Angle : 0.558 7.999 26500 Z= 0.292 Chirality : 0.041 0.151 2961 Planarity : 0.004 0.077 3405 Dihedral : 6.764 65.548 2649 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.83 % Allowed : 20.52 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % Cis-general : 0.04 % Twisted Proline : 1.98 % 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: -1.10 (0.17), residues: 2353 helix: 1.16 (0.16), residues: 1131 sheet: -1.18 (0.32), residues: 233 loop : -3.02 (0.17), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 298 HIS 0.006 0.001 HIS D 411 PHE 0.020 0.001 PHE D 586 TYR 0.038 0.001 TYR D 410 ARG 0.004 0.000 ARG C 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 128 time to evaluate : 2.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 PHE cc_start: 0.9429 (OUTLIER) cc_final: 0.8781 (t80) REVERT: A 404 ASP cc_start: 0.8813 (t0) cc_final: 0.8452 (t0) REVERT: B 149 MET cc_start: 0.8116 (mtt) cc_final: 0.7858 (mtt) REVERT: B 289 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8023 (tm-30) REVERT: B 480 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7580 (pp) REVERT: D 74 MET cc_start: 0.7363 (mmp) cc_final: 0.7117 (mmp) REVERT: D 201 MET cc_start: 0.8146 (ptm) cc_final: 0.7692 (ppp) REVERT: D 327 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8981 (mm) REVERT: D 425 MET cc_start: 0.7867 (mmt) cc_final: 0.7603 (mmt) REVERT: D 429 TYR cc_start: 0.8407 (t80) cc_final: 0.7947 (t80) REVERT: D 455 PHE cc_start: 0.8699 (m-10) cc_final: 0.8481 (m-80) REVERT: C 495 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9215 (mm) REVERT: C 630 LYS cc_start: 0.6549 (OUTLIER) cc_final: 0.6177 (mtmm) outliers start: 83 outliers final: 41 residues processed: 202 average time/residue: 0.3154 time to fit residues: 102.2117 Evaluate side-chains 157 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 111 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 467 HIS Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 257 TYR Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 407 ASN Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 530 GLN Chi-restraints excluded: chain D residue 597 ASN Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 505 ASN Chi-restraints excluded: chain C residue 630 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 120 optimal weight: 0.0570 chunk 67 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 216 optimal weight: 0.8980 chunk 233 optimal weight: 0.9990 chunk 192 optimal weight: 3.9990 chunk 214 optimal weight: 0.0040 chunk 73 optimal weight: 7.9990 chunk 173 optimal weight: 10.0000 overall best weight: 0.5912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 467 HIS ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 HIS C 589 GLN C 623 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19602 Z= 0.150 Angle : 0.533 7.966 26500 Z= 0.276 Chirality : 0.040 0.144 2961 Planarity : 0.004 0.075 3405 Dihedral : 5.436 59.302 2599 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.50 % Allowed : 20.98 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % Cis-general : 0.04 % Twisted Proline : 1.98 % 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: -0.42 (0.18), residues: 2353 helix: 1.70 (0.16), residues: 1134 sheet: -0.78 (0.33), residues: 239 loop : -2.70 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 313 HIS 0.015 0.001 HIS A 467 PHE 0.012 0.001 PHE D 492 TYR 0.043 0.001 TYR D 549 ARG 0.003 0.000 ARG C 628 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 121 time to evaluate : 2.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 PHE cc_start: 0.9421 (OUTLIER) cc_final: 0.8695 (t80) REVERT: A 404 ASP cc_start: 0.8835 (t0) cc_final: 0.8517 (t0) REVERT: B 149 MET cc_start: 0.8200 (mtt) cc_final: 0.7900 (mtt) REVERT: B 289 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8014 (tm-30) REVERT: B 566 MET cc_start: 0.8503 (tpp) cc_final: 0.8261 (tpp) REVERT: B 599 TYR cc_start: 0.8234 (t80) cc_final: 0.7815 (t80) REVERT: D 201 MET cc_start: 0.8093 (ptm) cc_final: 0.7646 (ppp) REVERT: D 327 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8989 (mm) REVERT: D 420 LYS cc_start: 0.8985 (mmmt) cc_final: 0.8776 (mmmt) REVERT: D 425 MET cc_start: 0.7863 (mmt) cc_final: 0.7574 (mmt) REVERT: C 495 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9193 (mm) REVERT: C 630 LYS cc_start: 0.6578 (OUTLIER) cc_final: 0.6108 (mtmm) outliers start: 76 outliers final: 46 residues processed: 191 average time/residue: 0.2751 time to fit residues: 84.8180 Evaluate side-chains 160 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 110 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 575 GLN Chi-restraints excluded: chain D residue 597 ASN Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 630 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 0.0470 chunk 162 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 103 optimal weight: 0.0170 chunk 145 optimal weight: 8.9990 chunk 217 optimal weight: 6.9990 chunk 230 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 overall best weight: 1.3120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 507 HIS ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS D 458 ASN D 488 ASN C 623 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19602 Z= 0.223 Angle : 0.565 8.852 26500 Z= 0.292 Chirality : 0.042 0.144 2961 Planarity : 0.004 0.077 3405 Dihedral : 5.299 55.073 2594 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 4.70 % Allowed : 20.79 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % Cis-general : 0.04 % Twisted Proline : 1.98 % 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: -0.13 (0.18), residues: 2353 helix: 1.93 (0.16), residues: 1136 sheet: -0.58 (0.33), residues: 243 loop : -2.56 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 298 HIS 0.005 0.001 HIS D 419 PHE 0.017 0.001 PHE D 586 TYR 0.039 0.001 TYR D 410 ARG 0.003 0.000 ARG C 628 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 123 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 PHE cc_start: 0.9447 (OUTLIER) cc_final: 0.8696 (t80) REVERT: A 404 ASP cc_start: 0.8890 (t0) cc_final: 0.8503 (t0) REVERT: B 149 MET cc_start: 0.8011 (mtt) cc_final: 0.7783 (mtt) REVERT: B 289 GLU cc_start: 0.8667 (tm-30) cc_final: 0.7841 (tm-30) REVERT: B 599 TYR cc_start: 0.8333 (t80) cc_final: 0.7810 (t80) REVERT: D 272 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7199 (mt) REVERT: D 327 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8984 (mm) REVERT: D 425 MET cc_start: 0.7873 (mmt) cc_final: 0.7582 (mmt) REVERT: D 476 GLU cc_start: 0.9369 (OUTLIER) cc_final: 0.8979 (pt0) REVERT: C 236 ASP cc_start: 0.8970 (OUTLIER) cc_final: 0.8651 (m-30) REVERT: C 422 MET cc_start: 0.8964 (ttm) cc_final: 0.8741 (ttm) REVERT: C 630 LYS cc_start: 0.6865 (OUTLIER) cc_final: 0.6281 (mtmm) outliers start: 102 outliers final: 67 residues processed: 220 average time/residue: 0.2715 time to fit residues: 96.3991 Evaluate side-chains 186 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 113 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 467 HIS Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 654 HIS Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 597 ASN Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 630 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 171 optimal weight: 6.9990 chunk 94 optimal weight: 0.6980 chunk 196 optimal weight: 0.9990 chunk 159 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 117 optimal weight: 0.4980 chunk 206 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 623 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19602 Z= 0.185 Angle : 0.549 10.262 26500 Z= 0.283 Chirality : 0.041 0.144 2961 Planarity : 0.004 0.074 3405 Dihedral : 5.197 52.772 2593 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.33 % Allowed : 21.21 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % Cis-general : 0.04 % Twisted Proline : 1.98 % 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: 0.04 (0.18), residues: 2353 helix: 2.04 (0.16), residues: 1136 sheet: -0.46 (0.34), residues: 241 loop : -2.45 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 298 HIS 0.004 0.001 HIS D 419 PHE 0.011 0.001 PHE D 602 TYR 0.041 0.001 TYR D 410 ARG 0.005 0.000 ARG A 666 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 119 time to evaluate : 2.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.7773 (mtp) cc_final: 0.7511 (mtp) REVERT: A 315 PHE cc_start: 0.9433 (OUTLIER) cc_final: 0.8697 (t80) REVERT: A 404 ASP cc_start: 0.8893 (t0) cc_final: 0.8496 (t0) REVERT: B 289 GLU cc_start: 0.8662 (tm-30) cc_final: 0.7956 (tm-30) REVERT: B 566 MET cc_start: 0.8529 (tpp) cc_final: 0.8045 (tpp) REVERT: B 571 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8785 (mp0) REVERT: B 599 TYR cc_start: 0.8320 (t80) cc_final: 0.7842 (t80) REVERT: D 201 MET cc_start: 0.8324 (ptm) cc_final: 0.7322 (ppp) REVERT: D 327 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8993 (mm) REVERT: D 425 MET cc_start: 0.7857 (mmt) cc_final: 0.7552 (mmt) REVERT: C 236 ASP cc_start: 0.8947 (OUTLIER) cc_final: 0.8612 (m-30) REVERT: C 495 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9181 (mm) REVERT: C 623 GLN cc_start: 0.7486 (tp40) cc_final: 0.6955 (pp30) outliers start: 94 outliers final: 74 residues processed: 210 average time/residue: 0.2695 time to fit residues: 91.9698 Evaluate side-chains 194 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 116 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 467 HIS Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 654 HIS Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 597 ASN Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 230 optimal weight: 0.9990 chunk 191 optimal weight: 0.0770 chunk 106 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 120 optimal weight: 20.0000 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 19602 Z= 0.159 Angle : 0.540 11.039 26500 Z= 0.275 Chirality : 0.040 0.152 2961 Planarity : 0.004 0.073 3405 Dihedral : 4.891 51.947 2588 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.96 % Allowed : 21.95 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % Cis-general : 0.04 % Twisted Proline : 1.98 % 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: 0.27 (0.18), residues: 2353 helix: 2.23 (0.16), residues: 1136 sheet: -0.38 (0.35), residues: 237 loop : -2.33 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 298 HIS 0.004 0.001 HIS C 487 PHE 0.021 0.001 PHE D 586 TYR 0.043 0.001 TYR D 410 ARG 0.004 0.000 ARG C 628 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 123 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.7688 (mtp) cc_final: 0.7427 (mtp) REVERT: A 315 PHE cc_start: 0.9426 (OUTLIER) cc_final: 0.8680 (t80) REVERT: A 404 ASP cc_start: 0.8882 (t0) cc_final: 0.8484 (t0) REVERT: B 149 MET cc_start: 0.8034 (mtt) cc_final: 0.7725 (mtt) REVERT: B 289 GLU cc_start: 0.8613 (tm-30) cc_final: 0.7939 (tm-30) REVERT: B 566 MET cc_start: 0.8458 (tpp) cc_final: 0.7943 (tpp) REVERT: B 571 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8799 (mp0) REVERT: B 599 TYR cc_start: 0.8328 (t80) cc_final: 0.7952 (t80) REVERT: D 201 MET cc_start: 0.8220 (ptm) cc_final: 0.7381 (ppp) REVERT: D 327 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9001 (mm) REVERT: D 425 MET cc_start: 0.7841 (mmt) cc_final: 0.7518 (mmt) REVERT: C 236 ASP cc_start: 0.8932 (OUTLIER) cc_final: 0.8594 (m-30) REVERT: C 458 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8115 (t0) REVERT: C 495 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9180 (mm) outliers start: 86 outliers final: 71 residues processed: 206 average time/residue: 0.2794 time to fit residues: 92.2575 Evaluate side-chains 192 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 116 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 467 HIS Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 654 HIS Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 597 ASN Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 168 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 193 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 229 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN C 623 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19602 Z= 0.229 Angle : 0.566 11.044 26500 Z= 0.289 Chirality : 0.041 0.145 2961 Planarity : 0.004 0.075 3405 Dihedral : 4.976 52.943 2588 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.75 % Allowed : 21.62 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % Cis-general : 0.04 % Twisted Proline : 1.98 % 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: 0.37 (0.18), residues: 2353 helix: 2.26 (0.15), residues: 1181 sheet: -0.37 (0.35), residues: 243 loop : -2.44 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 298 HIS 0.004 0.001 HIS D 419 PHE 0.010 0.001 PHE D 602 TYR 0.042 0.001 TYR D 410 ARG 0.007 0.000 ARG A 666 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 116 time to evaluate : 2.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.8206 (mtp) cc_final: 0.7952 (mtp) REVERT: A 315 PHE cc_start: 0.9441 (OUTLIER) cc_final: 0.8696 (t80) REVERT: A 404 ASP cc_start: 0.8906 (t0) cc_final: 0.8492 (t0) REVERT: B 149 MET cc_start: 0.8009 (mtt) cc_final: 0.7728 (mtt) REVERT: B 289 GLU cc_start: 0.8653 (tm-30) cc_final: 0.7930 (tm-30) REVERT: B 566 MET cc_start: 0.8481 (tpp) cc_final: 0.8127 (tpp) REVERT: B 571 GLU cc_start: 0.9108 (mt-10) cc_final: 0.8797 (mp0) REVERT: B 599 TYR cc_start: 0.8303 (t80) cc_final: 0.7969 (t80) REVERT: D 201 MET cc_start: 0.8258 (ptm) cc_final: 0.7423 (ppp) REVERT: D 327 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9002 (mm) REVERT: D 425 MET cc_start: 0.7910 (mmt) cc_final: 0.7583 (mmt) REVERT: D 476 GLU cc_start: 0.9372 (OUTLIER) cc_final: 0.9047 (pt0) REVERT: C 236 ASP cc_start: 0.8934 (OUTLIER) cc_final: 0.8597 (m-30) REVERT: C 458 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.8131 (t0) REVERT: C 495 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9190 (mm) outliers start: 103 outliers final: 83 residues processed: 214 average time/residue: 0.2786 time to fit residues: 97.1192 Evaluate side-chains 204 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 115 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 467 HIS Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 654 HIS Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN C 623 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19602 Z= 0.223 Angle : 0.574 11.332 26500 Z= 0.292 Chirality : 0.041 0.174 2961 Planarity : 0.004 0.075 3405 Dihedral : 4.995 52.373 2588 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 4.66 % Allowed : 22.08 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % Cis-general : 0.04 % Twisted Proline : 1.98 % 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: 0.42 (0.18), residues: 2353 helix: 2.29 (0.15), residues: 1181 sheet: -0.32 (0.35), residues: 243 loop : -2.40 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 298 HIS 0.007 0.001 HIS D 419 PHE 0.025 0.001 PHE D 586 TYR 0.041 0.001 TYR D 410 ARG 0.006 0.000 ARG A 666 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 116 time to evaluate : 2.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.8193 (mtp) cc_final: 0.7906 (mtp) REVERT: A 315 PHE cc_start: 0.9442 (OUTLIER) cc_final: 0.8700 (t80) REVERT: A 404 ASP cc_start: 0.8911 (t0) cc_final: 0.8495 (t0) REVERT: A 640 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8143 (tp30) REVERT: B 149 MET cc_start: 0.8010 (mtt) cc_final: 0.7734 (mtt) REVERT: B 289 GLU cc_start: 0.8660 (tm-30) cc_final: 0.7932 (tm-30) REVERT: B 566 MET cc_start: 0.8490 (tpp) cc_final: 0.8188 (tpp) REVERT: B 571 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8819 (mt-10) REVERT: B 599 TYR cc_start: 0.8392 (t80) cc_final: 0.8098 (t80) REVERT: D 201 MET cc_start: 0.8254 (ptm) cc_final: 0.7416 (ppp) REVERT: D 327 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8975 (mm) REVERT: D 425 MET cc_start: 0.7931 (mmt) cc_final: 0.7590 (mmt) REVERT: D 476 GLU cc_start: 0.9369 (OUTLIER) cc_final: 0.9038 (pt0) REVERT: C 236 ASP cc_start: 0.8932 (OUTLIER) cc_final: 0.8586 (m-30) REVERT: C 495 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9189 (mm) REVERT: C 623 GLN cc_start: 0.7502 (tp40) cc_final: 0.6884 (pp30) outliers start: 101 outliers final: 86 residues processed: 213 average time/residue: 0.2627 time to fit residues: 91.2408 Evaluate side-chains 206 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 114 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 467 HIS Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 654 HIS Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 597 ASN Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 10.0000 chunk 219 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 213 optimal weight: 0.0020 chunk 128 optimal weight: 9.9990 chunk 93 optimal weight: 0.7980 chunk 167 optimal weight: 3.9990 chunk 65 optimal weight: 0.0270 chunk 193 optimal weight: 0.5980 chunk 202 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 overall best weight: 0.4646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 19602 Z= 0.143 Angle : 0.548 11.753 26500 Z= 0.275 Chirality : 0.040 0.160 2961 Planarity : 0.004 0.071 3405 Dihedral : 4.792 52.725 2588 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.81 % Allowed : 23.79 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % Cis-general : 0.04 % Twisted Proline : 1.98 % 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: 0.52 (0.18), residues: 2353 helix: 2.39 (0.16), residues: 1137 sheet: -0.21 (0.34), residues: 237 loop : -2.15 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 313 HIS 0.004 0.001 HIS D 419 PHE 0.010 0.001 PHE D 455 TYR 0.046 0.001 TYR D 410 ARG 0.005 0.000 ARG A 666 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 123 time to evaluate : 2.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 PHE cc_start: 0.9410 (OUTLIER) cc_final: 0.8704 (t80) REVERT: A 404 ASP cc_start: 0.8889 (t0) cc_final: 0.8461 (t0) REVERT: B 149 MET cc_start: 0.8039 (mtt) cc_final: 0.7734 (mtt) REVERT: B 289 GLU cc_start: 0.8588 (tm-30) cc_final: 0.7925 (tm-30) REVERT: B 566 MET cc_start: 0.8481 (tpp) cc_final: 0.8119 (tpp) REVERT: B 571 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8878 (mt-10) REVERT: B 599 TYR cc_start: 0.8374 (t80) cc_final: 0.8110 (t80) REVERT: D 68 ASP cc_start: 0.8322 (m-30) cc_final: 0.8012 (p0) REVERT: D 201 MET cc_start: 0.8171 (ptm) cc_final: 0.7673 (tmm) REVERT: D 327 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8822 (mm) REVERT: D 425 MET cc_start: 0.7918 (mmt) cc_final: 0.7538 (mmt) REVERT: D 476 GLU cc_start: 0.9390 (OUTLIER) cc_final: 0.9073 (pt0) REVERT: C 236 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8574 (m-30) REVERT: C 422 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8620 (ttm) REVERT: C 489 MET cc_start: 0.8996 (mmm) cc_final: 0.8778 (mmm) REVERT: C 495 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9135 (mm) outliers start: 61 outliers final: 51 residues processed: 181 average time/residue: 0.2723 time to fit residues: 80.1799 Evaluate side-chains 173 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 116 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 467 HIS Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 422 MET Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 226 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 107 optimal weight: 0.0980 chunk 157 optimal weight: 4.9990 chunk 237 optimal weight: 6.9990 chunk 218 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 115 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN C 623 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19602 Z= 0.228 Angle : 0.587 11.258 26500 Z= 0.296 Chirality : 0.042 0.153 2961 Planarity : 0.004 0.075 3405 Dihedral : 4.913 52.523 2588 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.32 % Allowed : 23.47 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % Cis-general : 0.04 % Twisted Proline : 1.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.18), residues: 2353 helix: 2.39 (0.15), residues: 1183 sheet: -0.22 (0.34), residues: 243 loop : -2.27 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 244 HIS 0.006 0.001 HIS D 419 PHE 0.028 0.001 PHE D 586 TYR 0.045 0.001 TYR D 410 ARG 0.005 0.000 ARG A 666 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4706 Ramachandran restraints generated. 2353 Oldfield, 0 Emsley, 2353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 117 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 PHE cc_start: 0.9438 (OUTLIER) cc_final: 0.8684 (t80) REVERT: A 397 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7899 (mp0) REVERT: A 404 ASP cc_start: 0.8885 (t0) cc_final: 0.8467 (t0) REVERT: B 289 GLU cc_start: 0.8659 (tm-30) cc_final: 0.7945 (tm-30) REVERT: B 571 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8873 (mt-10) REVERT: B 599 TYR cc_start: 0.8384 (t80) cc_final: 0.8108 (t80) REVERT: D 201 MET cc_start: 0.8220 (ptm) cc_final: 0.7650 (tmm) REVERT: D 327 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9010 (mm) REVERT: D 425 MET cc_start: 0.7843 (mmt) cc_final: 0.7494 (mmt) REVERT: D 476 GLU cc_start: 0.9371 (OUTLIER) cc_final: 0.9030 (pt0) REVERT: C 236 ASP cc_start: 0.8935 (OUTLIER) cc_final: 0.8593 (m-30) REVERT: C 422 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8633 (ttm) REVERT: C 495 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9151 (mm) REVERT: C 623 GLN cc_start: 0.7462 (tp40) cc_final: 0.6969 (pp30) outliers start: 72 outliers final: 62 residues processed: 186 average time/residue: 0.2917 time to fit residues: 86.7492 Evaluate side-chains 184 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 115 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 467 HIS Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 422 MET Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 201 optimal weight: 6.9990 chunk 57 optimal weight: 0.0670 chunk 174 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 189 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.080147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.059919 restraints weight = 58849.529| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.28 r_work: 0.2976 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19602 Z= 0.206 Angle : 0.579 11.278 26500 Z= 0.293 Chirality : 0.041 0.151 2961 Planarity : 0.004 0.073 3405 Dihedral : 4.922 52.368 2588 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.55 % Allowed : 23.47 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.96 % Cis-general : 0.04 % Twisted Proline : 1.98 % 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: 0.60 (0.18), residues: 2353 helix: 2.39 (0.15), residues: 1182 sheet: -0.20 (0.34), residues: 243 loop : -2.24 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 313 HIS 0.006 0.001 HIS D 419 PHE 0.009 0.001 PHE C 512 TYR 0.046 0.001 TYR D 410 ARG 0.005 0.000 ARG A 666 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3821.46 seconds wall clock time: 70 minutes 30.72 seconds (4230.72 seconds total)