Starting phenix.real_space_refine (version: dev) on Fri Feb 17 21:51:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xvg_33486/02_2023/7xvg_33486.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xvg_33486/02_2023/7xvg_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_33486/02_2023/7xvg_33486.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xvg_33486/02_2023/7xvg_33486.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xvg_33486/02_2023/7xvg_33486.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xvg_33486/02_2023/7xvg_33486.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 4.07, 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: 2.60 Conformation dependent library (CDL) restraints added in 1.1 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: 0.36 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: 1.63 Time building geometry restraints manager: 2.79 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 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. 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: 0.780 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: 4.330 Check model and map are aligned: 0.100 Process input model: 19.970 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.060 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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 : 12.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.90 % Favored : 93.97 % Rotamer Outliers : 0.28 % 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: -0.97 (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 *********************** 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 : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 107 average time/residue: 0.1795 time to fit residues: 26.2644 Evaluate side-chains 86 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 0.800 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2932 time to fit residues: 1.8472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 6576 Z= 0.191 Angle : 0.649 9.831 8882 Z= 0.314 Chirality : 0.044 0.137 996 Planarity : 0.004 0.041 1116 Dihedral : 4.447 16.677 854 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 1.38 % 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: -0.99 (0.31), residues: 780 helix: 0.53 (0.29), residues: 335 sheet: -2.81 (0.68), residues: 61 loop : -1.35 (0.32), residues: 384 *********************** 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 104 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.817 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 97 average time/residue: 0.1688 time to fit residues: 23.1017 Evaluate side-chains 89 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 0.812 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0706 time to fit residues: 1.9187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 76 optimal weight: 0.1980 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.7770 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 6576 Z= 0.180 Angle : 0.608 9.107 8882 Z= 0.297 Chirality : 0.043 0.172 996 Planarity : 0.004 0.038 1116 Dihedral : 4.361 18.144 854 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer Outliers : 1.52 % 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: 0.62 (0.29), residues: 333 sheet: -2.76 (0.67), residues: 61 loop : -1.25 (0.32), residues: 386 *********************** 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 98 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 0.717 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 93 average time/residue: 0.1733 time to fit residues: 22.4640 Evaluate side-chains 84 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 0.744 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0830 time to fit residues: 1.6754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.0980 chunk 7 optimal weight: 20.0000 chunk 33 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 6576 Z= 0.203 Angle : 0.617 10.671 8882 Z= 0.303 Chirality : 0.044 0.148 996 Planarity : 0.004 0.043 1116 Dihedral : 4.377 20.681 854 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer Outliers : 2.48 % 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: -0.85 (0.31), residues: 780 helix: 0.60 (0.29), residues: 334 sheet: -2.81 (0.66), residues: 61 loop : -1.21 (0.32), residues: 385 *********************** 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 113 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 107 average time/residue: 0.1634 time to fit residues: 24.5854 Evaluate side-chains 97 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 0.801 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0789 time to fit residues: 2.3133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 64 optimal weight: 0.0970 chunk 52 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 6576 Z= 0.185 Angle : 0.629 12.186 8882 Z= 0.300 Chirality : 0.043 0.170 996 Planarity : 0.004 0.038 1116 Dihedral : 4.252 20.547 854 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 1.24 % 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 (0.31), residues: 780 helix: 0.68 (0.29), residues: 336 sheet: -2.94 (0.60), residues: 68 loop : -1.19 (0.33), residues: 376 *********************** 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 104 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 0.916 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 100 average time/residue: 0.1653 time to fit residues: 23.3471 Evaluate side-chains 87 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 0.975 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0690 time to fit residues: 1.8492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 6576 Z= 0.318 Angle : 0.706 11.396 8882 Z= 0.346 Chirality : 0.047 0.171 996 Planarity : 0.004 0.038 1116 Dihedral : 4.558 18.808 854 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer Outliers : 2.34 % 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: -1.04 (0.31), residues: 780 helix: 0.45 (0.29), residues: 336 sheet: -3.36 (0.57), residues: 72 loop : -1.14 (0.34), residues: 372 *********************** 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 111 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 106 average time/residue: 0.1693 time to fit residues: 25.0490 Evaluate side-chains 96 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 0.783 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0687 time to fit residues: 2.2146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 0.0770 chunk 75 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 34 optimal weight: 20.0000 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 overall best weight: 1.6342 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 6576 Z= 0.257 Angle : 0.686 11.328 8882 Z= 0.334 Chirality : 0.045 0.137 996 Planarity : 0.004 0.038 1116 Dihedral : 4.575 20.610 854 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer Outliers : 1.10 % 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: -0.99 (0.31), residues: 780 helix: 0.47 (0.29), residues: 336 sheet: -3.18 (0.59), residues: 68 loop : -1.15 (0.33), residues: 376 *********************** 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 106 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 100 average time/residue: 0.1764 time to fit residues: 24.2332 Evaluate side-chains 95 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.773 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0702 time to fit residues: 2.0277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.0050 chunk 47 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- 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 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6576 Z= 0.188 Angle : 0.653 11.322 8882 Z= 0.314 Chirality : 0.043 0.141 996 Planarity : 0.004 0.036 1116 Dihedral : 4.366 17.062 854 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer Outliers : 1.79 % 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: -0.87 (0.31), residues: 780 helix: 0.59 (0.29), residues: 336 sheet: -2.97 (0.60), residues: 67 loop : -1.15 (0.33), residues: 377 *********************** 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 104 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 96 average time/residue: 0.1666 time to fit residues: 22.3790 Evaluate side-chains 92 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.750 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0682 time to fit residues: 2.1001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 238 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6576 Z= 0.187 Angle : 0.676 11.219 8882 Z= 0.319 Chirality : 0.043 0.167 996 Planarity : 0.004 0.041 1116 Dihedral : 4.259 16.584 854 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer Outliers : 0.69 % 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: -0.76 (0.31), residues: 780 helix: 0.63 (0.29), residues: 335 sheet: -2.76 (0.61), residues: 65 loop : -1.08 (0.33), residues: 380 *********************** 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 98 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 95 average time/residue: 0.1803 time to fit residues: 23.7010 Evaluate side-chains 89 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 0.828 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0887 time to fit residues: 1.5702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.3980 chunk 71 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 57 optimal weight: 0.4980 chunk 9 optimal weight: 0.1980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2619 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= 0.181 Angle : 0.695 11.262 8882 Z= 0.330 Chirality : 0.043 0.173 996 Planarity : 0.004 0.037 1116 Dihedral : 4.246 16.453 854 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer Outliers : 0.41 % 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: -0.72 (0.31), residues: 780 helix: 0.72 (0.30), residues: 332 sheet: -2.72 (0.63), residues: 64 loop : -1.11 (0.33), residues: 384 ********************** 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 94 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 93 average time/residue: 0.1760 time to fit residues: 23.0031 Evaluate side-chains 92 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 0.912 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0817 time to fit residues: 1.4863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 0.3980 chunk 54 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 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 = 0.4085 r_free = 0.4085 target = 0.152941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.120198 restraints weight = 10804.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.121323 restraints weight = 6962.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.122237 restraints weight = 5547.119| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 6576 Z= 0.202 Angle : 0.698 11.195 8882 Z= 0.334 Chirality : 0.044 0.169 996 Planarity : 0.004 0.037 1116 Dihedral : 4.253 16.392 854 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.31), residues: 780 helix: 0.72 (0.29), residues: 333 sheet: -2.82 (0.61), residues: 67 loop : -1.13 (0.33), residues: 380 =============================================================================== Job complete usr+sys time: 1452.84 seconds wall clock time: 27 minutes 29.87 seconds (1649.87 seconds total)