Starting phenix.real_space_refine on Wed Feb 14 04:28:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wiu_32536/02_2024/7wiu_32536.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wiu_32536/02_2024/7wiu_32536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wiu_32536/02_2024/7wiu_32536.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wiu_32536/02_2024/7wiu_32536.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wiu_32536/02_2024/7wiu_32536.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wiu_32536/02_2024/7wiu_32536.pdb" } resolution = 3.48 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= 0.031 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 14 5.16 5 C 5501 2.51 5 N 1547 2.21 5 O 1553 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A ASP 396": "OD1" <-> "OD2" Residue "A ASP 397": "OD1" <-> "OD2" Residue "A TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 458": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 498": "OD1" <-> "OD2" Residue "A TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A ARG 523": "NH1" <-> "NH2" Residue "A PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "A PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 613": "OD1" <-> "OD2" Residue "A PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 620": "NH1" <-> "NH2" Residue "A ARG 658": "NH1" <-> "NH2" Residue "A ASP 661": "OD1" <-> "OD2" Residue "A GLU 663": "OE1" <-> "OE2" Residue "A ASP 680": "OD1" <-> "OD2" Residue "A GLU 692": "OE1" <-> "OE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A ARG 721": "NH1" <-> "NH2" Residue "A ARG 728": "NH1" <-> "NH2" Residue "A GLU 750": "OE1" <-> "OE2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "A PHE 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 777": "OD1" <-> "OD2" Residue "A ARG 803": "NH1" <-> "NH2" Residue "A ARG 809": "NH1" <-> "NH2" Residue "A ARG 820": "NH1" <-> "NH2" Residue "B ARG 16": "NH1" <-> "NH2" Residue "B PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ASP 71": "OD1" <-> "OD2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B ASP 95": "OD1" <-> "OD2" Residue "B PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B ARG 282": "NH1" <-> "NH2" Residue "B TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 285": "OE1" <-> "OE2" Residue "B ARG 301": "NH1" <-> "NH2" Residue "B ARG 324": "NH1" <-> "NH2" Residue "B PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 393": "OD1" <-> "OD2" Residue "B ASP 401": "OD1" <-> "OD2" Residue "B PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 424": "NH1" <-> "NH2" Residue "B ARG 444": "NH1" <-> "NH2" Residue "B ASP 449": "OD1" <-> "OD2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B ARG 482": "NH1" <-> "NH2" Residue "B ARG 532": "NH1" <-> "NH2" Residue "B PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 544": "NH1" <-> "NH2" Residue "B ASP 548": "OD1" <-> "OD2" Residue "B ARG 566": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8615 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4344 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 25, 'TRANS': 545} Chain: "B" Number of atoms: 4271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4271 Classifications: {'peptide': 576} Link IDs: {'PTRANS': 25, 'TRANS': 550} Time building chain proxies: 5.08, per 1000 atoms: 0.59 Number of scatterers: 8615 At special positions: 0 Unit cell: (70.52, 98.4, 136.12, 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 14 16.00 O 1553 8.00 N 1547 7.00 C 5501 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: 3.55 Conformation dependent library (CDL) restraints added in 1.9 seconds 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 5 sheets defined 65.1% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 290 through 309 Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.837A pdb=" N VAL A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 375 removed outlier: 4.011A pdb=" N PHE A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA A 360 " --> pdb=" O HIS A 356 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE A 362 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 386 removed outlier: 4.168A pdb=" N PHE A 382 " --> pdb=" O PRO A 378 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 407 removed outlier: 3.905A pdb=" N LYS A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 430 Proline residue: A 419 - end of helix removed outlier: 3.539A pdb=" N VAL A 429 " --> pdb=" O TYR A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 438 removed outlier: 4.263A pdb=" N ALA A 434 " --> pdb=" O ASP A 430 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 435 " --> pdb=" O TRP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 452 Processing helix chain 'A' and resid 457 through 479 Processing helix chain 'A' and resid 479 through 486 removed outlier: 3.869A pdb=" N ILE A 483 " --> pdb=" O GLY A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 509 Processing helix chain 'A' and resid 511 through 521 Processing helix chain 'A' and resid 523 through 541 removed outlier: 3.809A pdb=" N PHE A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 528 " --> pdb=" O PRO A 524 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 548 No H-bonds generated for 'chain 'A' and resid 546 through 548' Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'A' and resid 558 through 572 removed outlier: 3.776A pdb=" N GLY A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE A 566 " --> pdb=" O ARG A 562 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ALA A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 588 Processing helix chain 'A' and resid 650 through 655 Processing helix chain 'A' and resid 656 through 658 No H-bonds generated for 'chain 'A' and resid 656 through 658' Processing helix chain 'A' and resid 675 through 677 No H-bonds generated for 'chain 'A' and resid 675 through 677' Processing helix chain 'A' and resid 699 through 705 Processing helix chain 'A' and resid 714 through 722 Processing helix chain 'A' and resid 725 through 731 Processing helix chain 'A' and resid 734 through 738 removed outlier: 3.517A pdb=" N ASP A 737 " --> pdb=" O ASP A 734 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 738 " --> pdb=" O GLY A 735 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 734 through 738' Processing helix chain 'A' and resid 748 through 763 removed outlier: 3.771A pdb=" N ARG A 753 " --> pdb=" O GLY A 749 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU A 754 " --> pdb=" O GLU A 750 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 761 " --> pdb=" O ALA A 757 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY A 762 " --> pdb=" O ARG A 758 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP A 763 " --> pdb=" O ALA A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 774 No H-bonds generated for 'chain 'A' and resid 772 through 774' Processing helix chain 'A' and resid 781 through 790 Processing helix chain 'A' and resid 803 through 808 removed outlier: 3.817A pdb=" N ILE A 807 " --> pdb=" O ARG A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 832 Processing helix chain 'A' and resid 835 through 841 Processing helix chain 'B' and resid 14 through 46 removed outlier: 3.524A pdb=" N ARG B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) Proline residue: B 40 - end of helix removed outlier: 4.402A pdb=" N ALA B 43 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA B 44 " --> pdb=" O PRO B 40 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 97 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 101 through 105 removed outlier: 3.515A pdb=" N TRP B 104 " --> pdb=" O ARG B 101 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE B 105 " --> pdb=" O LEU B 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 101 through 105' Processing helix chain 'B' and resid 108 through 117 removed outlier: 3.703A pdb=" N ILE B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.634A pdb=" N VAL B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY B 126 " --> pdb=" O PRO B 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 121 through 126' Processing helix chain 'B' and resid 131 through 150 removed outlier: 3.510A pdb=" N LEU B 140 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) Proline residue: B 142 - end of helix Processing helix chain 'B' and resid 153 through 202 removed outlier: 3.514A pdb=" N VAL B 158 " --> pdb=" O TRP B 154 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA B 159 " --> pdb=" O GLN B 155 " (cutoff:3.500A) Proline residue: B 165 - end of helix removed outlier: 4.947A pdb=" N ARG B 195 " --> pdb=" O ALA B 191 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ILE B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG B 201 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR B 202 " --> pdb=" O GLU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 209 removed outlier: 3.830A pdb=" N ARG B 207 " --> pdb=" O GLN B 203 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA B 208 " --> pdb=" O GLN B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 226 removed outlier: 3.757A pdb=" N ALA B 215 " --> pdb=" O ARG B 211 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 242 Proline residue: B 239 - end of helix Processing helix chain 'B' and resid 243 through 266 removed outlier: 3.613A pdb=" N GLY B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 284 removed outlier: 3.822A pdb=" N ILE B 274 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ALA B 275 " --> pdb=" O PRO B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 293 removed outlier: 3.975A pdb=" N THR B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 312 Processing helix chain 'B' and resid 370 through 381 removed outlier: 3.529A pdb=" N THR B 374 " --> pdb=" O CYS B 370 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU B 376 " --> pdb=" O LYS B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 428 Processing helix chain 'B' and resid 435 through 446 Processing helix chain 'B' and resid 448 through 454 Processing helix chain 'B' and resid 472 through 486 removed outlier: 3.737A pdb=" N LYS B 486 " --> pdb=" O ARG B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 514 Processing helix chain 'B' and resid 527 through 532 Processing helix chain 'B' and resid 550 through 558 removed outlier: 3.609A pdb=" N GLY B 558 " --> pdb=" O LEU B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 569 removed outlier: 3.815A pdb=" N PHE B 564 " --> pdb=" O ARG B 560 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 668 through 669 removed outlier: 3.586A pdb=" N VAL A 669 " --> pdb=" O GLN A 672 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN A 672 " --> pdb=" O VAL A 669 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 687 through 689 Processing sheet with id=AA3, first strand: chain 'A' and resid 813 through 815 removed outlier: 3.868A pdb=" N GLU A 823 " --> pdb=" O VAL A 815 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 410 through 411 Processing sheet with id=AA5, first strand: chain 'B' and resid 537 through 540 removed outlier: 6.822A pdb=" N VAL B 537 " --> pdb=" O ASP B 548 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ASP B 548 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE B 539 " --> pdb=" O VAL B 546 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1431 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: 2.46 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1407 1.32 - 1.44: 2237 1.44 - 1.56: 5111 1.56 - 1.68: 0 1.68 - 1.81: 23 Bond restraints: 8778 Sorted by residual: bond pdb=" C ILE B 392 " pdb=" O ILE B 392 " ideal model delta sigma weight residual 1.237 1.200 0.037 9.80e-03 1.04e+04 1.45e+01 bond pdb=" C PRO B 385 " pdb=" O PRO B 385 " ideal model delta sigma weight residual 1.233 1.192 0.041 1.13e-02 7.83e+03 1.33e+01 bond pdb=" N TYR A 619 " pdb=" CA TYR A 619 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.10e+00 bond pdb=" N TRP A 277 " pdb=" CA TRP A 277 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.49e+00 bond pdb=" N HIS A 614 " pdb=" CA HIS A 614 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.22e+00 ... (remaining 8773 not shown) Histogram of bond angle deviations from ideal: 99.18 - 106.24: 234 106.24 - 113.29: 4986 113.29 - 120.35: 3386 120.35 - 127.40: 3274 127.40 - 134.45: 111 Bond angle restraints: 11991 Sorted by residual: angle pdb=" N GLY B 326 " pdb=" CA GLY B 326 " pdb=" C GLY B 326 " ideal model delta sigma weight residual 114.92 106.77 8.15 1.30e+00 5.92e-01 3.93e+01 angle pdb=" C ARG A 620 " pdb=" N PRO A 621 " pdb=" CA PRO A 621 " ideal model delta sigma weight residual 119.84 127.52 -7.68 1.25e+00 6.40e-01 3.77e+01 angle pdb=" N PRO B 385 " pdb=" CA PRO B 385 " pdb=" C PRO B 385 " ideal model delta sigma weight residual 110.80 102.13 8.67 1.51e+00 4.39e-01 3.29e+01 angle pdb=" N ARG A 278 " pdb=" CA ARG A 278 " pdb=" C ARG A 278 " ideal model delta sigma weight residual 111.07 117.01 -5.94 1.07e+00 8.73e-01 3.08e+01 angle pdb=" C THR B 395 " pdb=" CA THR B 395 " pdb=" CB THR B 395 " ideal model delta sigma weight residual 113.45 102.59 10.86 1.98e+00 2.55e-01 3.01e+01 ... (remaining 11986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4701 17.97 - 35.94: 399 35.94 - 53.91: 82 53.91 - 71.88: 12 71.88 - 89.85: 7 Dihedral angle restraints: 5201 sinusoidal: 1940 harmonic: 3261 Sorted by residual: dihedral pdb=" CA ASP B 325 " pdb=" C ASP B 325 " pdb=" N GLY B 326 " pdb=" CA GLY B 326 " ideal model delta harmonic sigma weight residual 180.00 -152.94 -27.06 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA ASN B 11 " pdb=" C ASN B 11 " pdb=" N ASP B 12 " pdb=" CA ASP B 12 " ideal model delta harmonic sigma weight residual 180.00 153.01 26.99 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" C TYR A 619 " pdb=" N TYR A 619 " pdb=" CA TYR A 619 " pdb=" CB TYR A 619 " ideal model delta harmonic sigma weight residual -122.60 -135.20 12.60 0 2.50e+00 1.60e-01 2.54e+01 ... (remaining 5198 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1339 0.080 - 0.160: 107 0.160 - 0.240: 5 0.240 - 0.320: 5 0.320 - 0.400: 6 Chirality restraints: 1462 Sorted by residual: chirality pdb=" CA TYR A 619 " pdb=" N TYR A 619 " pdb=" C TYR A 619 " pdb=" CB TYR A 619 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" CA PHE A 612 " pdb=" N PHE A 612 " pdb=" C PHE A 612 " pdb=" CB PHE A 612 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CA ASP B 393 " pdb=" N ASP B 393 " pdb=" C ASP B 393 " pdb=" CB ASP B 393 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 ... (remaining 1459 not shown) Planarity restraints: 1536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 326 " -0.022 2.00e-02 2.50e+03 4.43e-02 1.96e+01 pdb=" C GLY B 326 " 0.077 2.00e-02 2.50e+03 pdb=" O GLY B 326 " -0.029 2.00e-02 2.50e+03 pdb=" N ALA B 327 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 14 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.11e+00 pdb=" C ARG B 14 " -0.052 2.00e-02 2.50e+03 pdb=" O ARG B 14 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA B 15 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 842 " 0.014 2.00e-02 2.50e+03 2.83e-02 8.02e+00 pdb=" C ASP A 842 " -0.049 2.00e-02 2.50e+03 pdb=" O ASP A 842 " 0.019 2.00e-02 2.50e+03 pdb=" N THR A 843 " 0.016 2.00e-02 2.50e+03 ... (remaining 1533 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 113 2.64 - 3.20: 8427 3.20 - 3.77: 12631 3.77 - 4.33: 16378 4.33 - 4.90: 27125 Nonbonded interactions: 64674 Sorted by model distance: nonbonded pdb=" OG1 THR B 395 " pdb=" N ASP B 396 " model vdw 2.070 2.520 nonbonded pdb=" O ARG A 620 " pdb=" NE ARG A 620 " model vdw 2.204 2.520 nonbonded pdb=" OG1 THR A 826 " pdb=" OE1 GLU A 829 " model vdw 2.209 2.440 nonbonded pdb=" O ASP B 336 " pdb=" NH1 ARG B 387 " model vdw 2.218 2.520 nonbonded pdb=" NH2 ARG A 620 " pdb=" N GLY A 622 " model vdw 2.231 3.200 ... (remaining 64669 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.740 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: 12.000 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 26.840 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8778 Z= 0.298 Angle : 0.941 10.863 11991 Z= 0.585 Chirality : 0.052 0.400 1462 Planarity : 0.005 0.044 1536 Dihedral : 14.542 89.849 3099 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.87 % Allowed : 11.72 % Favored : 87.40 % Rotamer: Outliers : 2.16 % Allowed : 6.93 % Favored : 90.91 % Cbeta Deviations : 0.48 % 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: -3.47 (0.22), residues: 1143 helix: -1.09 (0.18), residues: 710 sheet: -3.65 (0.61), residues: 40 loop : -4.44 (0.24), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 172 HIS 0.004 0.001 HIS B 383 PHE 0.027 0.001 PHE A 612 TYR 0.014 0.001 TYR A 619 ARG 0.004 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 277 TRP cc_start: 0.5109 (OUTLIER) cc_final: 0.4401 (m-10) REVERT: A 515 LYS cc_start: 0.9111 (mtmm) cc_final: 0.8591 (mtmm) REVERT: A 548 ASN cc_start: 0.9062 (m110) cc_final: 0.8849 (m-40) REVERT: A 582 HIS cc_start: 0.8374 (t-90) cc_final: 0.8157 (t-170) REVERT: B 22 LEU cc_start: 0.9073 (tt) cc_final: 0.8727 (mm) REVERT: B 48 GLU cc_start: 0.7886 (pp20) cc_final: 0.7636 (pp20) REVERT: B 123 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8084 (mp0) REVERT: B 130 ASN cc_start: 0.9357 (m-40) cc_final: 0.9109 (m-40) REVERT: B 368 SER cc_start: 0.8517 (t) cc_final: 0.7588 (t) REVERT: B 387 ARG cc_start: 0.6670 (OUTLIER) cc_final: 0.6319 (ptm-80) REVERT: B 389 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7642 (mtp85) REVERT: B 391 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8559 (mp) REVERT: B 393 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7932 (p0) REVERT: B 411 VAL cc_start: 0.9503 (t) cc_final: 0.9268 (m) outliers start: 19 outliers final: 9 residues processed: 165 average time/residue: 0.2068 time to fit residues: 46.6411 Evaluate side-chains 128 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 620 ARG Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 387 ARG Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 395 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 8.9990 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 66 optimal weight: 0.0000 chunk 103 optimal weight: 5.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 ASN A 548 ASN A 582 HIS A 597 HIS ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN B 241 GLN B 405 GLN B 420 HIS B 504 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8778 Z= 0.220 Angle : 0.721 10.012 11991 Z= 0.360 Chirality : 0.043 0.167 1462 Planarity : 0.005 0.060 1536 Dihedral : 6.832 53.844 1277 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.11 % Favored : 88.71 % Rotamer: Outliers : 2.50 % Allowed : 16.02 % Favored : 81.48 % 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: -1.90 (0.25), residues: 1143 helix: 0.18 (0.20), residues: 716 sheet: -2.93 (0.70), residues: 40 loop : -3.95 (0.25), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 172 HIS 0.004 0.001 HIS A 614 PHE 0.017 0.001 PHE A 612 TYR 0.021 0.001 TYR A 619 ARG 0.008 0.000 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: A 277 TRP cc_start: 0.5460 (OUTLIER) cc_final: 0.4767 (m-10) REVERT: A 316 GLU cc_start: 0.8082 (tp30) cc_final: 0.7782 (tp30) REVERT: A 392 LYS cc_start: 0.8841 (tmmt) cc_final: 0.8427 (tmtt) REVERT: A 515 LYS cc_start: 0.9118 (mtmm) cc_final: 0.8648 (mtmm) REVERT: A 518 MET cc_start: 0.8147 (ttm) cc_final: 0.7943 (tpp) REVERT: A 582 HIS cc_start: 0.8279 (t70) cc_final: 0.7886 (t-170) REVERT: B 22 LEU cc_start: 0.9050 (tt) cc_final: 0.8804 (mm) REVERT: B 48 GLU cc_start: 0.7931 (pp20) cc_final: 0.7626 (pp20) REVERT: B 123 GLU cc_start: 0.8276 (mt-10) cc_final: 0.8059 (mp0) REVERT: B 130 ASN cc_start: 0.9304 (m-40) cc_final: 0.9090 (m-40) REVERT: B 393 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.8084 (p0) REVERT: B 411 VAL cc_start: 0.9395 (t) cc_final: 0.9112 (p) REVERT: B 492 LEU cc_start: 0.9022 (pp) cc_final: 0.8697 (pp) outliers start: 22 outliers final: 10 residues processed: 139 average time/residue: 0.1897 time to fit residues: 37.8741 Evaluate side-chains 126 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 415 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 5.9990 chunk 32 optimal weight: 0.0040 chunk 86 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 92 optimal weight: 0.4980 chunk 102 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8778 Z= 0.182 Angle : 0.674 10.148 11991 Z= 0.334 Chirality : 0.042 0.164 1462 Planarity : 0.005 0.050 1536 Dihedral : 6.015 53.654 1257 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.50 % Favored : 89.15 % Rotamer: Outliers : 3.18 % Allowed : 17.61 % Favored : 79.20 % 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: -1.20 (0.25), residues: 1143 helix: 0.74 (0.20), residues: 720 sheet: -2.58 (0.72), residues: 40 loop : -3.74 (0.25), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.002 0.000 HIS A 614 PHE 0.009 0.001 PHE A 775 TYR 0.019 0.001 TYR A 619 ARG 0.005 0.000 ARG B 324 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 125 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 277 TRP cc_start: 0.5474 (OUTLIER) cc_final: 0.4937 (m-10) REVERT: A 316 GLU cc_start: 0.8048 (tp30) cc_final: 0.7789 (tp30) REVERT: A 392 LYS cc_start: 0.8874 (tmmt) cc_final: 0.8541 (tmtt) REVERT: A 397 ASP cc_start: 0.8424 (m-30) cc_final: 0.8140 (m-30) REVERT: A 515 LYS cc_start: 0.9112 (mtmm) cc_final: 0.8699 (mtmm) REVERT: A 582 HIS cc_start: 0.8315 (t70) cc_final: 0.7838 (t-170) REVERT: B 22 LEU cc_start: 0.9046 (tt) cc_final: 0.8720 (mm) REVERT: B 48 GLU cc_start: 0.7969 (pp20) cc_final: 0.7637 (pp20) REVERT: B 130 ASN cc_start: 0.9283 (m-40) cc_final: 0.9069 (m-40) REVERT: B 156 LEU cc_start: 0.9257 (mm) cc_final: 0.9012 (tp) REVERT: B 393 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.8002 (p0) REVERT: B 411 VAL cc_start: 0.9389 (t) cc_final: 0.9104 (p) REVERT: B 492 LEU cc_start: 0.8979 (pp) cc_final: 0.8696 (pp) outliers start: 28 outliers final: 12 residues processed: 142 average time/residue: 0.1629 time to fit residues: 34.3360 Evaluate side-chains 134 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 415 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 0.0970 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 GLN B 569 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8778 Z= 0.162 Angle : 0.645 8.346 11991 Z= 0.318 Chirality : 0.041 0.199 1462 Planarity : 0.004 0.051 1536 Dihedral : 5.689 58.231 1255 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.06 % Favored : 89.59 % Rotamer: Outliers : 3.86 % Allowed : 19.77 % Favored : 76.36 % 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: -0.83 (0.26), residues: 1143 helix: 1.00 (0.21), residues: 724 sheet: -2.22 (0.77), residues: 40 loop : -3.60 (0.26), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.002 0.000 HIS A 614 PHE 0.017 0.001 PHE A 559 TYR 0.016 0.001 TYR A 619 ARG 0.004 0.000 ARG B 544 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 134 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 277 TRP cc_start: 0.5466 (OUTLIER) cc_final: 0.5002 (m-10) REVERT: A 392 LYS cc_start: 0.8859 (tmmt) cc_final: 0.8514 (tmtt) REVERT: A 514 LYS cc_start: 0.7905 (mptt) cc_final: 0.7418 (mttt) REVERT: A 515 LYS cc_start: 0.9143 (mtmm) cc_final: 0.8694 (mtmm) REVERT: A 522 THR cc_start: 0.9047 (m) cc_final: 0.8801 (t) REVERT: A 582 HIS cc_start: 0.8353 (t70) cc_final: 0.7844 (t-170) REVERT: B 29 VAL cc_start: 0.8807 (t) cc_final: 0.8570 (p) REVERT: B 48 GLU cc_start: 0.7988 (pp20) cc_final: 0.7626 (pp20) REVERT: B 130 ASN cc_start: 0.9263 (m-40) cc_final: 0.9046 (m-40) REVERT: B 186 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8157 (p0) REVERT: B 411 VAL cc_start: 0.9383 (t) cc_final: 0.9121 (p) REVERT: B 492 LEU cc_start: 0.8934 (pp) cc_final: 0.8673 (pp) outliers start: 34 outliers final: 17 residues processed: 154 average time/residue: 0.1908 time to fit residues: 42.4133 Evaluate side-chains 141 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 661 ASP Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 569 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 45 optimal weight: 0.0470 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 27 optimal weight: 0.4980 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN B 569 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8778 Z= 0.179 Angle : 0.655 9.715 11991 Z= 0.322 Chirality : 0.041 0.147 1462 Planarity : 0.004 0.053 1536 Dihedral : 5.657 59.737 1255 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.97 % Favored : 89.68 % Rotamer: Outliers : 3.41 % Allowed : 21.02 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.26), residues: 1143 helix: 1.08 (0.20), residues: 729 sheet: -1.96 (0.81), residues: 38 loop : -3.51 (0.27), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.007 0.000 HIS B 569 PHE 0.011 0.001 PHE A 775 TYR 0.015 0.001 TYR A 619 ARG 0.003 0.000 ARG A 329 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 124 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: A 277 TRP cc_start: 0.5339 (OUTLIER) cc_final: 0.4901 (m100) REVERT: A 397 ASP cc_start: 0.8405 (m-30) cc_final: 0.8145 (m-30) REVERT: A 514 LYS cc_start: 0.7912 (mptt) cc_final: 0.7423 (mttt) REVERT: A 515 LYS cc_start: 0.9151 (mtmm) cc_final: 0.8638 (mtmm) REVERT: A 522 THR cc_start: 0.9029 (m) cc_final: 0.8798 (t) REVERT: A 529 TRP cc_start: 0.9023 (t60) cc_final: 0.8797 (t-100) REVERT: A 582 HIS cc_start: 0.8376 (t70) cc_final: 0.8173 (t-170) REVERT: B 48 GLU cc_start: 0.7992 (pp20) cc_final: 0.7625 (pp20) REVERT: B 130 ASN cc_start: 0.9260 (m-40) cc_final: 0.9045 (m-40) REVERT: B 156 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8811 (tp) REVERT: B 186 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8127 (p0) REVERT: B 280 MET cc_start: 0.7844 (mmt) cc_final: 0.7612 (mmt) REVERT: B 411 VAL cc_start: 0.9400 (t) cc_final: 0.9132 (p) REVERT: B 492 LEU cc_start: 0.8949 (pp) cc_final: 0.8683 (pp) outliers start: 30 outliers final: 20 residues processed: 144 average time/residue: 0.2159 time to fit residues: 44.3947 Evaluate side-chains 146 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 661 ASP Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 415 HIS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 569 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 0.1980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 805 HIS B 569 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8778 Z= 0.232 Angle : 0.668 10.288 11991 Z= 0.331 Chirality : 0.042 0.209 1462 Planarity : 0.005 0.052 1536 Dihedral : 5.693 59.693 1255 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.06 % Favored : 89.59 % Rotamer: Outliers : 4.09 % Allowed : 21.59 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.26), residues: 1143 helix: 1.11 (0.20), residues: 725 sheet: -1.71 (0.83), residues: 38 loop : -3.53 (0.26), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.008 0.001 HIS B 569 PHE 0.012 0.001 PHE A 559 TYR 0.016 0.001 TYR A 619 ARG 0.003 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 124 time to evaluate : 1.028 Fit side-chains REVERT: A 277 TRP cc_start: 0.5367 (OUTLIER) cc_final: 0.4934 (m100) REVERT: A 397 ASP cc_start: 0.8421 (m-30) cc_final: 0.8147 (m-30) REVERT: A 514 LYS cc_start: 0.7920 (mptt) cc_final: 0.7435 (mttt) REVERT: A 515 LYS cc_start: 0.9147 (mtmm) cc_final: 0.8710 (mtmm) REVERT: A 529 TRP cc_start: 0.9061 (t60) cc_final: 0.8808 (t-100) REVERT: B 48 GLU cc_start: 0.7967 (pp20) cc_final: 0.7604 (pp20) REVERT: B 130 ASN cc_start: 0.9261 (m-40) cc_final: 0.9038 (m-40) REVERT: B 186 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8148 (p0) REVERT: B 492 LEU cc_start: 0.8976 (pp) cc_final: 0.8597 (pp) outliers start: 36 outliers final: 26 residues processed: 144 average time/residue: 0.2060 time to fit residues: 42.6461 Evaluate side-chains 149 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 121 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 544 MET Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 661 ASP Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 415 HIS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 569 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 61 optimal weight: 0.0970 chunk 109 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 HIS B 569 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8778 Z= 0.172 Angle : 0.670 10.496 11991 Z= 0.325 Chirality : 0.041 0.181 1462 Planarity : 0.004 0.054 1536 Dihedral : 5.611 58.815 1255 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.27 % Favored : 90.38 % Rotamer: Outliers : 3.75 % Allowed : 22.27 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.26), residues: 1143 helix: 1.30 (0.21), residues: 719 sheet: -1.62 (0.84), residues: 38 loop : -3.50 (0.26), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.005 0.000 HIS B 569 PHE 0.009 0.001 PHE B 419 TYR 0.014 0.001 TYR A 619 ARG 0.002 0.000 ARG A 329 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 122 time to evaluate : 0.989 Fit side-chains REVERT: A 277 TRP cc_start: 0.5226 (OUTLIER) cc_final: 0.4839 (m100) REVERT: A 514 LYS cc_start: 0.7894 (mptt) cc_final: 0.7436 (mttt) REVERT: A 529 TRP cc_start: 0.9019 (t60) cc_final: 0.8800 (t-100) REVERT: A 661 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7749 (m-30) REVERT: B 48 GLU cc_start: 0.7989 (pp20) cc_final: 0.7611 (pp20) REVERT: B 130 ASN cc_start: 0.9235 (m-40) cc_final: 0.9014 (m-40) REVERT: B 186 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8128 (p0) REVERT: B 492 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8669 (pp) outliers start: 33 outliers final: 22 residues processed: 142 average time/residue: 0.1797 time to fit residues: 37.6164 Evaluate side-chains 149 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 123 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 661 ASP Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 415 HIS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 569 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 105 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: A 582 HIS B 569 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8778 Z= 0.187 Angle : 0.680 11.530 11991 Z= 0.328 Chirality : 0.042 0.214 1462 Planarity : 0.005 0.054 1536 Dihedral : 5.595 59.365 1255 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.89 % Favored : 89.85 % Rotamer: Outliers : 3.52 % Allowed : 21.82 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.26), residues: 1143 helix: 1.39 (0.21), residues: 712 sheet: -1.55 (0.86), residues: 38 loop : -3.46 (0.27), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.019 0.001 HIS A 582 PHE 0.012 0.001 PHE A 559 TYR 0.014 0.001 TYR A 619 ARG 0.003 0.000 ARG A 562 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 122 time to evaluate : 1.065 Fit side-chains REVERT: A 277 TRP cc_start: 0.5186 (OUTLIER) cc_final: 0.4829 (m100) REVERT: A 514 LYS cc_start: 0.7912 (mptt) cc_final: 0.7457 (mttt) REVERT: A 529 TRP cc_start: 0.9021 (t60) cc_final: 0.8814 (t-100) REVERT: A 661 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7796 (m-30) REVERT: B 48 GLU cc_start: 0.7990 (pp20) cc_final: 0.7628 (pp20) REVERT: B 130 ASN cc_start: 0.9232 (m-40) cc_final: 0.9011 (m-40) REVERT: B 186 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8131 (p0) REVERT: B 492 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8715 (pp) outliers start: 31 outliers final: 22 residues processed: 140 average time/residue: 0.1794 time to fit residues: 36.6333 Evaluate side-chains 146 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 661 ASP Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 415 HIS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 569 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 105 optimal weight: 0.0980 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 92 optimal weight: 4.9990 chunk 67 optimal weight: 0.3980 chunk 108 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 HIS B 569 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8778 Z= 0.160 Angle : 0.678 12.187 11991 Z= 0.326 Chirality : 0.041 0.166 1462 Planarity : 0.005 0.055 1536 Dihedral : 5.517 59.364 1255 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.36 % Favored : 90.38 % Rotamer: Outliers : 3.18 % Allowed : 22.05 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.26), residues: 1143 helix: 1.48 (0.21), residues: 712 sheet: -1.53 (0.88), residues: 38 loop : -3.43 (0.27), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.015 0.001 HIS A 582 PHE 0.008 0.001 PHE B 419 TYR 0.013 0.001 TYR A 619 ARG 0.003 0.000 ARG A 581 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 128 time to evaluate : 0.986 Fit side-chains REVERT: A 277 TRP cc_start: 0.5137 (OUTLIER) cc_final: 0.4839 (m100) REVERT: A 514 LYS cc_start: 0.7901 (mptt) cc_final: 0.7446 (mttt) REVERT: A 515 LYS cc_start: 0.9187 (mtmm) cc_final: 0.8901 (mtmm) REVERT: A 661 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7818 (m-30) REVERT: B 48 GLU cc_start: 0.7975 (pp20) cc_final: 0.7612 (pp20) REVERT: B 186 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.8102 (p0) REVERT: B 492 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8694 (pp) outliers start: 28 outliers final: 19 residues processed: 146 average time/residue: 0.1795 time to fit residues: 38.7026 Evaluate side-chains 144 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 661 ASP Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 415 HIS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 569 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 113 optimal weight: 0.0040 chunk 104 optimal weight: 0.7980 chunk 90 optimal weight: 0.0470 chunk 9 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 55 optimal weight: 0.0970 chunk 71 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.3488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 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 0.042 8778 Z= 0.154 Angle : 0.689 12.934 11991 Z= 0.327 Chirality : 0.042 0.224 1462 Planarity : 0.005 0.056 1536 Dihedral : 5.358 57.742 1253 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.27 % Favored : 90.46 % Rotamer: Outliers : 2.84 % Allowed : 22.50 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.26), residues: 1143 helix: 1.50 (0.20), residues: 715 sheet: -1.50 (0.88), residues: 38 loop : -3.31 (0.27), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 529 HIS 0.014 0.001 HIS B 569 PHE 0.011 0.001 PHE A 559 TYR 0.011 0.001 TYR A 619 ARG 0.003 0.000 ARG A 329 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 128 time to evaluate : 1.034 Fit side-chains REVERT: A 277 TRP cc_start: 0.5188 (OUTLIER) cc_final: 0.4901 (m100) REVERT: A 514 LYS cc_start: 0.7930 (mptt) cc_final: 0.7498 (mttt) REVERT: A 515 LYS cc_start: 0.9195 (mtmm) cc_final: 0.8876 (mtmm) REVERT: A 661 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7827 (m-30) REVERT: A 777 ASP cc_start: 0.7676 (p0) cc_final: 0.7453 (p0) REVERT: B 48 GLU cc_start: 0.7944 (pp20) cc_final: 0.7569 (pp20) REVERT: B 186 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.8104 (p0) REVERT: B 492 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8664 (pp) outliers start: 25 outliers final: 18 residues processed: 144 average time/residue: 0.1795 time to fit residues: 37.6536 Evaluate side-chains 144 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 661 ASP Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 415 HIS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 569 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.6980 chunk 13 optimal weight: 0.0570 chunk 25 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.097869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.085485 restraints weight = 21041.126| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.81 r_work: 0.3297 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8778 Z= 0.168 Angle : 0.693 13.255 11991 Z= 0.328 Chirality : 0.042 0.222 1462 Planarity : 0.005 0.055 1536 Dihedral : 5.308 56.912 1253 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.45 % Favored : 90.29 % Rotamer: Outliers : 2.95 % Allowed : 23.41 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.26), residues: 1143 helix: 1.58 (0.20), residues: 709 sheet: -1.44 (0.89), residues: 38 loop : -3.32 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 529 HIS 0.011 0.001 HIS A 582 PHE 0.008 0.001 PHE B 419 TYR 0.012 0.001 TYR B 283 ARG 0.002 0.000 ARG A 385 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2088.94 seconds wall clock time: 38 minutes 24.03 seconds (2304.03 seconds total)