Starting phenix.real_space_refine on Fri Feb 16 05:46:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7f_23211/02_2024/7l7f_23211.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7f_23211/02_2024/7l7f_23211.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7f_23211/02_2024/7l7f_23211.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7f_23211/02_2024/7l7f_23211.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7f_23211/02_2024/7l7f_23211.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7f_23211/02_2024/7l7f_23211.pdb" } resolution = 3.24 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 9310 2.51 5 N 2428 2.21 5 O 2724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 23": "OE1" <-> "OE2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B GLU 37": "OE1" <-> "OE2" Residue "B ASP 38": "OD1" <-> "OD2" Residue "B TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 56": "OE1" <-> "OE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B ASP 111": "OD1" <-> "OD2" Residue "B ARG 115": "NH1" <-> "NH2" Residue "B TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 136": "OD1" <-> "OD2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 192": "NH1" <-> "NH2" Residue "B TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 213": "OD1" <-> "OD2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B ASP 225": "OD1" <-> "OD2" Residue "B ARG 245": "NH1" <-> "NH2" Residue "B TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 269": "OD1" <-> "OD2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B ASP 295": "OD1" <-> "OD2" Residue "B ASP 299": "OD1" <-> "OD2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B GLU 312": "OE1" <-> "OE2" Residue "B ASP 335": "OD1" <-> "OD2" Residue "B ASP 355": "OD1" <-> "OD2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 430": "OE1" <-> "OE2" Residue "B GLU 435": "OE1" <-> "OE2" Residue "B ASP 471": "OD1" <-> "OD2" Residue "B PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 518": "NH1" <-> "NH2" Residue "B TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 609": "OD1" <-> "OD2" Residue "B ASP 630": "OD1" <-> "OD2" Residue "B GLU 634": "OE1" <-> "OE2" Residue "B GLU 639": "OE1" <-> "OE2" Residue "B PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 669": "OD1" <-> "OD2" Residue "B ARG 671": "NH1" <-> "NH2" Residue "B ARG 678": "NH1" <-> "NH2" Residue "B PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 701": "OE1" <-> "OE2" Residue "B ASP 713": "OD1" <-> "OD2" Residue "B ARG 716": "NH1" <-> "NH2" Residue "B PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 346": "NH1" <-> "NH2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 403": "NH1" <-> "NH2" Residue "E TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 442": "OD1" <-> "OD2" Residue "E TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 465": "OE1" <-> "OE2" Residue "E GLU 471": "OE1" <-> "OE2" Residue "E TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 516": "OE1" <-> "OE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D GLU 37": "OE1" <-> "OE2" Residue "D ASP 38": "OD1" <-> "OD2" Residue "D TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D ASP 111": "OD1" <-> "OD2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 136": "OD1" <-> "OD2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 213": "OD1" <-> "OD2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D ASP 225": "OD1" <-> "OD2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 269": "OD1" <-> "OD2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D ASP 295": "OD1" <-> "OD2" Residue "D ASP 299": "OD1" <-> "OD2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D GLU 312": "OE1" <-> "OE2" Residue "D ASP 335": "OD1" <-> "OD2" Residue "D ASP 355": "OD1" <-> "OD2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 430": "OE1" <-> "OE2" Residue "D GLU 435": "OE1" <-> "OE2" Residue "D ASP 471": "OD1" <-> "OD2" Residue "D PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 609": "OD1" <-> "OD2" Residue "D ASP 630": "OD1" <-> "OD2" Residue "D GLU 634": "OE1" <-> "OE2" Residue "D GLU 639": "OE1" <-> "OE2" Residue "D PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 669": "OD1" <-> "OD2" Residue "D ARG 671": "NH1" <-> "NH2" Residue "D ARG 678": "NH1" <-> "NH2" Residue "D PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 701": "OE1" <-> "OE2" Residue "D ASP 713": "OD1" <-> "OD2" Residue "D ARG 716": "NH1" <-> "NH2" Residue "D PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 346": "NH1" <-> "NH2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 403": "NH1" <-> "NH2" Residue "F TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 442": "OD1" <-> "OD2" Residue "F TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 465": "OE1" <-> "OE2" Residue "F GLU 471": "OE1" <-> "OE2" Residue "F TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 516": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14542 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 5809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5809 Classifications: {'peptide': 711} Link IDs: {'PTRANS': 31, 'TRANS': 679} Chain: "E" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1462 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "D" Number of atoms: 5809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5809 Classifications: {'peptide': 711} Link IDs: {'PTRANS': 31, 'TRANS': 679} Chain: "F" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1462 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Time building chain proxies: 8.06, per 1000 atoms: 0.55 Number of scatterers: 14542 At special positions: 0 Unit cell: (120.93, 143.55, 138.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2724 8.00 N 2428 7.00 C 9310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 141 " distance=2.04 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.02 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.02 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.04 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " 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: 5.81 Conformation dependent library (CDL) restraints added in 3.0 seconds 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3380 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 12 sheets defined 49.3% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'B' and resid 21 through 53 removed outlier: 4.256A pdb=" N ALA B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N HIS B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU B 37 " --> pdb=" O ASN B 33 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN B 53 " --> pdb=" O ASN B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 80 removed outlier: 3.995A pdb=" N ASN B 64 " --> pdb=" O GLN B 60 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 83 No H-bonds generated for 'chain 'B' and resid 81 through 83' Processing helix chain 'B' and resid 84 through 88 removed outlier: 3.978A pdb=" N GLU B 87 " --> pdb=" O PRO B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 101 Processing helix chain 'B' and resid 109 through 129 Processing helix chain 'B' and resid 147 through 155 Processing helix chain 'B' and resid 157 through 173 removed outlier: 3.512A pdb=" N TRP B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG B 169 " --> pdb=" O TRP B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 193 removed outlier: 4.009A pdb=" N GLU B 182 " --> pdb=" O PRO B 178 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL B 185 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 220 through 231 removed outlier: 3.970A pdb=" N GLU B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 249 removed outlier: 3.824A pdb=" N HIS B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 Processing helix chain 'B' and resid 294 through 298 Processing helix chain 'B' and resid 303 through 318 removed outlier: 4.090A pdb=" N ILE B 307 " --> pdb=" O ASP B 303 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 removed outlier: 3.588A pdb=" N ASN B 330 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER B 331 " --> pdb=" O PHE B 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 326 through 331' Processing helix chain 'B' and resid 365 through 383 removed outlier: 3.940A pdb=" N HIS B 373 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N HIS B 378 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 393 removed outlier: 3.715A pdb=" N ARG B 393 " --> pdb=" O PHE B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 413 removed outlier: 3.585A pdb=" N GLY B 405 " --> pdb=" O HIS B 401 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N MET B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER B 409 " --> pdb=" O GLY B 405 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 411 " --> pdb=" O ILE B 407 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA B 413 " --> pdb=" O SER B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 422 removed outlier: 3.830A pdb=" N GLY B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 447 removed outlier: 4.110A pdb=" N THR B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 466 removed outlier: 3.529A pdb=" N THR B 453 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 466 " --> pdb=" O MET B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 484 removed outlier: 4.336A pdb=" N TRP B 478 " --> pdb=" O MET B 474 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG B 482 " --> pdb=" O TRP B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 513 through 530 removed outlier: 3.509A pdb=" N THR B 517 " --> pdb=" O ILE B 513 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR B 519 " --> pdb=" O TYR B 515 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B 520 " --> pdb=" O TYR B 516 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 removed outlier: 3.537A pdb=" N LYS B 541 " --> pdb=" O PRO B 538 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS B 542 " --> pdb=" O LEU B 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 538 through 542' Processing helix chain 'B' and resid 548 through 559 removed outlier: 3.679A pdb=" N GLN B 552 " --> pdb=" O THR B 548 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG B 559 " --> pdb=" O PHE B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 570 Processing helix chain 'B' and resid 581 through 588 removed outlier: 3.677A pdb=" N PHE B 588 " --> pdb=" O LEU B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 599 removed outlier: 3.991A pdb=" N TRP B 594 " --> pdb=" O PRO B 590 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP B 597 " --> pdb=" O THR B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 629 Processing helix chain 'B' and resid 636 through 660 removed outlier: 3.867A pdb=" N MET B 640 " --> pdb=" O ASN B 636 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN B 660 " --> pdb=" O LEU B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 707 removed outlier: 3.517A pdb=" N VAL B 700 " --> pdb=" O PRO B 696 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER B 707 " --> pdb=" O ALA B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 716 removed outlier: 3.659A pdb=" N ILE B 711 " --> pdb=" O SER B 707 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE B 715 " --> pdb=" O ILE B 711 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 342 Processing helix chain 'E' and resid 405 through 410 removed outlier: 5.765A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'D' and resid 22 through 53 removed outlier: 3.863A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN D 53 " --> pdb=" O ASN D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 80 removed outlier: 3.996A pdb=" N ASN D 64 " --> pdb=" O GLN D 60 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.977A pdb=" N GLU D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 173 removed outlier: 3.512A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 193 removed outlier: 4.010A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 Processing helix chain 'D' and resid 220 through 231 removed outlier: 3.970A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 249 removed outlier: 3.824A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 282 Processing helix chain 'D' and resid 294 through 298 Processing helix chain 'D' and resid 303 through 318 removed outlier: 4.089A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.587A pdb=" N ASN D 330 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 326 through 331' Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.941A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.715A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.585A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA D 413 " --> pdb=" O SER D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 3.830A pdb=" N GLY D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 447 removed outlier: 4.110A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 removed outlier: 3.530A pdb=" N THR D 453 " --> pdb=" O THR D 449 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY D 466 " --> pdb=" O MET D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 removed outlier: 4.336A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 530 removed outlier: 3.509A pdb=" N THR D 517 " --> pdb=" O ILE D 513 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.537A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS D 542 " --> pdb=" O LEU D 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 538 through 542' Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.679A pdb=" N GLN D 552 " --> pdb=" O THR D 548 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 570 Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.678A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.991A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 629 Processing helix chain 'D' and resid 636 through 660 removed outlier: 3.867A pdb=" N MET D 640 " --> pdb=" O ASN D 636 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN D 660 " --> pdb=" O LEU D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 696 through 707 removed outlier: 3.517A pdb=" N VAL D 700 " --> pdb=" O PRO D 696 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER D 707 " --> pdb=" O ALA D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 716 removed outlier: 3.659A pdb=" N ILE D 711 " --> pdb=" O SER D 707 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE D 715 " --> pdb=" O ILE D 711 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 342 Processing helix chain 'F' and resid 405 through 410 removed outlier: 5.764A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'B' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'B' and resid 262 through 263 removed outlier: 6.077A pdb=" N LEU B 262 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 670 through 673 removed outlier: 4.828A pdb=" N LYS B 619 " --> pdb=" O LEU B 725 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 356 through 358 removed outlier: 3.759A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASP E 398 " --> pdb=" O VAL E 512 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL E 512 " --> pdb=" O ASP E 398 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS E 432 " --> pdb=" O LEU E 513 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR E 376 " --> pdb=" O ALA E 435 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 452 through 454 removed outlier: 3.516A pdb=" N TYR E 453 " --> pdb=" O GLN E 493 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN E 493 " --> pdb=" O TYR E 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AA8, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.077A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AB1, first strand: chain 'D' and resid 670 through 673 removed outlier: 4.829A pdb=" N LYS D 619 " --> pdb=" O LEU D 725 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 356 through 358 removed outlier: 3.759A pdb=" N VAL F 395 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP F 398 " --> pdb=" O VAL F 512 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL F 512 " --> pdb=" O ASP F 398 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS F 432 " --> pdb=" O LEU F 513 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR F 376 " --> pdb=" O ALA F 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 452 through 454 removed outlier: 3.516A pdb=" N TYR F 453 " --> pdb=" O GLN F 493 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN F 493 " --> pdb=" O TYR F 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 558 hydrogen bonds defined for protein. 1596 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: 4.45 Time building geometry restraints manager: 6.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4704 1.35 - 1.47: 3865 1.47 - 1.59: 6235 1.59 - 1.71: 0 1.71 - 1.84: 130 Bond restraints: 14934 Sorted by residual: bond pdb=" N LYS F 386 " pdb=" CA LYS F 386 " ideal model delta sigma weight residual 1.455 1.487 -0.033 1.38e-02 5.25e+03 5.63e+00 bond pdb=" N LYS E 386 " pdb=" CA LYS E 386 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.38e-02 5.25e+03 5.51e+00 bond pdb=" N TYR E 489 " pdb=" CA TYR E 489 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.25e-02 6.40e+03 5.38e+00 bond pdb=" C GLU D 35 " pdb=" O GLU D 35 " ideal model delta sigma weight residual 1.236 1.253 -0.017 1.22e-02 6.72e+03 1.83e+00 bond pdb=" C GLU B 35 " pdb=" O GLU B 35 " ideal model delta sigma weight residual 1.236 1.252 -0.016 1.22e-02 6.72e+03 1.79e+00 ... (remaining 14929 not shown) Histogram of bond angle deviations from ideal: 99.05 - 106.04: 331 106.04 - 113.04: 7648 113.04 - 120.04: 5668 120.04 - 127.04: 6412 127.04 - 134.03: 209 Bond angle restraints: 20268 Sorted by residual: angle pdb=" C GLU B 171 " pdb=" N VAL B 172 " pdb=" CA VAL B 172 " ideal model delta sigma weight residual 122.66 119.02 3.64 9.70e-01 1.06e+00 1.41e+01 angle pdb=" C GLU D 171 " pdb=" N VAL D 172 " pdb=" CA VAL D 172 " ideal model delta sigma weight residual 122.66 119.10 3.56 9.70e-01 1.06e+00 1.35e+01 angle pdb=" CA CYS E 432 " pdb=" CB CYS E 432 " pdb=" SG CYS E 432 " ideal model delta sigma weight residual 114.40 122.65 -8.25 2.30e+00 1.89e-01 1.29e+01 angle pdb=" CA CYS F 432 " pdb=" CB CYS F 432 " pdb=" SG CYS F 432 " ideal model delta sigma weight residual 114.40 122.63 -8.23 2.30e+00 1.89e-01 1.28e+01 angle pdb=" N LYS F 386 " pdb=" CA LYS F 386 " pdb=" C LYS F 386 " ideal model delta sigma weight residual 113.61 108.53 5.08 1.50e+00 4.44e-01 1.15e+01 ... (remaining 20263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 7669 17.34 - 34.68: 945 34.68 - 52.02: 180 52.02 - 69.36: 46 69.36 - 86.70: 22 Dihedral angle restraints: 8862 sinusoidal: 3604 harmonic: 5258 Sorted by residual: dihedral pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " pdb=" SG CYS E 432 " pdb=" CB CYS E 432 " ideal model delta sinusoidal sigma weight residual 93.00 11.89 81.11 1 1.00e+01 1.00e-02 8.12e+01 dihedral pdb=" CB CYS F 379 " pdb=" SG CYS F 379 " pdb=" SG CYS F 432 " pdb=" CB CYS F 432 " ideal model delta sinusoidal sigma weight residual 93.00 11.90 81.10 1 1.00e+01 1.00e-02 8.11e+01 dihedral pdb=" CA CYS E 336 " pdb=" C CYS E 336 " pdb=" N PRO E 337 " pdb=" CA PRO E 337 " ideal model delta harmonic sigma weight residual 180.00 157.24 22.76 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 8859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1065 0.029 - 0.058: 677 0.058 - 0.087: 255 0.087 - 0.117: 107 0.117 - 0.146: 20 Chirality restraints: 2124 Sorted by residual: chirality pdb=" CA ILE E 434 " pdb=" N ILE E 434 " pdb=" C ILE E 434 " pdb=" CB ILE E 434 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA PRO B 688 " pdb=" N PRO B 688 " pdb=" C PRO B 688 " pdb=" CB PRO B 688 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CA PRO D 688 " pdb=" N PRO D 688 " pdb=" C PRO D 688 " pdb=" CB PRO D 688 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.21e-01 ... (remaining 2121 not shown) Planarity restraints: 2632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS E 488 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" C CYS E 488 " -0.036 2.00e-02 2.50e+03 pdb=" O CYS E 488 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR E 489 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 283 " 0.029 5.00e-02 4.00e+02 4.33e-02 2.99e+00 pdb=" N PRO D 284 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 284 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 284 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 687 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO D 688 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 688 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 688 " 0.024 5.00e-02 4.00e+02 ... (remaining 2629 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1106 2.73 - 3.27: 13838 3.27 - 3.82: 21239 3.82 - 4.36: 24872 4.36 - 4.90: 44383 Nonbonded interactions: 105438 Sorted by model distance: nonbonded pdb=" OE1 GLU B 435 " pdb=" NE2 HIS B 540 " model vdw 2.189 2.520 nonbonded pdb=" OE1 GLU D 435 " pdb=" NE2 HIS D 540 " model vdw 2.189 2.520 nonbonded pdb=" NE2 GLN B 524 " pdb=" N ASN B 580 " model vdw 2.266 3.200 nonbonded pdb=" NE2 GLN D 524 " pdb=" N ASN D 580 " model vdw 2.267 3.200 nonbonded pdb=" O THR E 470 " pdb=" OG1 THR E 470 " model vdw 2.295 2.440 ... (remaining 105433 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 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 19.650 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 40.600 Find NCS groups from input model: 0.700 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 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 : 0.005 0.036 14934 Z= 0.299 Angle : 0.680 9.552 20268 Z= 0.397 Chirality : 0.044 0.146 2124 Planarity : 0.005 0.043 2632 Dihedral : 15.832 86.698 5446 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 0.25 % Allowed : 16.35 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.17), residues: 1780 helix: -1.34 (0.17), residues: 810 sheet: -1.95 (0.54), residues: 80 loop : -3.71 (0.15), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 594 HIS 0.004 0.001 HIS B 241 PHE 0.014 0.001 PHE D 684 TYR 0.019 0.001 TYR B 183 ARG 0.002 0.000 ARG D 306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 190 time to evaluate : 1.704 Fit side-chains revert: symmetry clash REVERT: B 35 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7529 (mt-10) REVERT: B 249 MET cc_start: 0.8277 (mtp) cc_final: 0.8063 (mtp) REVERT: B 557 MET cc_start: 0.9167 (tmm) cc_final: 0.8964 (tmm) REVERT: B 582 ARG cc_start: 0.7107 (mmm160) cc_final: 0.6821 (tpt170) REVERT: E 407 VAL cc_start: 0.7864 (m) cc_final: 0.7584 (t) REVERT: E 455 LEU cc_start: 0.7359 (tp) cc_final: 0.7152 (tp) REVERT: E 474 GLN cc_start: 0.7525 (tt0) cc_final: 0.7182 (tm-30) REVERT: E 511 VAL cc_start: 0.6877 (t) cc_final: 0.6643 (p) REVERT: D 249 MET cc_start: 0.8348 (mtp) cc_final: 0.8142 (mtp) REVERT: D 349 TRP cc_start: 0.8687 (m100) cc_final: 0.8309 (m100) REVERT: D 582 ARG cc_start: 0.7134 (mmm160) cc_final: 0.6820 (tpt170) REVERT: F 403 ARG cc_start: 0.7788 (ptt180) cc_final: 0.7447 (ptm-80) REVERT: F 434 ILE cc_start: 0.7784 (mt) cc_final: 0.7540 (mt) REVERT: F 474 GLN cc_start: 0.7773 (tt0) cc_final: 0.7265 (tm-30) REVERT: F 486 PHE cc_start: 0.6447 (t80) cc_final: 0.6159 (t80) REVERT: F 487 ASN cc_start: 0.7712 (m-40) cc_final: 0.7107 (m-40) outliers start: 4 outliers final: 0 residues processed: 194 average time/residue: 0.2821 time to fit residues: 79.6213 Evaluate side-chains 131 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 72 optimal weight: 0.0570 chunk 139 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS B 42 GLN B 154 ASN B 239 HIS B 330 ASN B 345 HIS B 374 HIS B 380 GLN B 429 GLN B 437 ASN B 442 GLN B 524 GLN B 586 ASN B 599 ASN B 601 ASN B 638 ASN ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 ASN E 370 ASN ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 GLN E 501 ASN D 102 GLN D 154 ASN D 239 HIS D 330 ASN D 374 HIS D 380 GLN D 429 GLN D 437 ASN D 442 GLN D 524 GLN D 586 ASN D 599 ASN D 601 ASN ** D 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 GLN F 370 ASN F 493 GLN F 501 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14934 Z= 0.172 Angle : 0.520 8.273 20268 Z= 0.273 Chirality : 0.042 0.162 2124 Planarity : 0.004 0.036 2632 Dihedral : 4.467 24.668 1952 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.15 % Allowed : 16.29 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.19), residues: 1780 helix: -0.11 (0.19), residues: 804 sheet: -1.38 (0.61), residues: 80 loop : -3.01 (0.17), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 594 HIS 0.009 0.001 HIS B 34 PHE 0.023 0.001 PHE E 486 TYR 0.013 0.001 TYR D 50 ARG 0.002 0.000 ARG D 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 139 time to evaluate : 1.807 Fit side-chains REVERT: B 35 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7548 (mt-10) REVERT: B 51 ASN cc_start: 0.8350 (OUTLIER) cc_final: 0.8108 (m110) REVERT: B 582 ARG cc_start: 0.6833 (mmm160) cc_final: 0.6471 (tpt170) REVERT: E 474 GLN cc_start: 0.7502 (tt0) cc_final: 0.7245 (tm-30) REVERT: D 35 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7459 (mt-10) REVERT: D 582 ARG cc_start: 0.6789 (mmm160) cc_final: 0.6366 (tpt170) REVERT: F 464 PHE cc_start: 0.6861 (m-80) cc_final: 0.6376 (m-80) REVERT: F 474 GLN cc_start: 0.7636 (tt0) cc_final: 0.7245 (tm-30) outliers start: 34 outliers final: 15 residues processed: 168 average time/residue: 0.2437 time to fit residues: 62.9939 Evaluate side-chains 141 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 636 ASN Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 465 LYS Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 chunk 161 optimal weight: 0.5980 chunk 174 optimal weight: 20.0000 chunk 144 optimal weight: 8.9990 chunk 160 optimal weight: 9.9990 chunk 55 optimal weight: 0.3980 chunk 129 optimal weight: 8.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN B 345 HIS B 638 ASN B 653 GLN E 487 ASN D 24 GLN D 638 ASN D 653 GLN F 487 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14934 Z= 0.160 Angle : 0.505 7.986 20268 Z= 0.260 Chirality : 0.041 0.162 2124 Planarity : 0.004 0.037 2632 Dihedral : 4.169 22.774 1952 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.72 % Allowed : 17.87 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.19), residues: 1780 helix: 0.33 (0.19), residues: 804 sheet: -1.06 (0.63), residues: 80 loop : -2.70 (0.18), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 436 HIS 0.008 0.001 HIS B 345 PHE 0.028 0.001 PHE E 486 TYR 0.010 0.001 TYR D 183 ARG 0.001 0.000 ARG D 460 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 138 time to evaluate : 1.899 Fit side-chains REVERT: B 35 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7617 (mt-10) REVERT: B 51 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7988 (m110) REVERT: B 582 ARG cc_start: 0.6801 (mmm160) cc_final: 0.6256 (tpt170) REVERT: E 474 GLN cc_start: 0.7537 (tt0) cc_final: 0.7285 (tm-30) REVERT: D 24 GLN cc_start: 0.5381 (OUTLIER) cc_final: 0.5159 (mt0) REVERT: D 35 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7434 (mt-10) REVERT: F 464 PHE cc_start: 0.6833 (m-80) cc_final: 0.6373 (m-80) REVERT: F 474 GLN cc_start: 0.7639 (tt0) cc_final: 0.7299 (tm-30) outliers start: 43 outliers final: 21 residues processed: 173 average time/residue: 0.2360 time to fit residues: 63.2310 Evaluate side-chains 149 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 636 ASN Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 465 LYS Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 108 optimal weight: 0.0040 chunk 162 optimal weight: 6.9990 chunk 172 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 345 HIS B 653 GLN D 638 ASN F 487 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14934 Z= 0.136 Angle : 0.481 8.072 20268 Z= 0.247 Chirality : 0.040 0.160 2124 Planarity : 0.003 0.034 2632 Dihedral : 3.957 21.332 1952 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.34 % Allowed : 19.20 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.20), residues: 1780 helix: 0.51 (0.19), residues: 816 sheet: -0.83 (0.63), residues: 80 loop : -2.60 (0.18), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 436 HIS 0.007 0.001 HIS B 345 PHE 0.016 0.001 PHE E 486 TYR 0.010 0.001 TYR D 50 ARG 0.001 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 135 time to evaluate : 1.799 Fit side-chains REVERT: B 35 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7572 (mt-10) REVERT: E 474 GLN cc_start: 0.7533 (tt0) cc_final: 0.7304 (tm-30) REVERT: D 35 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7427 (mt-10) REVERT: F 474 GLN cc_start: 0.7597 (tt0) cc_final: 0.7270 (tm-30) REVERT: F 487 ASN cc_start: 0.6370 (m-40) cc_final: 0.6113 (m-40) outliers start: 37 outliers final: 21 residues processed: 162 average time/residue: 0.2474 time to fit residues: 61.0616 Evaluate side-chains 144 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 636 ASN Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 405 ASP Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 465 LYS Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 128 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 154 optimal weight: 0.1980 chunk 43 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14934 Z= 0.167 Angle : 0.498 9.969 20268 Z= 0.258 Chirality : 0.041 0.151 2124 Planarity : 0.003 0.034 2632 Dihedral : 3.958 20.600 1952 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.72 % Allowed : 19.01 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.20), residues: 1780 helix: 0.66 (0.19), residues: 816 sheet: -0.74 (0.63), residues: 80 loop : -2.48 (0.18), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 168 HIS 0.003 0.001 HIS D 241 PHE 0.011 0.001 PHE B 684 TYR 0.011 0.001 TYR D 183 ARG 0.003 0.000 ARG D 582 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 129 time to evaluate : 1.825 Fit side-chains REVERT: B 35 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7525 (mt-10) REVERT: E 474 GLN cc_start: 0.7624 (tt0) cc_final: 0.7395 (tm-30) REVERT: D 35 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7466 (mt-10) REVERT: F 474 GLN cc_start: 0.7627 (tt0) cc_final: 0.7337 (tm-30) REVERT: F 487 ASN cc_start: 0.6982 (m-40) cc_final: 0.6606 (m-40) outliers start: 43 outliers final: 23 residues processed: 161 average time/residue: 0.2577 time to fit residues: 62.8963 Evaluate side-chains 147 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 636 ASN Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 405 ASP Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 465 LYS Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 172 optimal weight: 0.0070 chunk 142 optimal weight: 4.9990 chunk 79 optimal weight: 0.0040 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 166 optimal weight: 10.0000 overall best weight: 0.4010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 661 GLN D 24 GLN D 661 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14934 Z= 0.119 Angle : 0.464 8.535 20268 Z= 0.236 Chirality : 0.040 0.155 2124 Planarity : 0.003 0.033 2632 Dihedral : 3.680 22.678 1952 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.90 % Allowed : 19.26 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.20), residues: 1780 helix: 0.90 (0.20), residues: 816 sheet: -0.56 (0.64), residues: 80 loop : -2.28 (0.18), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 436 HIS 0.001 0.000 HIS D 373 PHE 0.010 0.001 PHE E 400 TYR 0.008 0.001 TYR D 50 ARG 0.004 0.000 ARG B 582 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 128 time to evaluate : 1.857 Fit side-chains REVERT: B 35 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7556 (mt-10) REVERT: E 403 ARG cc_start: 0.7482 (ptm-80) cc_final: 0.7153 (ptm-80) REVERT: E 412 PRO cc_start: 0.6346 (Cg_endo) cc_final: 0.6056 (Cg_exo) REVERT: E 474 GLN cc_start: 0.7541 (tt0) cc_final: 0.7306 (tm-30) REVERT: D 35 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7499 (mt-10) REVERT: F 380 TYR cc_start: 0.4220 (OUTLIER) cc_final: 0.2263 (m-80) REVERT: F 474 GLN cc_start: 0.7617 (tt0) cc_final: 0.7351 (tm-30) outliers start: 30 outliers final: 17 residues processed: 147 average time/residue: 0.2653 time to fit residues: 58.9834 Evaluate side-chains 143 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 636 ASN Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 405 ASP Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain F residue 380 TYR Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 97 optimal weight: 0.3980 chunk 144 optimal weight: 7.9990 chunk 96 optimal weight: 0.7980 chunk 171 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN E 487 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14934 Z= 0.153 Angle : 0.483 8.459 20268 Z= 0.248 Chirality : 0.041 0.153 2124 Planarity : 0.003 0.032 2632 Dihedral : 3.745 22.052 1952 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.71 % Allowed : 19.58 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.20), residues: 1780 helix: 0.97 (0.19), residues: 830 sheet: -0.56 (0.64), residues: 80 loop : -2.23 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 168 HIS 0.003 0.001 HIS D 241 PHE 0.019 0.001 PHE E 486 TYR 0.011 0.001 TYR D 183 ARG 0.002 0.000 ARG D 582 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 124 time to evaluate : 1.771 Fit side-chains REVERT: B 35 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7515 (mt-10) REVERT: E 368 LEU cc_start: 0.7729 (mt) cc_final: 0.7379 (mp) REVERT: E 412 PRO cc_start: 0.6373 (Cg_endo) cc_final: 0.6060 (Cg_exo) REVERT: E 474 GLN cc_start: 0.7624 (tt0) cc_final: 0.7354 (tm-30) REVERT: D 24 GLN cc_start: 0.5441 (OUTLIER) cc_final: 0.4795 (mt0) REVERT: D 35 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7491 (mt-10) REVERT: F 474 GLN cc_start: 0.7626 (tt0) cc_final: 0.7319 (tm-30) outliers start: 27 outliers final: 19 residues processed: 145 average time/residue: 0.2479 time to fit residues: 55.2646 Evaluate side-chains 139 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 636 ASN Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 405 ASP Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 84 optimal weight: 0.0010 chunk 15 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 156 optimal weight: 0.0370 chunk 164 optimal weight: 5.9990 overall best weight: 0.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN E 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14934 Z= 0.123 Angle : 0.465 8.072 20268 Z= 0.237 Chirality : 0.040 0.155 2124 Planarity : 0.003 0.031 2632 Dihedral : 3.590 21.487 1952 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.09 % Allowed : 19.14 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.20), residues: 1780 helix: 1.18 (0.20), residues: 816 sheet: -0.53 (0.65), residues: 80 loop : -2.11 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 436 HIS 0.002 0.000 HIS D 373 PHE 0.013 0.001 PHE E 486 TYR 0.009 0.001 TYR D 50 ARG 0.003 0.000 ARG D 582 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 129 time to evaluate : 1.791 Fit side-chains REVERT: B 35 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7493 (mt-10) REVERT: E 403 ARG cc_start: 0.7557 (ptm-80) cc_final: 0.7326 (ptm-80) REVERT: E 412 PRO cc_start: 0.6422 (Cg_endo) cc_final: 0.6129 (Cg_exo) REVERT: E 474 GLN cc_start: 0.7622 (tt0) cc_final: 0.7309 (tm-30) REVERT: E 487 ASN cc_start: 0.6738 (m-40) cc_final: 0.6096 (m-40) REVERT: D 24 GLN cc_start: 0.5298 (OUTLIER) cc_final: 0.4752 (mt0) REVERT: D 35 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7451 (mt-10) REVERT: F 380 TYR cc_start: 0.4002 (OUTLIER) cc_final: 0.3037 (m-80) REVERT: F 474 GLN cc_start: 0.7655 (tt0) cc_final: 0.7248 (tm-30) REVERT: F 487 ASN cc_start: 0.7015 (m-40) cc_final: 0.6649 (m-40) outliers start: 33 outliers final: 21 residues processed: 153 average time/residue: 0.2423 time to fit residues: 57.0900 Evaluate side-chains 145 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 636 ASN Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 405 ASP Chi-restraints excluded: chain E residue 409 GLN Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 380 TYR Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 2.9990 chunk 159 optimal weight: 0.0000 chunk 164 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 125 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 144 optimal weight: 8.9990 chunk 151 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN E 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14934 Z= 0.163 Angle : 0.495 8.042 20268 Z= 0.254 Chirality : 0.041 0.152 2124 Planarity : 0.003 0.031 2632 Dihedral : 3.699 20.105 1952 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.15 % Allowed : 18.88 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.20), residues: 1780 helix: 1.17 (0.19), residues: 828 sheet: -0.49 (0.65), residues: 80 loop : -2.14 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 168 HIS 0.003 0.001 HIS D 241 PHE 0.013 0.001 PHE E 486 TYR 0.012 0.001 TYR D 183 ARG 0.003 0.000 ARG D 582 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 121 time to evaluate : 1.864 Fit side-chains REVERT: B 35 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7472 (mt-10) REVERT: B 208 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7739 (tp30) REVERT: E 398 ASP cc_start: 0.5572 (OUTLIER) cc_final: 0.5265 (p0) REVERT: E 403 ARG cc_start: 0.7498 (ptm-80) cc_final: 0.7222 (ptm-80) REVERT: E 474 GLN cc_start: 0.7625 (tt0) cc_final: 0.7313 (tm-30) REVERT: D 24 GLN cc_start: 0.5406 (OUTLIER) cc_final: 0.4715 (mt0) REVERT: D 35 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7448 (mt-10) REVERT: F 380 TYR cc_start: 0.3977 (OUTLIER) cc_final: 0.2997 (m-80) REVERT: F 474 GLN cc_start: 0.7707 (tt0) cc_final: 0.7304 (tm-30) outliers start: 34 outliers final: 23 residues processed: 148 average time/residue: 0.2580 time to fit residues: 58.7320 Evaluate side-chains 146 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 636 ASN Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 405 ASP Chi-restraints excluded: chain E residue 409 GLN Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 380 TYR Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 3.9990 chunk 80 optimal weight: 30.0000 chunk 117 optimal weight: 0.7980 chunk 177 optimal weight: 6.9990 chunk 163 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 14 optimal weight: 0.0770 chunk 109 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN B 340 GLN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN D 661 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14934 Z= 0.233 Angle : 0.548 8.037 20268 Z= 0.284 Chirality : 0.043 0.162 2124 Planarity : 0.004 0.033 2632 Dihedral : 4.053 19.037 1952 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.22 % Allowed : 18.76 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.20), residues: 1780 helix: 0.99 (0.19), residues: 832 sheet: -0.49 (0.64), residues: 80 loop : -2.13 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 168 HIS 0.005 0.001 HIS D 241 PHE 0.015 0.001 PHE E 486 TYR 0.018 0.001 TYR B 183 ARG 0.002 0.000 ARG D 582 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 120 time to evaluate : 1.606 Fit side-chains REVERT: B 35 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7528 (mt-10) REVERT: B 208 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7838 (tp30) REVERT: E 398 ASP cc_start: 0.5484 (OUTLIER) cc_final: 0.5182 (p0) REVERT: E 474 GLN cc_start: 0.7729 (tt0) cc_final: 0.7344 (tm-30) REVERT: D 24 GLN cc_start: 0.5663 (OUTLIER) cc_final: 0.4847 (mt0) REVERT: D 35 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7424 (mt-10) REVERT: F 380 TYR cc_start: 0.3920 (OUTLIER) cc_final: 0.2938 (m-80) REVERT: F 474 GLN cc_start: 0.7688 (tt0) cc_final: 0.7216 (tm-30) outliers start: 35 outliers final: 27 residues processed: 148 average time/residue: 0.2425 time to fit residues: 56.2062 Evaluate side-chains 149 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 118 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 636 ASN Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 405 ASP Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 380 TYR Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain F residue 511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 17 optimal weight: 0.0370 chunk 26 optimal weight: 0.0970 chunk 124 optimal weight: 2.9990 chunk 8 optimal weight: 0.0870 overall best weight: 0.4234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 472 GLN D 472 GLN D 661 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.138965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.107088 restraints weight = 23167.493| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.61 r_work: 0.3087 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14934 Z= 0.122 Angle : 0.477 8.360 20268 Z= 0.243 Chirality : 0.040 0.153 2124 Planarity : 0.003 0.032 2632 Dihedral : 3.620 20.840 1952 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.71 % Allowed : 19.39 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.20), residues: 1780 helix: 1.29 (0.20), residues: 816 sheet: -0.25 (0.67), residues: 80 loop : -2.01 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 436 HIS 0.002 0.000 HIS D 373 PHE 0.012 0.001 PHE E 486 TYR 0.008 0.001 TYR D 50 ARG 0.003 0.000 ARG B 582 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3287.93 seconds wall clock time: 60 minutes 15.74 seconds (3615.74 seconds total)