Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 23:17:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rph_24614/04_2023/7rph_24614.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rph_24614/04_2023/7rph_24614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rph_24614/04_2023/7rph_24614.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rph_24614/04_2023/7rph_24614.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rph_24614/04_2023/7rph_24614.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rph_24614/04_2023/7rph_24614.pdb" } resolution = 2.5 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= 0.006 sd= 0.579 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: 5 Type Number sf(0) Gaussians S 65 5.16 5 Na 3 4.78 5 C 5742 2.51 5 N 1185 2.21 5 O 1578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 258": "OE1" <-> "OE2" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "A ARG 382": "NH1" <-> "NH2" Residue "A GLU 472": "OE1" <-> "OE2" Residue "A TYR 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 552": "OE1" <-> "OE2" Residue "A GLU 591": "OE1" <-> "OE2" Residue "A GLU 698": "OE1" <-> "OE2" Residue "A GLU 746": "OE1" <-> "OE2" Residue "A GLU 807": "OE1" <-> "OE2" Residue "A GLU 842": "OE1" <-> "OE2" Residue "A GLU 852": "OE1" <-> "OE2" Residue "A GLU 859": "OE1" <-> "OE2" Residue "A GLU 882": "OE1" <-> "OE2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "A ARG 897": "NH1" <-> "NH2" Residue "A PHE 929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 944": "OE1" <-> "OE2" Residue "A GLU 958": "OE1" <-> "OE2" Residue "A GLU 970": "OE1" <-> "OE2" Residue "A ARG 1059": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8573 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8573 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1048, 8565 Unusual residues: {' NA': 3, 'AV0': 2, 'NAG': 5, 'Y01': 26} Classifications: {'peptide': 926, 'undetermined': 36, 'water': 86} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 885, None: 122} Not linked: pdbres="PHE A1143 " pdbres=" NA A1601 " Not linked: pdbres=" NA A1601 " pdbres=" NA A1602 " Not linked: pdbres=" NA A1602 " pdbres=" NA A1603 " Not linked: pdbres=" NA A1603 " pdbres="Y01 A1604 " Not linked: pdbres="Y01 A1604 " pdbres="Y01 A1605 " ... (remaining 117 not shown) Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Conformer: "B" Number of residues, atoms: 1048, 8565 Unusual residues: {' NA': 3, 'AV0': 2, 'NAG': 5, 'Y01': 26} Classifications: {'peptide': 926, 'undetermined': 36, 'water': 86} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 885, None: 122} Not linked: pdbres="PHE A1143 " pdbres=" NA A1601 " Not linked: pdbres=" NA A1601 " pdbres=" NA A1602 " Not linked: pdbres=" NA A1602 " pdbres=" NA A1603 " Not linked: pdbres=" NA A1603 " pdbres="Y01 A1604 " Not linked: pdbres="Y01 A1604 " pdbres="Y01 A1605 " ... (remaining 117 not shown) Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 bond proxies already assigned to first conformer: 8749 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AMET A 557 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 557 " occ=0.50 Time building chain proxies: 8.95, per 1000 atoms: 1.04 Number of scatterers: 8573 At special positions: 0 Unit cell: (88.51, 88.51, 127.755, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 Na 3 11.00 O 1578 8.00 N 1185 7.00 C 5742 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 348 " distance=2.02 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 366 " distance=2.05 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 417 " distance=2.02 Simple disulfide: pdb=" SG CYS A 397 " - pdb=" SG CYS A 410 " distance=2.04 Simple disulfide: pdb=" SG CYS A 829 " - pdb=" SG CYS A 849 " distance=2.05 Simple disulfide: pdb=" SG CYS A 863 " - pdb=" SG CYS A 872 " distance=2.03 Simple disulfide: pdb=" SG CYS A 871 " - pdb=" SG CYS A 887 " distance=2.05 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 Links applied NAG-ASN " NAG A1632 " - " ASN A 915 " " NAG A1633 " - " ASN A 475 " " NAG A1634 " - " ASN A 834 " " NAG A1635 " - " ASN A 362 " " NAG A1636 " - " ASN A 390 " Time building additional restraints: 3.40 Conformation dependent library (CDL) restraints added in 2.3 seconds 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1766 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 3 sheets defined 67.8% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 179 through 187 Processing helix chain 'A' and resid 187 through 209 removed outlier: 3.550A pdb=" N VAL A 191 " --> pdb=" O TRP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 242 Processing helix chain 'A' and resid 253 through 262 removed outlier: 3.606A pdb=" N ARG A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 329 removed outlier: 3.547A pdb=" N CYS A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'A' and resid 352 through 361 Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 370 through 390 removed outlier: 3.518A pdb=" N VAL A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LYS A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N HIS A 387 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A 388 " --> pdb=" O CYS A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 removed outlier: 3.973A pdb=" N THR A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS A 419 " --> pdb=" O ARG A 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 414 through 419' Processing helix chain 'A' and resid 421 through 430 Processing helix chain 'A' and resid 437 through 442 removed outlier: 4.001A pdb=" N ASP A 442 " --> pdb=" O PRO A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 471 Processing helix chain 'A' and resid 491 through 493 No H-bonds generated for 'chain 'A' and resid 491 through 493' Processing helix chain 'A' and resid 494 through 502 removed outlier: 3.567A pdb=" N TYR A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 522 Processing helix chain 'A' and resid 523 through 548 removed outlier: 3.813A pdb=" N LEU A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 559 Processing helix chain 'A' and resid 560 through 569 Processing helix chain 'A' and resid 570 through 587 Processing helix chain 'A' and resid 591 through 621 removed outlier: 5.641A pdb=" N LEU A 605 " --> pdb=" O GLN A 601 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N SER A 606 " --> pdb=" O HIS A 602 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR A 614 " --> pdb=" O THR A 610 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 624 No H-bonds generated for 'chain 'A' and resid 622 through 624' Processing helix chain 'A' and resid 626 through 648 Processing helix chain 'A' and resid 649 through 662 Processing helix chain 'A' and resid 682 through 706 Processing helix chain 'A' and resid 706 through 715 removed outlier: 3.581A pdb=" N CYS A 710 " --> pdb=" O LYS A 706 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE A 715 " --> pdb=" O ILE A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 736 removed outlier: 3.527A pdb=" N ILE A 721 " --> pdb=" O TYR A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 750 Processing helix chain 'A' and resid 757 through 765 removed outlier: 3.646A pdb=" N ASP A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 769 Processing helix chain 'A' and resid 770 through 779 removed outlier: 4.013A pdb=" N HIS A 776 " --> pdb=" O PHE A 772 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS A 777 " --> pdb=" O GLU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 834 removed outlier: 3.547A pdb=" N ASN A 834 " --> pdb=" O GLN A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 859 removed outlier: 3.763A pdb=" N THR A 853 " --> pdb=" O CYS A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 872 Proline residue: A 870 - end of helix Processing helix chain 'A' and resid 880 through 899 removed outlier: 4.099A pdb=" N LYS A 889 " --> pdb=" O GLU A 885 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A 897 " --> pdb=" O MET A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 954 removed outlier: 3.514A pdb=" N GLN A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 1002 Processing helix chain 'A' and resid 1003 through 1028 Processing helix chain 'A' and resid 1033 through 1061 removed outlier: 3.719A pdb=" N VAL A1038 " --> pdb=" O VAL A1034 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A1040 " --> pdb=" O GLU A1036 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER A1041 " --> pdb=" O SER A1037 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A1044 " --> pdb=" O ILE A1040 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ASP A1049 " --> pdb=" O GLY A1045 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N PHE A1050 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ALA A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1094 removed outlier: 5.233A pdb=" N SER A1079 " --> pdb=" O SER A1075 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ALA A1080 " --> pdb=" O ARG A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1123 Processing helix chain 'A' and resid 1123 through 1133 Processing sheet with id=AA1, first strand: chain 'A' and resid 450 through 458 removed outlier: 3.952A pdb=" N SER A 300 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ARG A 301 " --> pdb=" O ILE A 486 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ILE A 486 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 303 " --> pdb=" O THR A 484 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 341 through 343 removed outlier: 4.828A pdb=" N THR A 343 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 346 " --> pdb=" O THR A 343 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 910 through 912 removed outlier: 7.955A pdb=" N LEU A 923 " --> pdb=" O TRP A 789 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N TRP A 789 " --> pdb=" O LEU A 923 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N PHE A 925 " --> pdb=" O VAL A 787 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL A 787 " --> pdb=" O PHE A 925 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N SER A 927 " --> pdb=" O ILE A 785 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE A 785 " --> pdb=" O SER A 927 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHE A 929 " --> pdb=" O MET A 783 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1287 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1239 1.29 - 1.42: 2196 1.42 - 1.56: 4867 1.56 - 1.69: 367 1.69 - 1.83: 98 Bond restraints: 8767 Sorted by residual: bond pdb=" C LEU A1086 " pdb=" O LEU A1086 " ideal model delta sigma weight residual 1.237 1.156 0.081 1.17e-02 7.31e+03 4.75e+01 bond pdb=" C THR A 613 " pdb=" O THR A 613 " ideal model delta sigma weight residual 1.236 1.150 0.086 1.26e-02 6.30e+03 4.71e+01 bond pdb=" C ALA A 615 " pdb=" O ALA A 615 " ideal model delta sigma weight residual 1.237 1.159 0.078 1.16e-02 7.43e+03 4.53e+01 bond pdb=" C PHE A 608 " pdb=" O PHE A 608 " ideal model delta sigma weight residual 1.237 1.162 0.075 1.16e-02 7.43e+03 4.18e+01 bond pdb=" C ALA A 573 " pdb=" O ALA A 573 " ideal model delta sigma weight residual 1.237 1.161 0.076 1.19e-02 7.06e+03 4.08e+01 ... (remaining 8762 not shown) Histogram of bond angle deviations from ideal: 98.94 - 106.29: 421 106.29 - 113.65: 4784 113.65 - 121.00: 4592 121.00 - 128.35: 2212 128.35 - 135.70: 57 Bond angle restraints: 12066 Sorted by residual: angle pdb=" N PHE A 612 " pdb=" CA PHE A 612 " pdb=" C PHE A 612 " ideal model delta sigma weight residual 111.71 121.40 -9.69 1.15e+00 7.56e-01 7.10e+01 angle pdb=" N LEU A1086 " pdb=" CA LEU A1086 " pdb=" C LEU A1086 " ideal model delta sigma weight residual 111.28 119.12 -7.84 1.09e+00 8.42e-01 5.17e+01 angle pdb=" CA PHE A 759 " pdb=" CB PHE A 759 " pdb=" CG PHE A 759 " ideal model delta sigma weight residual 113.80 120.09 -6.29 1.00e+00 1.00e+00 3.96e+01 angle pdb=" N ASP A1049 " pdb=" CA ASP A1049 " pdb=" C ASP A1049 " ideal model delta sigma weight residual 111.07 117.58 -6.51 1.07e+00 8.73e-01 3.70e+01 angle pdb=" N ASP A 571 " pdb=" CA ASP A 571 " pdb=" C ASP A 571 " ideal model delta sigma weight residual 111.33 118.66 -7.33 1.21e+00 6.83e-01 3.67e+01 ... (remaining 12061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.95: 4638 27.95 - 55.91: 171 55.91 - 83.86: 20 83.86 - 111.82: 2 111.82 - 139.77: 3 Dihedral angle restraints: 4834 sinusoidal: 2106 harmonic: 2728 Sorted by residual: dihedral pdb=" CB CYS A 863 " pdb=" SG CYS A 863 " pdb=" SG CYS A 872 " pdb=" CB CYS A 872 " ideal model delta sinusoidal sigma weight residual -86.00 -163.15 77.15 1 1.00e+01 1.00e-02 7.46e+01 dihedral pdb=" CA VAL A1048 " pdb=" C VAL A1048 " pdb=" N ASP A1049 " pdb=" CA ASP A1049 " ideal model delta harmonic sigma weight residual -180.00 -152.08 -27.92 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CB CYS A 384 " pdb=" SG CYS A 384 " pdb=" SG CYS A 417 " pdb=" CB CYS A 417 " ideal model delta sinusoidal sigma weight residual 93.00 134.34 -41.34 1 1.00e+01 1.00e-02 2.39e+01 ... (remaining 4831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 971 0.109 - 0.219: 384 0.219 - 0.328: 70 0.328 - 0.437: 14 0.437 - 0.546: 2 Chirality restraints: 1441 Sorted by residual: chirality pdb=" CA LEU A1086 " pdb=" N LEU A1086 " pdb=" C LEU A1086 " pdb=" CB LEU A1086 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.46e+00 chirality pdb=" CA PHE A 612 " pdb=" N PHE A 612 " pdb=" C PHE A 612 " pdb=" CB PHE A 612 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.45 2.00e-01 2.50e+01 4.95e+00 chirality pdb=" CA GLN A 334 " pdb=" N GLN A 334 " pdb=" C GLN A 334 " pdb=" CB GLN A 334 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.71e+00 ... (remaining 1438 not shown) Planarity restraints: 1345 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 475 " 0.125 2.00e-02 2.50e+03 1.32e-01 2.17e+02 pdb=" CG ASN A 475 " -0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN A 475 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 475 " -0.202 2.00e-02 2.50e+03 pdb=" C1 NAG A1633 " 0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 313 " 0.134 2.00e-02 2.50e+03 6.63e-02 1.10e+02 pdb=" CG TRP A 313 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A 313 " -0.072 2.00e-02 2.50e+03 pdb=" CD2 TRP A 313 " -0.037 2.00e-02 2.50e+03 pdb=" NE1 TRP A 313 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TRP A 313 " 0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP A 313 " -0.079 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 313 " 0.078 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 313 " -0.045 2.00e-02 2.50e+03 pdb=" CH2 TRP A 313 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 351 " -0.106 2.00e-02 2.50e+03 5.66e-02 8.00e+01 pdb=" CG TRP A 351 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TRP A 351 " 0.084 2.00e-02 2.50e+03 pdb=" CD2 TRP A 351 " 0.026 2.00e-02 2.50e+03 pdb=" NE1 TRP A 351 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 351 " -0.017 2.00e-02 2.50e+03 pdb=" CE3 TRP A 351 " 0.082 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 351 " -0.050 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 351 " 0.026 2.00e-02 2.50e+03 pdb=" CH2 TRP A 351 " -0.052 2.00e-02 2.50e+03 ... (remaining 1342 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 19 2.54 - 3.13: 6250 3.13 - 3.72: 12578 3.72 - 4.31: 19701 4.31 - 4.90: 31303 Nonbonded interactions: 69851 Sorted by model distance: nonbonded pdb=" OD1 ASP A 571 " pdb="NA NA A1602 " model vdw 1.952 2.470 nonbonded pdb=" OD1 ASP A1049 " pdb="NA NA A1601 " model vdw 2.174 2.470 nonbonded pdb=" O GLY A 567 " pdb="NA NA A1602 " model vdw 2.186 2.470 nonbonded pdb=" OG1 THR A 613 " pdb="NA NA A1601 " model vdw 2.201 2.470 nonbonded pdb=" OD2 ASP A 572 " pdb="NA NA A1603 " model vdw 2.251 2.470 ... (remaining 69846 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 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: 0.010 Extract box with map and model: 7.650 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 31.110 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 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 : 0.017 0.128 8767 Z= 1.014 Angle : 1.889 9.687 12066 Z= 1.230 Chirality : 0.115 0.546 1441 Planarity : 0.014 0.105 1340 Dihedral : 14.717 139.770 3044 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 2.50 % 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: -0.70 (0.25), residues: 921 helix: -0.48 (0.19), residues: 563 sheet: -0.16 (0.97), residues: 29 loop : -0.11 (0.34), residues: 329 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 146 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 148 average time/residue: 1.2299 time to fit residues: 194.1897 Evaluate side-chains 101 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.877 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2501 ------------------------------------------------------------------------------- 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: 0.9980 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN A 367 GLN A 376 HIS ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN A 856 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 8767 Z= 0.183 Angle : 0.672 8.759 12066 Z= 0.321 Chirality : 0.044 0.284 1441 Planarity : 0.004 0.041 1340 Dihedral : 12.487 148.370 1373 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.51 (0.28), residues: 921 helix: 1.36 (0.21), residues: 578 sheet: 0.07 (0.92), residues: 31 loop : 0.64 (0.39), residues: 312 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 137 average time/residue: 1.0648 time to fit residues: 157.0910 Evaluate side-chains 98 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 0.896 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 2.1975 time to fit residues: 3.5554 ------------------------------------------------------------------------------- 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: 0.8980 chunk 29 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 94 optimal weight: 9.9990 chunk 102 optimal weight: 50.0000 chunk 84 optimal weight: 0.0970 chunk 93 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN A 968 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 8767 Z= 0.159 Angle : 0.607 7.638 12066 Z= 0.288 Chirality : 0.041 0.230 1441 Planarity : 0.004 0.038 1340 Dihedral : 11.749 148.976 1373 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 3.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.99 (0.28), residues: 921 helix: 1.80 (0.21), residues: 579 sheet: 0.44 (0.90), residues: 31 loop : 0.65 (0.39), residues: 311 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 93 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 111 average time/residue: 1.0518 time to fit residues: 126.2201 Evaluate side-chains 99 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.920 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.8157 time to fit residues: 3.8491 ------------------------------------------------------------------------------- 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: 9.9990 chunk 71 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 100 optimal weight: 50.0000 chunk 89 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 8767 Z= 0.196 Angle : 0.626 7.206 12066 Z= 0.297 Chirality : 0.042 0.241 1441 Planarity : 0.004 0.039 1340 Dihedral : 11.839 148.545 1373 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 3.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.91 (0.28), residues: 921 helix: 1.78 (0.21), residues: 579 sheet: 0.48 (0.90), residues: 31 loop : 0.53 (0.38), residues: 311 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 91 time to evaluate : 0.932 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 12 residues processed: 113 average time/residue: 1.1560 time to fit residues: 140.9538 Evaluate side-chains 97 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 0.958 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.1411 time to fit residues: 1.5010 ------------------------------------------------------------------------------- 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: 0.9990 chunk 1 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 8767 Z= 0.230 Angle : 0.653 7.029 12066 Z= 0.309 Chirality : 0.043 0.212 1441 Planarity : 0.004 0.039 1340 Dihedral : 11.803 146.684 1373 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer Outliers : 3.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.73 (0.28), residues: 921 helix: 1.79 (0.21), residues: 569 sheet: 0.47 (0.90), residues: 31 loop : 0.15 (0.36), residues: 321 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 88 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 15 residues processed: 111 average time/residue: 1.1314 time to fit residues: 135.1224 Evaluate side-chains 104 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 89 time to evaluate : 0.831 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 3 average time/residue: 0.4511 time to fit residues: 2.7462 ------------------------------------------------------------------------------- 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: 2.9990 chunk 19 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 100 optimal weight: 50.0000 chunk 83 optimal weight: 0.5980 chunk 46 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 97 optimal weight: 50.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 8767 Z= 0.291 Angle : 0.718 10.247 12066 Z= 0.336 Chirality : 0.045 0.237 1441 Planarity : 0.004 0.039 1340 Dihedral : 12.138 144.744 1373 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 3.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.49 (0.28), residues: 921 helix: 1.61 (0.21), residues: 569 sheet: 0.35 (0.89), residues: 31 loop : 0.03 (0.36), residues: 321 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 90 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 16 residues processed: 110 average time/residue: 1.1032 time to fit residues: 131.0401 Evaluate side-chains 102 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 0.955 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.6085 time to fit residues: 2.6738 ------------------------------------------------------------------------------- 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: 3.9990 chunk 57 optimal weight: 0.3980 chunk 73 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 100 optimal weight: 50.0000 chunk 62 optimal weight: 0.0980 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 8767 Z= 0.155 Angle : 0.587 8.643 12066 Z= 0.273 Chirality : 0.040 0.202 1441 Planarity : 0.004 0.039 1340 Dihedral : 11.516 145.083 1373 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 3.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.92 (0.28), residues: 921 helix: 1.95 (0.22), residues: 571 sheet: 0.44 (0.88), residues: 31 loop : 0.20 (0.37), residues: 319 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 18 residues processed: 112 average time/residue: 1.0889 time to fit residues: 132.0166 Evaluate side-chains 109 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 0.930 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.6671 time to fit residues: 4.3074 ------------------------------------------------------------------------------- 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: 1.9990 chunk 19 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 9 optimal weight: 0.0020 chunk 78 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 96 optimal weight: 40.0000 chunk 87 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN A 856 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 8767 Z= 0.179 Angle : 0.607 10.542 12066 Z= 0.285 Chirality : 0.040 0.200 1441 Planarity : 0.004 0.040 1340 Dihedral : 11.503 140.321 1373 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer Outliers : 2.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.95 (0.28), residues: 921 helix: 1.98 (0.22), residues: 571 sheet: 0.49 (0.88), residues: 31 loop : 0.21 (0.37), residues: 319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 17 residues processed: 104 average time/residue: 1.0729 time to fit residues: 120.4661 Evaluate side-chains 103 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 0.888 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 0.4738 time to fit residues: 2.8356 ------------------------------------------------------------------------------- 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: 30.0000 chunk 56 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 73 optimal weight: 0.4980 chunk 28 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 98 optimal weight: 50.0000 chunk 60 optimal weight: 0.9990 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 856 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 8767 Z= 0.163 Angle : 0.595 11.419 12066 Z= 0.275 Chirality : 0.040 0.304 1441 Planarity : 0.004 0.039 1340 Dihedral : 11.331 138.824 1373 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 2.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 (0.28), residues: 921 helix: 2.04 (0.22), residues: 571 sheet: 0.41 (0.88), residues: 31 loop : 0.24 (0.37), residues: 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 17 residues processed: 108 average time/residue: 1.1169 time to fit residues: 130.3877 Evaluate side-chains 108 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.993 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 0.4832 time to fit residues: 2.9698 ------------------------------------------------------------------------------- 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: 4.9990 chunk 68 optimal weight: 4.9990 chunk 103 optimal weight: 50.0000 chunk 95 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 87 optimal weight: 0.2980 chunk 25 optimal weight: 0.0770 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN A 856 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 8767 Z= 0.172 Angle : 0.631 12.679 12066 Z= 0.293 Chirality : 0.044 0.648 1441 Planarity : 0.004 0.039 1340 Dihedral : 11.361 138.418 1373 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 2.01 (0.28), residues: 921 helix: 2.02 (0.22), residues: 571 sheet: 0.42 (0.89), residues: 31 loop : 0.26 (0.37), residues: 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 15 residues processed: 107 average time/residue: 1.0946 time to fit residues: 126.5008 Evaluate side-chains 107 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.926 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 0.1288 time to fit residues: 1.4469 ------------------------------------------------------------------------------- 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: 0.8980 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 34 optimal weight: 0.1980 chunk 84 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 4 optimal weight: 0.0570 chunk 59 optimal weight: 4.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.183002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.137491 restraints weight = 18160.830| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.06 r_work: 0.3397 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 8767 Z= 0.147 Angle : 0.583 12.873 12066 Z= 0.269 Chirality : 0.041 0.533 1441 Planarity : 0.004 0.039 1340 Dihedral : 11.164 138.316 1373 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer Outliers : 2.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.29), residues: 921 helix: 2.12 (0.22), residues: 570 sheet: 0.47 (0.89), residues: 31 loop : 0.31 (0.37), residues: 320 =============================================================================== Job complete usr+sys time: 3081.22 seconds wall clock time: 55 minutes 29.29 seconds (3329.29 seconds total)