Starting phenix.real_space_refine on Mon Mar 11 00:55:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xvg_33486/03_2024/7xvg_33486.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xvg_33486/03_2024/7xvg_33486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xvg_33486/03_2024/7xvg_33486.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xvg_33486/03_2024/7xvg_33486.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xvg_33486/03_2024/7xvg_33486.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xvg_33486/03_2024/7xvg_33486.pdb" } resolution = 3.6 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= 0.047 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 26 5.16 5 C 4160 2.51 5 N 1066 2.21 5 O 1186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 441": "OD1" <-> "OD2" Residue "A TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 669": "OE1" <-> "OE2" Residue "A ASP 672": "OD1" <-> "OD2" Residue "A GLU 686": "OE1" <-> "OE2" Residue "A ARG 689": "NH1" <-> "NH2" Residue "A PHE 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 712": "OE1" <-> "OE2" Residue "A GLU 713": "OE1" <-> "OE2" Residue "A PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 844": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 885": "OD1" <-> "OD2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 6438 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3327 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 20, 'TRANS': 394} Chain breaks: 1 Chain: "B" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3111 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 368} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 4.08, per 1000 atoms: 0.63 Number of scatterers: 6438 At special positions: 0 Unit cell: (75.6, 94.08, 110.04, 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 26 16.00 O 1186 8.00 N 1066 7.00 C 4160 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: 2.35 Conformation dependent library (CDL) restraints added in 1.2 seconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1510 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 5 sheets defined 50.5% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 434 through 438 Processing helix chain 'A' and resid 446 through 457 Processing helix chain 'A' and resid 469 through 482 Processing helix chain 'A' and resid 502 through 514 removed outlier: 3.835A pdb=" N ASP A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 508 " --> pdb=" O MET A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 598 removed outlier: 3.532A pdb=" N LEU A 598 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 621 removed outlier: 3.701A pdb=" N ILE A 618 " --> pdb=" O PRO A 615 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLY A 619 " --> pdb=" O MET A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 665 Processing helix chain 'A' and resid 680 through 687 removed outlier: 3.672A pdb=" N VAL A 684 " --> pdb=" O ASP A 680 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 687 " --> pdb=" O PHE A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 690 No H-bonds generated for 'chain 'A' and resid 688 through 690' Processing helix chain 'A' and resid 707 through 718 removed outlier: 4.170A pdb=" N LEU A 711 " --> pdb=" O MET A 707 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A 713 " --> pdb=" O LYS A 709 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N MET A 718 " --> pdb=" O SER A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 792 Processing helix chain 'A' and resid 804 through 810 removed outlier: 3.833A pdb=" N PHE A 808 " --> pdb=" O ASN A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 844 removed outlier: 3.719A pdb=" N PHE A 844 " --> pdb=" O PRO A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 864 removed outlier: 3.795A pdb=" N ILE A 864 " --> pdb=" O ALA A 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 150 removed outlier: 4.252A pdb=" N TYR B 148 " --> pdb=" O ASP B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 193 removed outlier: 3.560A pdb=" N ASN B 189 " --> pdb=" O PHE B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 removed outlier: 4.365A pdb=" N ILE B 198 " --> pdb=" O LYS B 194 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 194 through 199' Processing helix chain 'B' and resid 211 through 226 Processing helix chain 'B' and resid 229 through 244 removed outlier: 3.984A pdb=" N ILE B 234 " --> pdb=" O PRO B 230 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N GLU B 235 " --> pdb=" O GLU B 231 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS B 243 " --> pdb=" O LYS B 239 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL B 244 " --> pdb=" O VAL B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 275 removed outlier: 3.552A pdb=" N ILE B 262 " --> pdb=" O PHE B 258 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN B 263 " --> pdb=" O ASN B 259 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N HIS B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS B 275 " --> pdb=" O HIS B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 290 through 317 removed outlier: 3.530A pdb=" N LYS B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B 302 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS B 308 " --> pdb=" O THR B 304 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE B 310 " --> pdb=" O LYS B 306 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ASP B 311 " --> pdb=" O MET B 307 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER B 312 " --> pdb=" O LYS B 308 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 322 removed outlier: 3.680A pdb=" N ILE B 322 " --> pdb=" O ASN B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 330 removed outlier: 4.281A pdb=" N ASP B 328 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 329 " --> pdb=" O MET B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 335 removed outlier: 3.565A pdb=" N SER B 334 " --> pdb=" O TRP B 331 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N HIS B 335 " --> pdb=" O GLN B 332 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 331 through 335' Processing helix chain 'B' and resid 336 through 347 removed outlier: 4.094A pdb=" N LEU B 343 " --> pdb=" O PHE B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 365 removed outlier: 3.835A pdb=" N SER B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER B 352 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 392 Processing helix chain 'B' and resid 393 through 396 Processing helix chain 'B' and resid 403 through 419 Processing helix chain 'B' and resid 423 through 441 removed outlier: 3.597A pdb=" N PHE B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 455 removed outlier: 3.757A pdb=" N LEU B 452 " --> pdb=" O PHE B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 483 Processing helix chain 'B' and resid 508 through 529 removed outlier: 4.253A pdb=" N LYS B 512 " --> pdb=" O LYS B 508 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU B 513 " --> pdb=" O HIS B 509 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL B 516 " --> pdb=" O LYS B 512 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N SER B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR B 518 " --> pdb=" O ASN B 514 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG B 529 " --> pdb=" O THR B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 553 removed outlier: 3.556A pdb=" N LEU B 544 " --> pdb=" O CYS B 540 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER B 553 " --> pdb=" O ASN B 549 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 444 through 445 removed outlier: 6.538A pdb=" N VAL A 496 " --> pdb=" O ILE A 490 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ILE A 490 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG A 500 " --> pdb=" O GLN A 486 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN A 486 " --> pdb=" O ARG A 500 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 581 through 583 Processing sheet with id=AA3, first strand: chain 'A' and resid 626 through 628 removed outlier: 6.848A pdb=" N LEU A 627 " --> pdb=" O TYR A 651 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP A 672 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ARG A 697 " --> pdb=" O ASP A 672 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP A 699 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP A 725 " --> pdb=" O LEU A 696 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 799 through 802 removed outlier: 7.512A pdb=" N LEU A 800 " --> pdb=" O ARG A 833 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 856 through 859 removed outlier: 3.857A pdb=" N PHE A 857 " --> pdb=" O ARG A 881 " (cutoff:3.500A) 230 hydrogen bonds defined for protein. 645 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: 1.54 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1132 1.32 - 1.44: 1657 1.44 - 1.57: 3744 1.57 - 1.69: 1 1.69 - 1.81: 42 Bond restraints: 6576 Sorted by residual: bond pdb=" N LEU A 879 " pdb=" CA LEU A 879 " ideal model delta sigma weight residual 1.455 1.490 -0.036 1.36e-02 5.41e+03 6.95e+00 bond pdb=" C PRO A 877 " pdb=" O PRO A 877 " ideal model delta sigma weight residual 1.235 1.203 0.032 1.30e-02 5.92e+03 6.21e+00 bond pdb=" N SER A 878 " pdb=" CA SER A 878 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.11e+00 bond pdb=" CA SER A 878 " pdb=" CB SER A 878 " ideal model delta sigma weight residual 1.530 1.488 0.042 1.69e-02 3.50e+03 6.11e+00 bond pdb=" N LEU A 690 " pdb=" CA LEU A 690 " ideal model delta sigma weight residual 1.462 1.490 -0.028 1.23e-02 6.61e+03 5.05e+00 ... (remaining 6571 not shown) Histogram of bond angle deviations from ideal: 99.42 - 106.34: 152 106.34 - 113.27: 3572 113.27 - 120.19: 2452 120.19 - 127.11: 2636 127.11 - 134.04: 70 Bond angle restraints: 8882 Sorted by residual: angle pdb=" N ILE B 318 " pdb=" CA ILE B 318 " pdb=" C ILE B 318 " ideal model delta sigma weight residual 111.91 108.20 3.71 8.90e-01 1.26e+00 1.73e+01 angle pdb=" N GLU A 478 " pdb=" CA GLU A 478 " pdb=" CB GLU A 478 " ideal model delta sigma weight residual 110.28 116.49 -6.21 1.55e+00 4.16e-01 1.61e+01 angle pdb=" N ARG A 689 " pdb=" CA ARG A 689 " pdb=" C ARG A 689 " ideal model delta sigma weight residual 112.89 108.19 4.70 1.24e+00 6.50e-01 1.43e+01 angle pdb=" C ASN A 477 " pdb=" N GLU A 478 " pdb=" CA GLU A 478 " ideal model delta sigma weight residual 120.31 115.12 5.19 1.52e+00 4.33e-01 1.17e+01 angle pdb=" C PRO A 850 " pdb=" N ARG A 851 " pdb=" CA ARG A 851 " ideal model delta sigma weight residual 122.56 117.89 4.67 1.50e+00 4.44e-01 9.71e+00 ... (remaining 8877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3547 17.95 - 35.90: 360 35.90 - 53.86: 45 53.86 - 71.81: 10 71.81 - 89.76: 5 Dihedral angle restraints: 3967 sinusoidal: 1638 harmonic: 2329 Sorted by residual: dihedral pdb=" CA LEU A 693 " pdb=" C LEU A 693 " pdb=" N ARG A 694 " pdb=" CA ARG A 694 " ideal model delta harmonic sigma weight residual 180.00 159.18 20.82 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CG ARG A 689 " pdb=" CD ARG A 689 " pdb=" NE ARG A 689 " pdb=" CZ ARG A 689 " ideal model delta sinusoidal sigma weight residual -90.00 -32.90 -57.10 2 1.50e+01 4.44e-03 1.50e+01 dihedral pdb=" CA LEU B 267 " pdb=" C LEU B 267 " pdb=" N GLN B 268 " pdb=" CA GLN B 268 " ideal model delta harmonic sigma weight residual 180.00 162.84 17.16 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 3964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 761 0.052 - 0.103: 195 0.103 - 0.155: 37 0.155 - 0.207: 0 0.207 - 0.259: 3 Chirality restraints: 996 Sorted by residual: chirality pdb=" CA ARG A 689 " pdb=" N ARG A 689 " pdb=" C ARG A 689 " pdb=" CB ARG A 689 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB ILE A 869 " pdb=" CA ILE A 869 " pdb=" CG1 ILE A 869 " pdb=" CG2 ILE A 869 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA LEU A 879 " pdb=" N LEU A 879 " pdb=" C LEU A 879 " pdb=" CB LEU A 879 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 993 not shown) Planarity restraints: 1116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 688 " -0.020 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C GLY A 688 " 0.069 2.00e-02 2.50e+03 pdb=" O GLY A 688 " -0.026 2.00e-02 2.50e+03 pdb=" N ARG A 689 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 876 " 0.018 2.00e-02 2.50e+03 3.51e-02 1.24e+01 pdb=" C LEU A 876 " -0.061 2.00e-02 2.50e+03 pdb=" O LEU A 876 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO A 877 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 689 " -0.161 9.50e-02 1.11e+02 7.23e-02 3.21e+00 pdb=" NE ARG A 689 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 689 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 689 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 689 " -0.006 2.00e-02 2.50e+03 ... (remaining 1113 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 84 2.64 - 3.20: 6170 3.20 - 3.77: 9567 3.77 - 4.33: 12956 4.33 - 4.90: 20683 Nonbonded interactions: 49460 Sorted by model distance: nonbonded pdb=" CD2 LEU A 879 " pdb=" N GLN A 880 " model vdw 2.074 3.540 nonbonded pdb=" O THR A 691 " pdb=" OG1 THR A 691 " model vdw 2.155 2.440 nonbonded pdb=" O GLU B 222 " pdb=" OG1 THR B 226 " model vdw 2.208 2.440 nonbonded pdb=" OG SER A 842 " pdb=" O ASN A 868 " model vdw 2.214 2.440 nonbonded pdb=" O GLU A 713 " pdb=" OG SER A 716 " model vdw 2.265 2.440 ... (remaining 49455 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 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: 0.000 Extract box with map and model: 5.660 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 20.840 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 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 0.055 6576 Z= 0.243 Angle : 0.728 10.242 8882 Z= 0.381 Chirality : 0.048 0.259 996 Planarity : 0.005 0.072 1116 Dihedral : 14.260 89.760 2457 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.90 % Favored : 93.97 % Rotamer: Outliers : 0.28 % Allowed : 0.83 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.31), residues: 780 helix: 0.51 (0.30), residues: 325 sheet: -2.62 (0.73), residues: 59 loop : -1.30 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 856 HIS 0.005 0.001 HIS B 359 PHE 0.028 0.002 PHE B 233 TYR 0.015 0.001 TYR A 460 ARG 0.003 0.000 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 486 GLN cc_start: 0.8144 (pm20) cc_final: 0.7928 (pm20) REVERT: B 195 ASP cc_start: 0.8268 (m-30) cc_final: 0.7995 (t0) REVERT: B 501 PHE cc_start: 0.7888 (m-80) cc_final: 0.7556 (m-80) REVERT: B 516 VAL cc_start: 0.8205 (t) cc_final: 0.7780 (t) outliers start: 2 outliers final: 2 residues processed: 107 average time/residue: 0.1763 time to fit residues: 25.7774 Evaluate side-chains 87 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 85 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 ARG Chi-restraints excluded: chain A residue 691 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 37 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 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 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 ASN A 729 ASN ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6576 Z= 0.193 Angle : 0.650 9.712 8882 Z= 0.316 Chirality : 0.044 0.137 996 Planarity : 0.004 0.039 1116 Dihedral : 5.024 56.522 859 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.38 % Allowed : 10.34 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.31), residues: 780 helix: 0.53 (0.29), residues: 333 sheet: -2.76 (0.69), residues: 61 loop : -1.33 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 453 HIS 0.008 0.001 HIS A 502 PHE 0.020 0.002 PHE A 703 TYR 0.014 0.001 TYR A 719 ARG 0.003 0.000 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 486 GLN cc_start: 0.8284 (pm20) cc_final: 0.8082 (pm20) REVERT: A 634 ILE cc_start: 0.6894 (tp) cc_final: 0.6642 (tp) REVERT: A 669 GLU cc_start: 0.6810 (tm-30) cc_final: 0.6599 (tm-30) REVERT: B 195 ASP cc_start: 0.8329 (m-30) cc_final: 0.8108 (t0) REVERT: B 501 PHE cc_start: 0.7875 (m-80) cc_final: 0.7534 (m-10) outliers start: 10 outliers final: 7 residues processed: 97 average time/residue: 0.1627 time to fit residues: 22.0926 Evaluate side-chains 92 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 719 TYR Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 509 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 76 optimal weight: 0.2980 chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6576 Z= 0.160 Angle : 0.603 9.294 8882 Z= 0.293 Chirality : 0.042 0.139 996 Planarity : 0.004 0.036 1116 Dihedral : 4.306 18.640 855 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.07 % Allowed : 13.66 % Favored : 84.28 % 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: -0.84 (0.31), residues: 780 helix: 0.66 (0.29), residues: 333 sheet: -2.67 (0.67), residues: 61 loop : -1.26 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 453 HIS 0.005 0.001 HIS A 502 PHE 0.020 0.001 PHE A 703 TYR 0.012 0.001 TYR B 383 ARG 0.002 0.000 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 GLN cc_start: 0.8324 (pm20) cc_final: 0.8120 (pm20) REVERT: A 634 ILE cc_start: 0.6895 (tp) cc_final: 0.6671 (tp) REVERT: B 233 PHE cc_start: 0.7284 (t80) cc_final: 0.7076 (t80) REVERT: B 501 PHE cc_start: 0.7824 (m-80) cc_final: 0.7503 (m-10) outliers start: 15 outliers final: 10 residues processed: 95 average time/residue: 0.1571 time to fit residues: 20.8639 Evaluate side-chains 87 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 719 TYR Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain A residue 729 ASN Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 509 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 4.9990 chunk 7 optimal weight: 20.0000 chunk 33 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 0.0770 chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 0.0970 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6576 Z= 0.158 Angle : 0.589 8.861 8882 Z= 0.286 Chirality : 0.042 0.147 996 Planarity : 0.003 0.036 1116 Dihedral : 4.248 20.025 855 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.34 % Allowed : 15.86 % Favored : 81.79 % 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: -0.80 (0.31), residues: 780 helix: 0.67 (0.29), residues: 333 sheet: -2.65 (0.66), residues: 61 loop : -1.22 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 356 HIS 0.004 0.001 HIS B 359 PHE 0.020 0.001 PHE A 703 TYR 0.012 0.001 TYR B 383 ARG 0.002 0.000 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 585 GLU cc_start: 0.7990 (pp20) cc_final: 0.7012 (pm20) REVERT: A 628 ASP cc_start: 0.8021 (t0) cc_final: 0.7808 (t0) REVERT: A 634 ILE cc_start: 0.6856 (tp) cc_final: 0.6619 (tp) REVERT: B 501 PHE cc_start: 0.7814 (m-80) cc_final: 0.7492 (m-10) outliers start: 17 outliers final: 12 residues processed: 99 average time/residue: 0.1731 time to fit residues: 23.9355 Evaluate side-chains 94 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 719 TYR Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain A residue 729 ASN Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 521 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 0.0870 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6576 Z= 0.166 Angle : 0.593 11.319 8882 Z= 0.286 Chirality : 0.042 0.139 996 Planarity : 0.003 0.038 1116 Dihedral : 4.163 20.728 855 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.76 % Allowed : 17.66 % Favored : 79.59 % 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: -0.72 (0.31), residues: 780 helix: 0.75 (0.29), residues: 333 sheet: -2.65 (0.65), residues: 61 loop : -1.19 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 356 HIS 0.018 0.001 HIS B 509 PHE 0.022 0.001 PHE B 448 TYR 0.012 0.001 TYR B 383 ARG 0.002 0.000 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 585 GLU cc_start: 0.7980 (pp20) cc_final: 0.7038 (pm20) REVERT: A 634 ILE cc_start: 0.6844 (tp) cc_final: 0.6593 (tp) REVERT: A 718 MET cc_start: 0.7347 (pmm) cc_final: 0.7020 (pmm) REVERT: A 881 ARG cc_start: 0.5903 (tpm170) cc_final: 0.5594 (tpm170) REVERT: B 437 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8408 (tt) REVERT: B 501 PHE cc_start: 0.7824 (m-80) cc_final: 0.7481 (m-10) outliers start: 20 outliers final: 13 residues processed: 103 average time/residue: 0.1614 time to fit residues: 23.2143 Evaluate side-chains 97 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain A residue 719 TYR Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain A residue 729 ASN Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 521 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 766 ASN ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 HIS ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.079 6576 Z= 0.631 Angle : 0.916 12.252 8882 Z= 0.467 Chirality : 0.055 0.251 996 Planarity : 0.006 0.057 1116 Dihedral : 5.458 20.348 854 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 4.41 % Allowed : 19.17 % Favored : 76.41 % 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: -1.59 (0.30), residues: 780 helix: -0.19 (0.27), residues: 328 sheet: -3.50 (0.66), residues: 59 loop : -1.36 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 856 HIS 0.022 0.002 HIS B 509 PHE 0.035 0.003 PHE A 700 TYR 0.042 0.003 TYR A 799 ARG 0.006 0.001 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 91 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 721 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7398 (mt) REVERT: A 881 ARG cc_start: 0.6401 (tpm170) cc_final: 0.6054 (tpm170) REVERT: B 472 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7791 (mm-30) REVERT: B 501 PHE cc_start: 0.7954 (m-80) cc_final: 0.7665 (m-80) outliers start: 32 outliers final: 21 residues processed: 111 average time/residue: 0.1609 time to fit residues: 24.9170 Evaluate side-chains 106 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 84 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 TRP Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 719 TYR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 521 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 0.0770 chunk 75 optimal weight: 0.9990 chunk 47 optimal weight: 0.2980 chunk 45 optimal weight: 0.4980 chunk 34 optimal weight: 20.0000 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 HIS ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6576 Z= 0.174 Angle : 0.670 12.525 8882 Z= 0.322 Chirality : 0.043 0.138 996 Planarity : 0.004 0.039 1116 Dihedral : 4.607 20.607 854 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.48 % Allowed : 20.83 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.31), residues: 780 helix: 0.50 (0.29), residues: 329 sheet: -3.12 (0.61), residues: 59 loop : -1.05 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 356 HIS 0.023 0.001 HIS B 509 PHE 0.019 0.002 PHE A 703 TYR 0.025 0.002 TYR B 518 ARG 0.002 0.000 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: A 440 GLU cc_start: 0.7826 (tt0) cc_final: 0.7215 (pm20) REVERT: A 585 GLU cc_start: 0.8094 (pp20) cc_final: 0.7197 (pm20) REVERT: A 628 ASP cc_start: 0.8402 (t0) cc_final: 0.8169 (t0) REVERT: A 718 MET cc_start: 0.7309 (pmm) cc_final: 0.7023 (pmm) REVERT: A 881 ARG cc_start: 0.6230 (tpm170) cc_final: 0.5811 (tpm170) REVERT: B 472 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7721 (mm-30) REVERT: B 501 PHE cc_start: 0.7857 (m-80) cc_final: 0.7481 (m-10) outliers start: 18 outliers final: 15 residues processed: 109 average time/residue: 0.1710 time to fit residues: 25.6267 Evaluate side-chains 107 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 719 TYR Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain A residue 729 ASN Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 521 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.6980 chunk 47 optimal weight: 0.0040 chunk 51 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6576 Z= 0.164 Angle : 0.652 11.866 8882 Z= 0.313 Chirality : 0.043 0.156 996 Planarity : 0.004 0.036 1116 Dihedral : 4.414 21.766 854 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.90 % Allowed : 21.66 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.31), residues: 780 helix: 0.72 (0.30), residues: 330 sheet: -2.89 (0.61), residues: 59 loop : -1.06 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 356 HIS 0.011 0.001 HIS B 509 PHE 0.028 0.002 PHE B 448 TYR 0.018 0.001 TYR B 518 ARG 0.001 0.000 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 97 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: A 440 GLU cc_start: 0.7868 (tt0) cc_final: 0.7124 (pm20) REVERT: A 585 GLU cc_start: 0.8094 (pp20) cc_final: 0.7195 (pm20) REVERT: A 628 ASP cc_start: 0.8400 (t0) cc_final: 0.8166 (t0) REVERT: A 881 ARG cc_start: 0.6187 (tpm170) cc_final: 0.5656 (tpm170) REVERT: B 232 GLU cc_start: 0.8074 (tp30) cc_final: 0.7380 (tp30) REVERT: B 236 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7190 (mt-10) REVERT: B 472 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7662 (mm-30) REVERT: B 501 PHE cc_start: 0.7825 (m-80) cc_final: 0.7481 (m-10) outliers start: 21 outliers final: 18 residues processed: 107 average time/residue: 0.1616 time to fit residues: 24.2617 Evaluate side-chains 109 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 719 TYR Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain A residue 729 ASN Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 766 ASN Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 521 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 21 optimal weight: 0.0980 chunk 63 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 chunk 69 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN B 509 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6576 Z= 0.168 Angle : 0.656 11.882 8882 Z= 0.314 Chirality : 0.042 0.148 996 Planarity : 0.004 0.044 1116 Dihedral : 4.305 19.108 854 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.76 % Allowed : 22.07 % Favored : 75.17 % 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: -0.64 (0.31), residues: 780 helix: 0.76 (0.30), residues: 330 sheet: -2.76 (0.61), residues: 59 loop : -1.06 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 863 HIS 0.004 0.001 HIS B 359 PHE 0.016 0.001 PHE A 703 TYR 0.025 0.001 TYR B 523 ARG 0.003 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: A 440 GLU cc_start: 0.7860 (tt0) cc_final: 0.7119 (pm20) REVERT: A 456 GLU cc_start: 0.7490 (tt0) cc_final: 0.6531 (pp20) REVERT: A 585 GLU cc_start: 0.8089 (pp20) cc_final: 0.7175 (pm20) REVERT: A 628 ASP cc_start: 0.8302 (t0) cc_final: 0.8067 (t0) REVERT: A 881 ARG cc_start: 0.6171 (tpm170) cc_final: 0.5655 (tpm170) REVERT: B 232 GLU cc_start: 0.8079 (tp30) cc_final: 0.7397 (tp30) REVERT: B 236 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7215 (mt-10) REVERT: B 472 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7647 (mm-30) REVERT: B 501 PHE cc_start: 0.7824 (m-80) cc_final: 0.7493 (m-10) outliers start: 20 outliers final: 17 residues processed: 108 average time/residue: 0.1775 time to fit residues: 26.5019 Evaluate side-chains 111 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 719 TYR Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 766 ASN Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 521 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 0.1980 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 9 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN B 509 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6576 Z= 0.174 Angle : 0.676 11.760 8882 Z= 0.318 Chirality : 0.042 0.138 996 Planarity : 0.004 0.039 1116 Dihedral : 4.240 16.478 854 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.62 % Allowed : 22.76 % Favored : 74.62 % 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: -0.59 (0.31), residues: 780 helix: 0.83 (0.30), residues: 329 sheet: -2.75 (0.62), residues: 61 loop : -1.03 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 863 HIS 0.004 0.001 HIS B 359 PHE 0.018 0.001 PHE B 448 TYR 0.022 0.001 TYR B 523 ARG 0.005 0.000 ARG A 689 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 94 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: A 440 GLU cc_start: 0.7866 (tt0) cc_final: 0.7122 (pm20) REVERT: A 585 GLU cc_start: 0.8091 (pp20) cc_final: 0.7173 (pm20) REVERT: A 628 ASP cc_start: 0.8331 (t0) cc_final: 0.8129 (t0) REVERT: A 881 ARG cc_start: 0.6150 (tpm170) cc_final: 0.5609 (mmp-170) REVERT: B 232 GLU cc_start: 0.8097 (tp30) cc_final: 0.7433 (tp30) REVERT: B 236 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7127 (mt-10) REVERT: B 318 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8313 (pt) REVERT: B 472 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7642 (mm-30) REVERT: B 501 PHE cc_start: 0.7813 (m-80) cc_final: 0.7496 (m-10) REVERT: B 521 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7854 (t80) outliers start: 19 outliers final: 16 residues processed: 104 average time/residue: 0.1597 time to fit residues: 23.2469 Evaluate side-chains 111 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 719 TYR Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 766 ASN Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 521 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.152757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.119890 restraints weight = 10901.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.120679 restraints weight = 7338.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.121649 restraints weight = 5860.048| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6576 Z= 0.196 Angle : 0.671 11.534 8882 Z= 0.318 Chirality : 0.043 0.134 996 Planarity : 0.004 0.040 1116 Dihedral : 4.241 16.468 854 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.03 % Allowed : 22.62 % Favored : 74.34 % 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: -0.60 (0.31), residues: 780 helix: 0.82 (0.30), residues: 330 sheet: -2.77 (0.62), residues: 61 loop : -1.05 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 863 HIS 0.009 0.001 HIS B 509 PHE 0.016 0.001 PHE A 703 TYR 0.022 0.001 TYR B 523 ARG 0.005 0.000 ARG A 689 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1624.77 seconds wall clock time: 30 minutes 57.32 seconds (1857.32 seconds total)