Starting phenix.real_space_refine on Tue Nov 14 06:58:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n74_24219/11_2023/7n74_24219_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n74_24219/11_2023/7n74_24219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n74_24219/11_2023/7n74_24219.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n74_24219/11_2023/7n74_24219.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n74_24219/11_2023/7n74_24219_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n74_24219/11_2023/7n74_24219_trim.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 49 5.16 5 C 5085 2.51 5 N 1322 2.21 5 O 1399 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 7859 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1043, 7859 Unusual residues: {' MG': 1, 'ATP': 1, 'Y01': 2} Classifications: {'peptide': 1036, 'undetermined': 4, 'water': 3} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 3, 'PTRANS': 69, 'TRANS': 963, None: 7} Not linked: pdbres="PRO A1168 " pdbres="ATP A1201 " Not linked: pdbres="ATP A1201 " pdbres=" MG A1202 " Not linked: pdbres=" MG A1202 " pdbres="Y01 A1203 " Not linked: pdbres="Y01 A1203 " pdbres="Y01 A1204 " Not linked: pdbres="Y01 A1204 " pdbres="HOH A1301 " ... (remaining 2 not shown) Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 264 Unresolved non-hydrogen angles: 335 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 177 Time building chain proxies: 4.70, per 1000 atoms: 0.60 Number of scatterers: 7859 At special positions: 0 Unit cell: (84.723, 85.634, 131.184, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 49 16.00 P 3 15.00 Mg 1 11.99 O 1399 8.00 N 1322 7.00 C 5085 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.16 Conformation dependent library (CDL) restraints added in 1.4 seconds 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1934 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 9 sheets defined 53.8% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 43 through 57 removed outlier: 3.539A pdb=" N VAL A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 68 Processing helix chain 'A' and resid 68 through 77 removed outlier: 3.911A pdb=" N GLY A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 200 through 212 removed outlier: 3.798A pdb=" N MET A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL A 206 " --> pdb=" O GLN A 202 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'A' and resid 233 through 249 Processing helix chain 'A' and resid 251 through 285 removed outlier: 3.576A pdb=" N MET A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 removed outlier: 3.753A pdb=" N GLY A 297 " --> pdb=" O ARG A 294 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU A 298 " --> pdb=" O PRO A 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 294 through 298' Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 393 through 396 Processing helix chain 'A' and resid 397 through 408 Processing helix chain 'A' and resid 419 through 445 removed outlier: 3.685A pdb=" N LEU A 430 " --> pdb=" O ALA A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 463 removed outlier: 3.655A pdb=" N VAL A 463 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 487 Processing helix chain 'A' and resid 494 through 500 removed outlier: 4.108A pdb=" N LEU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY A 500 " --> pdb=" O ILE A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 Processing helix chain 'A' and resid 544 through 553 Processing helix chain 'A' and resid 566 through 577 removed outlier: 3.806A pdb=" N THR A 576 " --> pdb=" O MET A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 659 Processing helix chain 'A' and resid 667 through 677 removed outlier: 3.626A pdb=" N TYR A 675 " --> pdb=" O MET A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 701 Processing helix chain 'A' and resid 703 through 709 Processing helix chain 'A' and resid 726 through 737 removed outlier: 3.678A pdb=" N VAL A 730 " --> pdb=" O GLN A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 759 Processing helix chain 'A' and resid 821 through 832 Processing helix chain 'A' and resid 835 through 842 Processing helix chain 'A' and resid 850 through 864 removed outlier: 3.600A pdb=" N LEU A 864 " --> pdb=" O GLU A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 877 through 884 Processing helix chain 'A' and resid 909 through 949 removed outlier: 3.692A pdb=" N ILE A 949 " --> pdb=" O ILE A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 964 Processing helix chain 'A' and resid 965 through 974 removed outlier: 4.493A pdb=" N SER A 974 " --> pdb=" O ALA A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1019 Processing helix chain 'A' and resid 1039 through 1061 removed outlier: 4.033A pdb=" N LEU A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1072 Processing helix chain 'A' and resid 1073 through 1093 Processing helix chain 'A' and resid 1097 through 1102 removed outlier: 3.562A pdb=" N LEU A1101 " --> pdb=" O LEU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1145 Proline residue: A1138 - end of helix Processing helix chain 'A' and resid 1152 through 1164 Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 41 removed outlier: 3.921A pdb=" N GLY A 39 " --> pdb=" O CYS A 80 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS A 41 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ARG A 78 " --> pdb=" O CYS A 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 90 Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 109 removed outlier: 5.777A pdb=" N ARG A 159 " --> pdb=" O TRP A 170 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 176 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 289 through 291 Processing sheet with id=AA5, first strand: chain 'A' and resid 312 through 315 removed outlier: 4.397A pdb=" N VAL A 386 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU A 387 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ASP A 325 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 347 through 350 removed outlier: 6.786A pdb=" N GLU A 332 " --> pdb=" O ALA A 378 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ALA A 378 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N MET A 334 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 488 through 490 removed outlier: 5.941A pdb=" N GLY A 887 " --> pdb=" O PHE A 901 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N SER A 903 " --> pdb=" O GLY A 887 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N SER A 889 " --> pdb=" O SER A 903 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ALA A 741 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N PHE A 846 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N MET A 743 " --> pdb=" O PHE A 846 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR A 844 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU A 818 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N PHE A 846 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU A 820 " --> pdb=" O PHE A 846 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N HIS A 767 " --> pdb=" O HIS A 817 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ALA A 819 " --> pdb=" O HIS A 767 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE A 769 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A 783 " --> pdb=" O THR A 774 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 520 through 525 removed outlier: 6.694A pdb=" N LEU A 685 " --> pdb=" O LEU A 714 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU A 716 " --> pdb=" O VAL A 683 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A 683 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL A 718 " --> pdb=" O ARG A 681 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG A 681 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG A 631 " --> pdb=" O PHE A 625 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE A 625 " --> pdb=" O ARG A 631 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA A 637 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL A 619 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 588 " --> pdb=" O VAL A 619 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 557 through 558 448 hydrogen bonds defined for protein. 1293 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: 3.31 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2000 1.33 - 1.45: 1310 1.45 - 1.57: 4636 1.57 - 1.69: 12 1.69 - 1.81: 73 Bond restraints: 8031 Sorted by residual: bond pdb=" C4 ATP A1201 " pdb=" C5 ATP A1201 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.78e+01 bond pdb=" C5 ATP A1201 " pdb=" C6 ATP A1201 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.39e+01 bond pdb=" C8 ATP A1201 " pdb=" N7 ATP A1201 " ideal model delta sigma weight residual 1.310 1.357 -0.047 1.00e-02 1.00e+04 2.18e+01 bond pdb=" C5 ATP A1201 " pdb=" N7 ATP A1201 " ideal model delta sigma weight residual 1.387 1.345 0.042 1.00e-02 1.00e+04 1.78e+01 bond pdb=" CAY Y01 A1203 " pdb=" OAW Y01 A1203 " ideal model delta sigma weight residual 1.332 1.413 -0.081 2.00e-02 2.50e+03 1.64e+01 ... (remaining 8026 not shown) Histogram of bond angle deviations from ideal: 93.21 - 101.75: 28 101.75 - 110.29: 1921 110.29 - 118.84: 4768 118.84 - 127.38: 4171 127.38 - 135.92: 98 Bond angle restraints: 10986 Sorted by residual: angle pdb=" PB ATP A1201 " pdb=" O3B ATP A1201 " pdb=" PG ATP A1201 " ideal model delta sigma weight residual 139.87 122.32 17.55 1.00e+00 1.00e+00 3.08e+02 angle pdb=" PA ATP A1201 " pdb=" O3A ATP A1201 " pdb=" PB ATP A1201 " ideal model delta sigma weight residual 136.83 121.71 15.12 1.00e+00 1.00e+00 2.29e+02 angle pdb=" C5 ATP A1201 " pdb=" C4 ATP A1201 " pdb=" N3 ATP A1201 " ideal model delta sigma weight residual 126.80 118.62 8.18 1.00e+00 1.00e+00 6.70e+01 angle pdb=" N3 ATP A1201 " pdb=" C4 ATP A1201 " pdb=" N9 ATP A1201 " ideal model delta sigma weight residual 127.04 134.83 -7.79 1.15e+00 7.59e-01 4.60e+01 angle pdb=" N LYS A 509 " pdb=" CA LYS A 509 " pdb=" C LYS A 509 " ideal model delta sigma weight residual 111.40 118.55 -7.15 1.22e+00 6.72e-01 3.44e+01 ... (remaining 10981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.02: 4260 15.02 - 30.03: 424 30.03 - 45.04: 93 45.04 - 60.06: 18 60.06 - 75.07: 5 Dihedral angle restraints: 4800 sinusoidal: 1806 harmonic: 2994 Sorted by residual: dihedral pdb=" CA SER A 889 " pdb=" C SER A 889 " pdb=" N LEU A 890 " pdb=" CA LEU A 890 " ideal model delta harmonic sigma weight residual 180.00 -158.29 -21.71 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA ILE A 965 " pdb=" C ILE A 965 " pdb=" N THR A 966 " pdb=" CA THR A 966 " ideal model delta harmonic sigma weight residual -180.00 -162.22 -17.78 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ARG A 207 " pdb=" C ARG A 207 " pdb=" N LYS A 208 " pdb=" CA LYS A 208 " ideal model delta harmonic sigma weight residual 180.00 162.29 17.71 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 4797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.356: 1327 0.356 - 0.711: 3 0.711 - 1.067: 0 1.067 - 1.423: 1 1.423 - 1.778: 3 Chirality restraints: 1334 Sorted by residual: chirality pdb=" CG LEU A 702 " pdb=" CB LEU A 702 " pdb=" CD1 LEU A 702 " pdb=" CD2 LEU A 702 " both_signs ideal model delta sigma weight residual False -2.59 -0.81 -1.78 2.00e-01 2.50e+01 7.91e+01 chirality pdb=" CG LEU A 723 " pdb=" CB LEU A 723 " pdb=" CD1 LEU A 723 " pdb=" CD2 LEU A 723 " both_signs ideal model delta sigma weight residual False -2.59 -0.95 -1.64 2.00e-01 2.50e+01 6.70e+01 chirality pdb=" CG LEU A 787 " pdb=" CB LEU A 787 " pdb=" CD1 LEU A 787 " pdb=" CD2 LEU A 787 " both_signs ideal model delta sigma weight residual False -2.59 -1.09 -1.50 2.00e-01 2.50e+01 5.66e+01 ... (remaining 1331 not shown) Planarity restraints: 1373 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1042 " -0.020 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" CG ASN A1042 " 0.068 2.00e-02 2.50e+03 pdb=" OD1 ASN A1042 " -0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN A1042 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 590 " 0.032 2.00e-02 2.50e+03 2.82e-02 1.39e+01 pdb=" CG PHE A 590 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 PHE A 590 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A 590 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 590 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 590 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 590 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1029 " -0.088 9.50e-02 1.11e+02 4.61e-02 7.94e+00 pdb=" NE ARG A1029 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A1029 " -0.045 2.00e-02 2.50e+03 pdb=" NH1 ARG A1029 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG A1029 " 0.012 2.00e-02 2.50e+03 ... (remaining 1370 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.46: 27 2.46 - 3.07: 5346 3.07 - 3.68: 11985 3.68 - 4.29: 18008 4.29 - 4.90: 30848 Nonbonded interactions: 66214 Sorted by model distance: nonbonded pdb=" OD1 ASN A 508 " pdb=" OG1 THR A 512 " model vdw 1.844 2.440 nonbonded pdb=" OG1 THR A 642 " pdb=" OE1 GLN A 643 " model vdw 1.982 2.440 nonbonded pdb=" OG SER A 633 " pdb=" OE2 GLU A 708 " model vdw 2.078 2.440 nonbonded pdb=" NH2 ARG A 740 " pdb=" O GLY A 843 " model vdw 2.100 2.520 nonbonded pdb=" OH TYR A 235 " pdb=" O PRO A 465 " model vdw 2.109 2.440 ... (remaining 66209 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.940 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: 11.130 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 26.180 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:14.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 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 : 0.006 0.081 8031 Z= 0.388 Angle : 0.887 17.547 10986 Z= 0.479 Chirality : 0.102 1.778 1334 Planarity : 0.006 0.060 1373 Dihedral : 12.925 75.073 2866 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 0.74 (0.26), residues: 1024 helix: 1.13 (0.23), residues: 499 sheet: -0.22 (0.39), residues: 167 loop : 0.13 (0.34), residues: 358 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.004 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 1.1332 time to fit residues: 127.0079 Evaluate side-chains 52 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.824 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 0.0870 chunk 60 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 ASN A1042 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8031 Z= 0.213 Angle : 0.604 7.925 10986 Z= 0.293 Chirality : 0.041 0.145 1334 Planarity : 0.005 0.046 1373 Dihedral : 5.504 53.644 1137 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.18 % Allowed : 7.74 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.29 (0.27), residues: 1024 helix: 1.69 (0.23), residues: 502 sheet: -0.01 (0.40), residues: 161 loop : 0.23 (0.34), residues: 361 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 61 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 4 residues processed: 73 average time/residue: 0.9768 time to fit residues: 77.4438 Evaluate side-chains 53 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.921 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.0833 time to fit residues: 1.3409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 94 optimal weight: 0.0040 chunk 102 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8031 Z= 0.188 Angle : 0.537 7.317 10986 Z= 0.259 Chirality : 0.040 0.140 1334 Planarity : 0.005 0.046 1373 Dihedral : 5.415 51.519 1137 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.78 % Allowed : 9.07 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.64 (0.27), residues: 1024 helix: 2.01 (0.23), residues: 505 sheet: 0.06 (0.40), residues: 159 loop : 0.37 (0.34), residues: 360 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 56 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 71 average time/residue: 0.9660 time to fit residues: 74.5283 Evaluate side-chains 63 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 0.902 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.6286 time to fit residues: 2.5867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 chunk 83 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8031 Z= 0.192 Angle : 0.528 7.930 10986 Z= 0.253 Chirality : 0.040 0.139 1334 Planarity : 0.005 0.047 1373 Dihedral : 5.277 52.053 1137 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.42 % Allowed : 10.28 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.84 (0.27), residues: 1024 helix: 2.20 (0.23), residues: 508 sheet: -0.01 (0.41), residues: 164 loop : 0.52 (0.34), residues: 352 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 56 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 70 average time/residue: 0.8356 time to fit residues: 64.2782 Evaluate side-chains 60 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.911 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.1171 time to fit residues: 1.3939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 51 optimal weight: 0.0370 chunk 90 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8031 Z= 0.211 Angle : 0.519 6.891 10986 Z= 0.251 Chirality : 0.040 0.138 1334 Planarity : 0.004 0.047 1373 Dihedral : 5.221 56.196 1137 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.42 % Allowed : 11.97 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.93 (0.27), residues: 1024 helix: 2.26 (0.23), residues: 508 sheet: -0.09 (0.41), residues: 158 loop : 0.65 (0.34), residues: 358 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 54 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 70 average time/residue: 1.0044 time to fit residues: 76.5930 Evaluate side-chains 63 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 0.881 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.1276 time to fit residues: 1.4114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.1980 chunk 19 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8031 Z= 0.226 Angle : 0.528 7.977 10986 Z= 0.253 Chirality : 0.040 0.139 1334 Planarity : 0.004 0.047 1373 Dihedral : 5.169 58.593 1137 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.14 % Allowed : 12.94 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.27), residues: 1024 helix: 2.32 (0.23), residues: 508 sheet: -0.06 (0.41), residues: 158 loop : 0.72 (0.34), residues: 358 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 57 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 13 residues processed: 77 average time/residue: 0.8334 time to fit residues: 70.5021 Evaluate side-chains 65 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 52 time to evaluate : 0.860 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 2 average time/residue: 0.1237 time to fit residues: 1.5391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8031 Z= 0.211 Angle : 0.531 7.659 10986 Z= 0.255 Chirality : 0.040 0.139 1334 Planarity : 0.004 0.046 1373 Dihedral : 5.094 53.971 1137 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.78 % Allowed : 14.15 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.27), residues: 1024 helix: 2.33 (0.23), residues: 511 sheet: -0.02 (0.40), residues: 160 loop : 0.78 (0.35), residues: 353 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 52 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 15 residues processed: 69 average time/residue: 0.9288 time to fit residues: 70.1125 Evaluate side-chains 69 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 54 time to evaluate : 0.918 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 3 average time/residue: 0.5065 time to fit residues: 3.0909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 93 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8031 Z= 0.177 Angle : 0.520 8.510 10986 Z= 0.246 Chirality : 0.040 0.138 1334 Planarity : 0.004 0.047 1373 Dihedral : 4.937 48.424 1137 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.42 % Allowed : 14.75 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.27), residues: 1024 helix: 2.42 (0.23), residues: 506 sheet: 0.08 (0.40), residues: 158 loop : 0.81 (0.35), residues: 360 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 52 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 70 average time/residue: 0.9056 time to fit residues: 69.3104 Evaluate side-chains 65 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 52 time to evaluate : 0.889 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.1249 time to fit residues: 1.4093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 73 optimal weight: 0.2980 chunk 28 optimal weight: 0.4980 chunk 84 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8031 Z= 0.174 Angle : 0.519 7.895 10986 Z= 0.245 Chirality : 0.040 0.139 1334 Planarity : 0.004 0.047 1373 Dihedral : 4.852 48.041 1137 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.06 % Allowed : 15.24 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.27), residues: 1024 helix: 2.51 (0.23), residues: 501 sheet: 0.08 (0.40), residues: 158 loop : 0.90 (0.35), residues: 365 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 53 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 13 residues processed: 68 average time/residue: 0.9777 time to fit residues: 72.2787 Evaluate side-chains 64 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 51 time to evaluate : 0.856 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 1 average time/residue: 0.2996 time to fit residues: 1.7225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 103 optimal weight: 0.3980 chunk 95 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8031 Z= 0.177 Angle : 0.538 11.101 10986 Z= 0.254 Chirality : 0.039 0.138 1334 Planarity : 0.004 0.047 1373 Dihedral : 4.769 48.036 1137 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.81 % Allowed : 15.60 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.27), residues: 1024 helix: 2.54 (0.23), residues: 501 sheet: 0.14 (0.40), residues: 158 loop : 0.90 (0.35), residues: 365 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 54 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 13 residues processed: 67 average time/residue: 1.0177 time to fit residues: 74.1731 Evaluate side-chains 66 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 0.903 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.1460 time to fit residues: 1.4384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.0060 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 0.0670 chunk 82 optimal weight: 0.0770 chunk 34 optimal weight: 10.0000 chunk 84 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 4 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 overall best weight: 0.2292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.092538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.067299 restraints weight = 15925.451| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.81 r_work: 0.2855 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8031 Z= 0.137 Angle : 0.521 8.590 10986 Z= 0.247 Chirality : 0.039 0.137 1334 Planarity : 0.004 0.047 1373 Dihedral : 4.689 49.825 1137 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.06 % Allowed : 15.84 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.27), residues: 1024 helix: 2.61 (0.23), residues: 501 sheet: 0.11 (0.40), residues: 158 loop : 0.97 (0.35), residues: 365 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2459.24 seconds wall clock time: 45 minutes 37.31 seconds (2737.31 seconds total)