Starting phenix.real_space_refine on Thu Mar 14 14:04:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqx_13606/03_2024/7pqx_13606.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqx_13606/03_2024/7pqx_13606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqx_13606/03_2024/7pqx_13606.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqx_13606/03_2024/7pqx_13606.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqx_13606/03_2024/7pqx_13606.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqx_13606/03_2024/7pqx_13606.pdb" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.105 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 24 5.16 5 C 5784 2.51 5 N 1572 2.21 5 O 1652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 112": "OD1" <-> "OD2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 138": "NH1" <-> "NH2" Residue "A ARG 143": "NH1" <-> "NH2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "A ARG 335": "NH1" <-> "NH2" Residue "A PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 368": "NH1" <-> "NH2" Residue "A PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A ASP 416": "OD1" <-> "OD2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 458": "NH1" <-> "NH2" Residue "A ARG 485": "NH1" <-> "NH2" Residue "A ASP 492": "OD1" <-> "OD2" Residue "A GLU 511": "OE1" <-> "OE2" Residue "A GLU 532": "OE1" <-> "OE2" Residue "A ARG 536": "NH1" <-> "NH2" Residue "A TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 570": "NH1" <-> "NH2" Residue "A ASP 595": "OD1" <-> "OD2" Residue "A GLU 626": "OE1" <-> "OE2" Residue "A ARG 662": "NH1" <-> "NH2" Residue "A ARG 667": "NH1" <-> "NH2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B ARG 115": "NH1" <-> "NH2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 138": "NH1" <-> "NH2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B ARG 335": "NH1" <-> "NH2" Residue "B PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 368": "NH1" <-> "NH2" Residue "B PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "B ASP 416": "OD1" <-> "OD2" Residue "B ARG 425": "NH1" <-> "NH2" Residue "B ARG 442": "NH1" <-> "NH2" Residue "B TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 458": "NH1" <-> "NH2" Residue "B ARG 485": "NH1" <-> "NH2" Residue "B ASP 492": "OD1" <-> "OD2" Residue "B GLU 511": "OE1" <-> "OE2" Residue "B GLU 532": "OE1" <-> "OE2" Residue "B ARG 536": "NH1" <-> "NH2" Residue "B TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 570": "NH1" <-> "NH2" Residue "B ASP 595": "OD1" <-> "OD2" Residue "B GLU 626": "OE1" <-> "OE2" Residue "B ARG 662": "NH1" <-> "NH2" Residue "B ARG 667": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9032 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4516 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 17, 'TRANS': 562} Chain: "B" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4516 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 17, 'TRANS': 562} Time building chain proxies: 5.03, per 1000 atoms: 0.56 Number of scatterers: 9032 At special positions: 0 Unit cell: (80.704, 118.976, 141.44, 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 24 16.00 O 1652 8.00 N 1572 7.00 C 5784 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.13 Conformation dependent library (CDL) restraints added in 1.6 seconds 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2164 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 8 sheets defined 67.3% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 95 through 103 removed outlier: 4.442A pdb=" N GLN A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 144 Proline residue: A 134 - end of helix Processing helix chain 'A' and resid 147 through 152 removed outlier: 3.520A pdb=" N GLY A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 205 removed outlier: 3.757A pdb=" N GLN A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 213 removed outlier: 3.729A pdb=" N HIS A 211 " --> pdb=" O ASP A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 239 Processing helix chain 'A' and resid 240 through 259 Processing helix chain 'A' and resid 260 through 309 removed outlier: 4.074A pdb=" N ALA A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LYS A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE A 288 " --> pdb=" O TRP A 284 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN A 309 " --> pdb=" O ASP A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 removed outlier: 3.614A pdb=" N PHE A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 371 removed outlier: 3.711A pdb=" N GLU A 322 " --> pdb=" O ASN A 318 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER A 336 " --> pdb=" O ALA A 332 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 392 removed outlier: 3.605A pdb=" N LEU A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL A 381 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 398 removed outlier: 4.021A pdb=" N GLY A 398 " --> pdb=" O ASN A 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 395 through 398' Processing helix chain 'A' and resid 399 through 418 removed outlier: 3.754A pdb=" N ARG A 405 " --> pdb=" O TYR A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 509 through 516 Processing helix chain 'A' and resid 531 through 537 Processing helix chain 'A' and resid 543 through 554 Processing helix chain 'A' and resid 556 through 562 Processing helix chain 'A' and resid 565 through 568 removed outlier: 3.612A pdb=" N GLN A 568 " --> pdb=" O HIS A 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 565 through 568' Processing helix chain 'A' and resid 579 through 595 Processing helix chain 'A' and resid 609 through 625 Processing helix chain 'A' and resid 660 through 666 removed outlier: 3.957A pdb=" N GLU A 666 " --> pdb=" O ARG A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 674 removed outlier: 4.309A pdb=" N GLU A 673 " --> pdb=" O VAL A 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 103 Processing helix chain 'B' and resid 109 through 144 Proline residue: B 134 - end of helix Processing helix chain 'B' and resid 147 through 152 removed outlier: 3.521A pdb=" N GLY B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 205 removed outlier: 3.757A pdb=" N GLN B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 213 removed outlier: 3.730A pdb=" N HIS B 211 " --> pdb=" O ASP B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 239 Processing helix chain 'B' and resid 240 through 259 Processing helix chain 'B' and resid 260 through 309 removed outlier: 4.074A pdb=" N ALA B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 286 " --> pdb=" O THR B 282 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LYS B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE B 288 " --> pdb=" O TRP B 284 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN B 309 " --> pdb=" O ASP B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 316 removed outlier: 3.614A pdb=" N PHE B 316 " --> pdb=" O ALA B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 371 removed outlier: 3.710A pdb=" N GLU B 322 " --> pdb=" O ASN B 318 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER B 336 " --> pdb=" O ALA B 332 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 392 removed outlier: 3.605A pdb=" N LEU B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL B 381 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 398 removed outlier: 4.021A pdb=" N GLY B 398 " --> pdb=" O ASN B 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 395 through 398' Processing helix chain 'B' and resid 399 through 418 removed outlier: 3.754A pdb=" N ARG B 405 " --> pdb=" O TYR B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 509 through 516 Processing helix chain 'B' and resid 531 through 537 Processing helix chain 'B' and resid 543 through 554 Processing helix chain 'B' and resid 556 through 562 Processing helix chain 'B' and resid 565 through 568 removed outlier: 3.611A pdb=" N GLN B 568 " --> pdb=" O HIS B 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 565 through 568' Processing helix chain 'B' and resid 579 through 595 Processing helix chain 'B' and resid 609 through 625 Processing helix chain 'B' and resid 660 through 666 removed outlier: 3.958A pdb=" N GLU B 666 " --> pdb=" O ARG B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 674 removed outlier: 4.309A pdb=" N GLU B 673 " --> pdb=" O VAL B 670 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 457 through 460 removed outlier: 5.481A pdb=" N ARG A 458 " --> pdb=" O PHE A 448 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N PHE A 448 " --> pdb=" O ARG A 458 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 460 removed outlier: 5.481A pdb=" N ARG A 458 " --> pdb=" O PHE A 448 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N PHE A 448 " --> pdb=" O ARG A 458 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL A 446 " --> pdb=" O GLN A 495 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLN A 495 " --> pdb=" O VAL A 446 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 517 through 518 removed outlier: 6.398A pdb=" N GLY A 518 " --> pdb=" O PHE A 600 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ASP A 602 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU A 599 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL A 634 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE A 601 " --> pdb=" O VAL A 634 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA A 635 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ALA A 471 " --> pdb=" O ILE A 648 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU A 650 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL A 473 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE A 647 " --> pdb=" O GLN A 658 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLN A 658 " --> pdb=" O ILE A 647 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL A 649 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL A 656 " --> pdb=" O VAL A 649 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 654 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 529 through 530 Processing sheet with id=AA5, first strand: chain 'B' and resid 457 through 460 removed outlier: 5.481A pdb=" N ARG B 458 " --> pdb=" O PHE B 448 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N PHE B 448 " --> pdb=" O ARG B 458 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 457 through 460 removed outlier: 5.481A pdb=" N ARG B 458 " --> pdb=" O PHE B 448 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N PHE B 448 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL B 446 " --> pdb=" O GLN B 495 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLN B 495 " --> pdb=" O VAL B 446 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 517 through 518 removed outlier: 6.398A pdb=" N GLY B 518 " --> pdb=" O PHE B 600 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ASP B 602 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU B 599 " --> pdb=" O LEU B 632 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL B 634 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE B 601 " --> pdb=" O VAL B 634 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA B 635 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ALA B 471 " --> pdb=" O ILE B 648 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU B 650 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL B 473 " --> pdb=" O LEU B 650 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE B 647 " --> pdb=" O GLN B 658 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLN B 658 " --> pdb=" O ILE B 647 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL B 649 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL B 656 " --> pdb=" O VAL B 649 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 654 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 529 through 530 590 hydrogen bonds defined for protein. 1746 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.81 Time building geometry restraints manager: 3.45 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: 2683 1.34 - 1.45: 1415 1.45 - 1.57: 5054 1.57 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 9196 Sorted by residual: bond pdb=" C TRP A 563 " pdb=" N PRO A 564 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.30e-02 5.92e+03 6.42e+00 bond pdb=" C TRP B 563 " pdb=" N PRO B 564 " ideal model delta sigma weight residual 1.335 1.367 -0.032 1.30e-02 5.92e+03 6.00e+00 bond pdb=" CB ARG B 170 " pdb=" CG ARG B 170 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.81e+00 bond pdb=" CB ARG A 170 " pdb=" CG ARG A 170 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.72e+00 bond pdb=" CB THR B 281 " pdb=" CG2 THR B 281 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.58e+00 ... (remaining 9191 not shown) Histogram of bond angle deviations from ideal: 92.27 - 100.71: 10 100.71 - 109.14: 785 109.14 - 117.58: 5910 117.58 - 126.01: 5655 126.01 - 134.45: 110 Bond angle restraints: 12470 Sorted by residual: angle pdb=" N GLU A 622 " pdb=" CA GLU A 622 " pdb=" CB GLU A 622 " ideal model delta sigma weight residual 110.39 118.50 -8.11 1.66e+00 3.63e-01 2.39e+01 angle pdb=" N GLU B 622 " pdb=" CA GLU B 622 " pdb=" CB GLU B 622 " ideal model delta sigma weight residual 110.39 118.46 -8.07 1.66e+00 3.63e-01 2.36e+01 angle pdb=" C GLU A 444 " pdb=" N ASN A 445 " pdb=" CA ASN A 445 " ideal model delta sigma weight residual 121.54 129.16 -7.62 1.91e+00 2.74e-01 1.59e+01 angle pdb=" OG1 THR B 482 " pdb=" CB THR B 482 " pdb=" CG2 THR B 482 " ideal model delta sigma weight residual 109.30 101.32 7.98 2.00e+00 2.50e-01 1.59e+01 angle pdb=" C GLU B 444 " pdb=" N ASN B 445 " pdb=" CA ASN B 445 " ideal model delta sigma weight residual 121.54 129.15 -7.61 1.91e+00 2.74e-01 1.59e+01 ... (remaining 12465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 4884 16.44 - 32.87: 498 32.87 - 49.31: 110 49.31 - 65.74: 14 65.74 - 82.18: 10 Dihedral angle restraints: 5516 sinusoidal: 2156 harmonic: 3360 Sorted by residual: dihedral pdb=" CA ASP B 502 " pdb=" C ASP B 502 " pdb=" N GLN B 503 " pdb=" CA GLN B 503 " ideal model delta harmonic sigma weight residual 180.00 157.22 22.78 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA ASP A 502 " pdb=" C ASP A 502 " pdb=" N GLN A 503 " pdb=" CA GLN A 503 " ideal model delta harmonic sigma weight residual 180.00 157.23 22.77 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA TYR B 451 " pdb=" C TYR B 451 " pdb=" N PRO B 452 " pdb=" CA PRO B 452 " ideal model delta harmonic sigma weight residual -180.00 -157.99 -22.01 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 5513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 874 0.048 - 0.095: 402 0.095 - 0.143: 137 0.143 - 0.190: 35 0.190 - 0.238: 16 Chirality restraints: 1464 Sorted by residual: chirality pdb=" CG LEU B 487 " pdb=" CB LEU B 487 " pdb=" CD1 LEU B 487 " pdb=" CD2 LEU B 487 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB ILE B 641 " pdb=" CA ILE B 641 " pdb=" CG1 ILE B 641 " pdb=" CG2 ILE B 641 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CG LEU A 487 " pdb=" CB LEU A 487 " pdb=" CD1 LEU A 487 " pdb=" CD2 LEU A 487 " both_signs ideal model delta sigma weight residual False -2.59 -2.82 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 1461 not shown) Planarity restraints: 1584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 388 " 0.030 2.00e-02 2.50e+03 2.21e-02 8.55e+00 pdb=" CG PHE A 388 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE A 388 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 388 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE A 388 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 388 " 0.024 2.00e-02 2.50e+03 pdb=" CZ PHE A 388 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 388 " -0.030 2.00e-02 2.50e+03 2.21e-02 8.52e+00 pdb=" CG PHE B 388 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE B 388 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 388 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE B 388 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 388 " -0.024 2.00e-02 2.50e+03 pdb=" CZ PHE B 388 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 454 " 0.045 5.00e-02 4.00e+02 6.89e-02 7.60e+00 pdb=" N PRO A 455 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 455 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 455 " 0.038 5.00e-02 4.00e+02 ... (remaining 1581 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2706 2.82 - 3.34: 8629 3.34 - 3.86: 15223 3.86 - 4.38: 17097 4.38 - 4.90: 29971 Nonbonded interactions: 73626 Sorted by model distance: nonbonded pdb=" O LEU A 206 " pdb=" OH TYR B 310 " model vdw 2.296 2.440 nonbonded pdb=" O GLU B 558 " pdb=" OG SER B 562 " model vdw 2.300 2.440 nonbonded pdb=" O GLU A 558 " pdb=" OG SER A 562 " model vdw 2.301 2.440 nonbonded pdb=" O GLY A 566 " pdb=" OG1 THR A 569 " model vdw 2.312 2.440 nonbonded pdb=" O GLY B 566 " pdb=" OG1 THR B 569 " model vdw 2.312 2.440 ... (remaining 73621 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' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.530 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: 7.070 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.270 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.103 9196 Z= 0.600 Angle : 1.108 11.381 12470 Z= 0.605 Chirality : 0.063 0.238 1464 Planarity : 0.007 0.069 1584 Dihedral : 14.204 82.177 3352 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % 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: -2.13 (0.21), residues: 1156 helix: -1.08 (0.16), residues: 740 sheet: 0.20 (0.67), residues: 60 loop : -2.15 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 284 HIS 0.007 0.002 HIS B 132 PHE 0.038 0.005 PHE A 388 TYR 0.028 0.003 TYR A 274 ARG 0.016 0.001 ARG B 425 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.876 Fit side-chains REVERT: A 532 GLU cc_start: 0.7287 (tp30) cc_final: 0.6662 (tp30) REVERT: B 401 TYR cc_start: 0.6469 (t80) cc_final: 0.6267 (t80) REVERT: B 532 GLU cc_start: 0.7289 (tp30) cc_final: 0.6705 (tp30) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2051 time to fit residues: 34.0396 Evaluate side-chains 96 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 9.9990 chunk 30 optimal weight: 0.2980 chunk 59 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 0.0070 chunk 55 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 HIS ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 HIS ** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9196 Z= 0.184 Angle : 0.581 7.791 12470 Z= 0.308 Chirality : 0.042 0.154 1464 Planarity : 0.004 0.046 1584 Dihedral : 5.092 22.173 1266 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.42 % Allowed : 7.28 % Favored : 92.31 % 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: -0.27 (0.24), residues: 1156 helix: 0.56 (0.18), residues: 758 sheet: 0.12 (0.66), residues: 60 loop : -1.84 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 284 HIS 0.002 0.001 HIS A 132 PHE 0.027 0.002 PHE A 355 TYR 0.010 0.001 TYR B 274 ARG 0.003 0.000 ARG B 536 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 SER cc_start: 0.8859 (p) cc_final: 0.8457 (m) REVERT: A 532 GLU cc_start: 0.7230 (tp30) cc_final: 0.6590 (tp30) REVERT: A 617 MET cc_start: 0.8840 (tpp) cc_final: 0.8531 (tpp) REVERT: B 532 GLU cc_start: 0.7253 (tp30) cc_final: 0.6608 (tp30) REVERT: B 617 MET cc_start: 0.8824 (tpp) cc_final: 0.8508 (tpp) outliers start: 4 outliers final: 4 residues processed: 127 average time/residue: 0.1479 time to fit residues: 29.1459 Evaluate side-chains 112 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 108 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 530 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 29 optimal weight: 0.0970 chunk 105 optimal weight: 0.0270 chunk 114 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 HIS B 557 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9196 Z= 0.170 Angle : 0.550 7.802 12470 Z= 0.286 Chirality : 0.041 0.148 1464 Planarity : 0.003 0.034 1584 Dihedral : 4.717 21.195 1266 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.94 % Allowed : 10.91 % Favored : 88.15 % 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: 0.62 (0.25), residues: 1156 helix: 1.31 (0.19), residues: 748 sheet: 0.24 (0.68), residues: 60 loop : -1.55 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 284 HIS 0.005 0.001 HIS B 555 PHE 0.021 0.002 PHE B 355 TYR 0.010 0.001 TYR A 274 ARG 0.003 0.000 ARG A 425 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 SER cc_start: 0.8727 (OUTLIER) cc_final: 0.8481 (m) REVERT: A 617 MET cc_start: 0.8839 (tpp) cc_final: 0.8532 (tpp) REVERT: B 617 MET cc_start: 0.8833 (tpp) cc_final: 0.8526 (tpp) outliers start: 9 outliers final: 3 residues processed: 116 average time/residue: 0.1613 time to fit residues: 28.9803 Evaluate side-chains 108 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 531 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 55 optimal weight: 0.3980 chunk 100 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 HIS ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9196 Z= 0.288 Angle : 0.577 7.150 12470 Z= 0.303 Chirality : 0.043 0.147 1464 Planarity : 0.003 0.033 1584 Dihedral : 4.650 20.118 1266 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.66 % Allowed : 12.47 % Favored : 85.86 % 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: 0.68 (0.25), residues: 1156 helix: 1.32 (0.19), residues: 758 sheet: 0.27 (0.68), residues: 60 loop : -1.49 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 284 HIS 0.005 0.001 HIS A 555 PHE 0.023 0.002 PHE B 355 TYR 0.017 0.001 TYR B 274 ARG 0.003 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 106 time to evaluate : 0.896 Fit side-chains REVERT: A 349 SER cc_start: 0.8952 (OUTLIER) cc_final: 0.8492 (m) REVERT: A 355 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7315 (t80) REVERT: A 522 GLN cc_start: 0.8316 (tp40) cc_final: 0.7987 (tp40) REVERT: A 617 MET cc_start: 0.8891 (tpp) cc_final: 0.8600 (tpp) REVERT: B 355 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.7393 (t80) REVERT: B 522 GLN cc_start: 0.8308 (tp40) cc_final: 0.7991 (tp40) REVERT: B 617 MET cc_start: 0.8882 (tpp) cc_final: 0.8602 (tpp) outliers start: 16 outliers final: 10 residues processed: 116 average time/residue: 0.1456 time to fit residues: 26.3050 Evaluate side-chains 113 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 531 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 95 optimal weight: 0.3980 chunk 77 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 HIS ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 HIS ** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9196 Z= 0.195 Angle : 0.536 6.832 12470 Z= 0.280 Chirality : 0.041 0.149 1464 Planarity : 0.003 0.031 1584 Dihedral : 4.525 19.954 1266 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.77 % Allowed : 13.51 % Favored : 84.72 % 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: 0.96 (0.25), residues: 1156 helix: 1.54 (0.19), residues: 758 sheet: 0.26 (0.67), residues: 60 loop : -1.37 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 284 HIS 0.006 0.001 HIS B 555 PHE 0.019 0.001 PHE B 355 TYR 0.010 0.001 TYR B 274 ARG 0.002 0.000 ARG B 425 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 100 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 SER cc_start: 0.8837 (OUTLIER) cc_final: 0.8531 (m) REVERT: A 355 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7329 (t80) REVERT: A 617 MET cc_start: 0.8893 (tpp) cc_final: 0.8615 (tpp) REVERT: B 355 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.7341 (t80) REVERT: B 617 MET cc_start: 0.8885 (tpp) cc_final: 0.8603 (tpp) outliers start: 17 outliers final: 3 residues processed: 110 average time/residue: 0.1396 time to fit residues: 24.5989 Evaluate side-chains 105 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 531 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.0870 chunk 100 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 65 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 112 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 chunk 9 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 HIS A 557 HIS ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 HIS B 557 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9196 Z= 0.172 Angle : 0.521 6.892 12470 Z= 0.272 Chirality : 0.041 0.162 1464 Planarity : 0.003 0.030 1584 Dihedral : 4.359 19.211 1266 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.46 % Allowed : 15.28 % Favored : 83.26 % 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: 1.26 (0.26), residues: 1156 helix: 1.81 (0.19), residues: 748 sheet: 0.24 (0.68), residues: 60 loop : -1.26 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 284 HIS 0.007 0.001 HIS B 555 PHE 0.029 0.002 PHE B 210 TYR 0.009 0.001 TYR A 274 ARG 0.001 0.000 ARG A 425 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 SER cc_start: 0.8729 (OUTLIER) cc_final: 0.8484 (m) REVERT: A 355 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.7330 (t80) REVERT: A 617 MET cc_start: 0.8888 (tpp) cc_final: 0.8586 (tpp) REVERT: B 355 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.7345 (t80) REVERT: B 617 MET cc_start: 0.8876 (tpp) cc_final: 0.8608 (tpp) outliers start: 14 outliers final: 9 residues processed: 107 average time/residue: 0.1466 time to fit residues: 25.1544 Evaluate side-chains 108 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 503 GLN Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 503 GLN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 531 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 62 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 51 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN A 555 HIS A 557 HIS ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 GLN B 555 HIS B 557 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9196 Z= 0.194 Angle : 0.536 7.120 12470 Z= 0.279 Chirality : 0.041 0.140 1464 Planarity : 0.003 0.030 1584 Dihedral : 4.338 18.516 1266 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.39 % Allowed : 14.76 % Favored : 82.85 % 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 (0.25), residues: 1156 helix: 1.86 (0.19), residues: 748 sheet: 0.32 (0.68), residues: 60 loop : -1.29 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 284 HIS 0.006 0.001 HIS A 555 PHE 0.017 0.002 PHE B 355 TYR 0.010 0.001 TYR B 274 ARG 0.002 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 101 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7869 (mp0) REVERT: A 349 SER cc_start: 0.8769 (OUTLIER) cc_final: 0.8492 (m) REVERT: A 355 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7330 (t80) REVERT: A 617 MET cc_start: 0.8884 (tpp) cc_final: 0.8595 (tpp) REVERT: B 319 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: B 355 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7345 (t80) REVERT: B 617 MET cc_start: 0.8878 (tpp) cc_final: 0.8600 (tpp) outliers start: 23 outliers final: 15 residues processed: 116 average time/residue: 0.1550 time to fit residues: 28.5825 Evaluate side-chains 118 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 503 GLN Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 503 GLN Chi-restraints excluded: chain B residue 522 GLN Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 613 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 0.0980 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 0.0370 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 HIS ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 HIS B 557 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9196 Z= 0.178 Angle : 0.541 7.266 12470 Z= 0.282 Chirality : 0.041 0.139 1464 Planarity : 0.003 0.027 1584 Dihedral : 4.314 18.375 1266 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.29 % Allowed : 15.38 % Favored : 82.33 % 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: 1.33 (0.25), residues: 1156 helix: 1.90 (0.19), residues: 748 sheet: 0.42 (0.69), residues: 60 loop : -1.33 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 284 HIS 0.006 0.001 HIS B 555 PHE 0.016 0.001 PHE B 355 TYR 0.009 0.001 TYR A 274 ARG 0.001 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7854 (mp0) REVERT: A 349 SER cc_start: 0.8731 (OUTLIER) cc_final: 0.8481 (m) REVERT: A 355 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.7318 (t80) REVERT: A 617 MET cc_start: 0.8882 (tpp) cc_final: 0.8601 (tpp) REVERT: B 319 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7992 (mp0) REVERT: B 355 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.7338 (t80) REVERT: B 617 MET cc_start: 0.8875 (tpp) cc_final: 0.8591 (tpp) outliers start: 22 outliers final: 12 residues processed: 114 average time/residue: 0.1442 time to fit residues: 25.9753 Evaluate side-chains 113 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 503 GLN Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 503 GLN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 630 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 GLN A 557 HIS ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 HIS B 557 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9196 Z= 0.214 Angle : 0.558 7.603 12470 Z= 0.290 Chirality : 0.042 0.141 1464 Planarity : 0.003 0.026 1584 Dihedral : 4.344 18.255 1266 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.49 % Allowed : 14.97 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.25), residues: 1156 helix: 1.86 (0.19), residues: 748 sheet: 0.47 (0.68), residues: 60 loop : -1.30 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 284 HIS 0.007 0.001 HIS B 555 PHE 0.018 0.001 PHE B 355 TYR 0.011 0.001 TYR A 274 ARG 0.002 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 102 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7881 (mp0) REVERT: A 349 SER cc_start: 0.8828 (OUTLIER) cc_final: 0.8517 (m) REVERT: A 355 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7383 (t80) REVERT: A 617 MET cc_start: 0.8880 (tpp) cc_final: 0.8607 (tpp) REVERT: B 319 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: B 355 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7400 (t80) REVERT: B 617 MET cc_start: 0.8879 (tpp) cc_final: 0.8605 (tpp) outliers start: 24 outliers final: 15 residues processed: 119 average time/residue: 0.1533 time to fit residues: 28.7976 Evaluate side-chains 118 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 503 GLN Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 503 GLN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 630 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 GLN A 557 HIS ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 HIS B 557 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9196 Z= 0.226 Angle : 0.568 7.920 12470 Z= 0.294 Chirality : 0.042 0.140 1464 Planarity : 0.003 0.025 1584 Dihedral : 4.349 18.233 1266 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.39 % Allowed : 15.18 % Favored : 82.43 % 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: 1.34 (0.25), residues: 1156 helix: 1.87 (0.19), residues: 748 sheet: 0.51 (0.68), residues: 60 loop : -1.26 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 284 HIS 0.007 0.001 HIS B 555 PHE 0.018 0.002 PHE B 355 TYR 0.012 0.001 TYR B 274 ARG 0.002 0.000 ARG A 170 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 100 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: A 349 SER cc_start: 0.8838 (OUTLIER) cc_final: 0.8518 (m) REVERT: A 355 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.7389 (t80) REVERT: A 617 MET cc_start: 0.8884 (tpp) cc_final: 0.8609 (tpp) REVERT: B 319 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: B 355 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.7403 (t80) REVERT: B 617 MET cc_start: 0.8878 (tpp) cc_final: 0.8602 (tpp) outliers start: 23 outliers final: 15 residues processed: 117 average time/residue: 0.1552 time to fit residues: 28.0409 Evaluate side-chains 116 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 503 GLN Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 503 GLN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 630 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 GLN A 557 HIS ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 HIS B 557 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.196719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.121773 restraints weight = 10496.222| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.09 r_work: 0.3267 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9196 Z= 0.187 Angle : 0.561 9.160 12470 Z= 0.290 Chirality : 0.041 0.138 1464 Planarity : 0.003 0.024 1584 Dihedral : 4.290 18.318 1266 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.29 % Allowed : 15.49 % Favored : 82.22 % 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: 1.44 (0.25), residues: 1156 helix: 1.96 (0.19), residues: 748 sheet: 0.55 (0.68), residues: 60 loop : -1.26 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 284 HIS 0.007 0.001 HIS B 555 PHE 0.016 0.001 PHE B 355 TYR 0.010 0.001 TYR A 274 ARG 0.001 0.000 ARG A 170 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2047.27 seconds wall clock time: 37 minutes 26.76 seconds (2246.76 seconds total)