Starting phenix.real_space_refine on Mon Mar 11 15:16:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rph_24614/03_2024/7rph_24614.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rph_24614/03_2024/7rph_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_24614/03_2024/7rph_24614.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rph_24614/03_2024/7rph_24614.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rph_24614/03_2024/7rph_24614.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rph_24614/03_2024/7rph_24614.pdb" } resolution = 2.5 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= 0.006 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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 dihedrals: 15 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 dihedrals: 15 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: 9.30, per 1000 atoms: 1.08 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: 3.53 Conformation dependent library (CDL) restraints added in 2.7 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: 1.02 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: 2.50 Time building geometry restraints manager: 3.77 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: 6352 27.95 - 55.91: 258 55.91 - 83.86: 25 83.86 - 111.82: 15 111.82 - 139.77: 9 Dihedral angle restraints: 6659 sinusoidal: 3931 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 6656 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: 1.970 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: 7.280 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 32.170 Find NCS groups from input model: 0.240 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:13.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.730 ------------------------------------------------------------------------------- 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 : 15.182 139.770 4869 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 % Allowed : 3.56 % Favored : 95.82 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.134 0.021 TRP A 313 HIS 0.019 0.004 HIS A 777 PHE 0.065 0.012 PHE A 929 TYR 0.110 0.020 TYR A 762 ARG 0.008 0.001 ARG A 833 *********************** 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 : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.6381 (mtm) cc_final: 0.5288 (mmp) REVERT: A 198 LEU cc_start: 0.7679 (mt) cc_final: 0.7339 (mt) REVERT: A 256 TYR cc_start: 0.6588 (t80) cc_final: 0.6197 (t80) REVERT: A 364 SER cc_start: 0.7742 (m) cc_final: 0.7072 (t) REVERT: A 449 LYS cc_start: 0.7677 (tttt) cc_final: 0.7436 (tttm) REVERT: A 478 ASP cc_start: 0.7320 (t0) cc_final: 0.7104 (t70) REVERT: A 524 MET cc_start: 0.6868 (tpt) cc_final: 0.6467 (tpt) REVERT: A 754 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.6093 (ptt90) REVERT: A 774 ARG cc_start: 0.6698 (mtp85) cc_final: 0.6093 (mtt-85) REVERT: A 840 GLN cc_start: 0.7642 (mt0) cc_final: 0.6944 (mp10) REVERT: A 846 PHE cc_start: 0.7302 (m-80) cc_final: 0.6841 (m-10) REVERT: A 852 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6715 (mt-10) REVERT: A 858 MET cc_start: 0.8132 (mmm) cc_final: 0.7691 (mmt) REVERT: A 936 GLU cc_start: 0.7275 (tp30) cc_final: 0.6898 (mp0) REVERT: A 968 ASN cc_start: 0.7907 (m-40) cc_final: 0.7029 (t0) REVERT: A 1095 MET cc_start: 0.8652 (mmm) cc_final: 0.8357 (mmp) outliers start: 4 outliers final: 0 residues processed: 148 average time/residue: 1.1750 time to fit residues: 185.4528 Evaluate side-chains 111 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 754 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7244 moved from start: 0.2071 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= 0.180 Angle : 0.692 9.132 12066 Z= 0.324 Chirality : 0.045 0.345 1441 Planarity : 0.004 0.041 1340 Dihedral : 12.191 169.276 3202 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.60 % Allowed : 7.62 % Favored : 90.79 % 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: 1.53 (0.28), residues: 921 helix: 1.38 (0.21), residues: 578 sheet: 0.07 (0.92), residues: 31 loop : 0.65 (0.39), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 313 HIS 0.004 0.001 HIS A 428 PHE 0.013 0.001 PHE A 608 TYR 0.017 0.002 TYR A 467 ARG 0.002 0.000 ARG A 415 *********************** 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 145 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 133 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.6198 (mtm) cc_final: 0.5107 (mmp) REVERT: A 198 LEU cc_start: 0.7533 (mt) cc_final: 0.7292 (mt) REVERT: A 259 GLU cc_start: 0.6635 (OUTLIER) cc_final: 0.6060 (tm-30) REVERT: A 478 ASP cc_start: 0.7324 (t0) cc_final: 0.6977 (t70) REVERT: A 515 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6499 (tp) REVERT: A 593 SER cc_start: 0.7439 (p) cc_final: 0.7190 (t) REVERT: A 754 ARG cc_start: 0.7459 (ptp-110) cc_final: 0.6024 (ptt90) REVERT: A 768 LYS cc_start: 0.6988 (mtmt) cc_final: 0.6444 (mttt) REVERT: A 774 ARG cc_start: 0.6694 (mtp85) cc_final: 0.6123 (mtt-85) REVERT: A 840 GLN cc_start: 0.7386 (mt0) cc_final: 0.6653 (mp10) REVERT: A 846 PHE cc_start: 0.7241 (m-80) cc_final: 0.7000 (m-80) REVERT: A 848 SER cc_start: 0.8593 (p) cc_final: 0.8349 (t) REVERT: A 882 GLU cc_start: 0.5983 (pm20) cc_final: 0.5496 (mp0) REVERT: A 924 GLU cc_start: 0.7585 (tt0) cc_final: 0.7260 (tt0) REVERT: A 936 GLU cc_start: 0.6982 (tp30) cc_final: 0.6695 (mp0) REVERT: A 937 LYS cc_start: 0.7223 (ttpt) cc_final: 0.6838 (tptp) REVERT: A 968 ASN cc_start: 0.7873 (m-40) cc_final: 0.7094 (t0) REVERT: A 1077 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7588 (mmm) outliers start: 12 outliers final: 5 residues processed: 139 average time/residue: 1.0954 time to fit residues: 163.3104 Evaluate side-chains 108 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1077 MET 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: 0.0670 chunk 78 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 102 optimal weight: 50.0000 chunk 84 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8767 Z= 0.232 Angle : 0.678 7.810 12066 Z= 0.323 Chirality : 0.045 0.234 1441 Planarity : 0.004 0.037 1340 Dihedral : 11.649 172.978 3198 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.07 % Allowed : 8.85 % Favored : 88.08 % 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: 1.71 (0.28), residues: 921 helix: 1.62 (0.21), residues: 578 sheet: 0.13 (0.88), residues: 31 loop : 0.47 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 650 HIS 0.004 0.001 HIS A 428 PHE 0.017 0.002 PHE A 608 TYR 0.020 0.002 TYR A 762 ARG 0.002 0.001 ARG A1130 *********************** 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 126 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 102 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.6187 (mtm) cc_final: 0.5119 (mmp) REVERT: A 198 LEU cc_start: 0.7556 (mt) cc_final: 0.7348 (mt) REVERT: A 259 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6448 (tt0) REVERT: A 472 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.6838 (tm-30) REVERT: A 478 ASP cc_start: 0.7295 (t0) cc_final: 0.6985 (t0) REVERT: A 515 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.6671 (tp) REVERT: A 552 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6837 (mp0) REVERT: A 593 SER cc_start: 0.7466 (p) cc_final: 0.7239 (t) REVERT: A 768 LYS cc_start: 0.6976 (mtmt) cc_final: 0.6357 (mttt) REVERT: A 774 ARG cc_start: 0.6652 (mtp85) cc_final: 0.5898 (mtt-85) REVERT: A 840 GLN cc_start: 0.7440 (mt0) cc_final: 0.6643 (mp10) REVERT: A 882 GLU cc_start: 0.6157 (pm20) cc_final: 0.5683 (mp0) REVERT: A 936 GLU cc_start: 0.7086 (tp30) cc_final: 0.6787 (mp0) REVERT: A 937 LYS cc_start: 0.7228 (ttpt) cc_final: 0.6793 (tptp) REVERT: A 954 SER cc_start: 0.7756 (OUTLIER) cc_final: 0.7550 (t) REVERT: A 1077 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7586 (mmm) outliers start: 24 outliers final: 10 residues processed: 117 average time/residue: 1.1935 time to fit residues: 149.6402 Evaluate side-chains 109 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1077 MET 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: 3.9990 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 100 optimal weight: 50.0000 chunk 89 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8767 Z= 0.293 Angle : 0.699 7.473 12066 Z= 0.333 Chirality : 0.046 0.233 1441 Planarity : 0.004 0.038 1340 Dihedral : 11.833 172.206 3198 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.69 % Allowed : 8.97 % Favored : 87.35 % 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: 1.46 (0.28), residues: 921 helix: 1.49 (0.21), residues: 575 sheet: 0.16 (0.88), residues: 31 loop : 0.23 (0.37), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 789 HIS 0.004 0.001 HIS A 332 PHE 0.017 0.002 PHE A 608 TYR 0.022 0.002 TYR A 762 ARG 0.003 0.001 ARG A 761 *********************** 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 120 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 91 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.6138 (mtm) cc_final: 0.5069 (mmp) REVERT: A 259 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.6311 (tt0) REVERT: A 421 ASN cc_start: 0.8217 (OUTLIER) cc_final: 0.7909 (m-40) REVERT: A 472 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.6882 (tm-30) REVERT: A 478 ASP cc_start: 0.7307 (t0) cc_final: 0.6932 (t70) REVERT: A 552 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6822 (mp0) REVERT: A 774 ARG cc_start: 0.6661 (mtp85) cc_final: 0.6396 (mtp180) REVERT: A 840 GLN cc_start: 0.7465 (mt0) cc_final: 0.6654 (mp10) REVERT: A 882 GLU cc_start: 0.6270 (pm20) cc_final: 0.5772 (mp0) REVERT: A 924 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7358 (tt0) REVERT: A 936 GLU cc_start: 0.7060 (tp30) cc_final: 0.6799 (mp0) REVERT: A 937 LYS cc_start: 0.7242 (ttpt) cc_final: 0.6811 (tptp) REVERT: A 1077 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7595 (mmm) outliers start: 29 outliers final: 10 residues processed: 110 average time/residue: 1.1038 time to fit residues: 130.4986 Evaluate side-chains 103 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 87 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1077 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.0970 chunk 1 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8767 Z= 0.151 Angle : 0.578 6.978 12066 Z= 0.271 Chirality : 0.041 0.216 1441 Planarity : 0.004 0.039 1340 Dihedral : 11.224 172.671 3198 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.69 % Allowed : 9.83 % Favored : 86.49 % 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: 1.89 (0.28), residues: 921 helix: 1.88 (0.22), residues: 571 sheet: 0.55 (0.92), residues: 31 loop : 0.28 (0.37), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 650 HIS 0.002 0.001 HIS A 428 PHE 0.010 0.001 PHE A 454 TYR 0.016 0.001 TYR A 256 ARG 0.002 0.000 ARG A 372 *********************** 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 122 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 93 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.6086 (mtm) cc_final: 0.4973 (mmp) REVERT: A 478 ASP cc_start: 0.7167 (t0) cc_final: 0.6925 (t0) REVERT: A 515 LEU cc_start: 0.7181 (mm) cc_final: 0.6526 (tp) REVERT: A 552 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.6949 (mp0) REVERT: A 774 ARG cc_start: 0.6609 (mtp85) cc_final: 0.6301 (mtp85) REVERT: A 840 GLN cc_start: 0.7348 (mt0) cc_final: 0.6512 (mp10) REVERT: A 882 GLU cc_start: 0.6366 (pm20) cc_final: 0.5840 (mp0) REVERT: A 924 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7227 (tt0) REVERT: A 936 GLU cc_start: 0.7038 (tp30) cc_final: 0.6771 (mp0) REVERT: A 937 LYS cc_start: 0.7222 (ttpt) cc_final: 0.6806 (tptp) REVERT: A 954 SER cc_start: 0.7624 (OUTLIER) cc_final: 0.7406 (t) REVERT: A 1077 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7480 (mmm) outliers start: 29 outliers final: 10 residues processed: 114 average time/residue: 1.1597 time to fit residues: 141.5381 Evaluate side-chains 107 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1077 MET 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: 2.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 100 optimal weight: 50.0000 chunk 83 optimal weight: 0.6980 chunk 46 optimal weight: 0.0670 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 97 optimal weight: 50.0000 overall best weight: 0.9322 ------------------------------------------------------------------------------- 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: 0.7288 moved from start: 0.2981 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= 0.177 Angle : 0.588 6.637 12066 Z= 0.278 Chirality : 0.041 0.212 1441 Planarity : 0.004 0.039 1340 Dihedral : 11.210 173.685 3198 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.19 % Allowed : 10.07 % Favored : 86.73 % 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: 1.90 (0.22), residues: 571 sheet: 0.46 (0.89), residues: 31 loop : 0.30 (0.37), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 650 HIS 0.003 0.001 HIS A 332 PHE 0.013 0.001 PHE A 608 TYR 0.016 0.002 TYR A 545 ARG 0.008 0.000 ARG A 382 *********************** 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 121 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.6019 (mtm) cc_final: 0.4970 (mmp) REVERT: A 256 TYR cc_start: 0.6503 (t80) cc_final: 0.6274 (t80) REVERT: A 421 ASN cc_start: 0.8021 (OUTLIER) cc_final: 0.7751 (m-40) REVERT: A 478 ASP cc_start: 0.7011 (t0) cc_final: 0.6790 (t0) REVERT: A 515 LEU cc_start: 0.7177 (mm) cc_final: 0.6534 (tp) REVERT: A 552 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6867 (mp0) REVERT: A 774 ARG cc_start: 0.6593 (mtp85) cc_final: 0.6391 (mtp-110) REVERT: A 840 GLN cc_start: 0.7408 (mt0) cc_final: 0.6593 (mp10) REVERT: A 882 GLU cc_start: 0.6428 (pm20) cc_final: 0.5890 (mp0) REVERT: A 924 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7281 (tt0) REVERT: A 936 GLU cc_start: 0.7006 (tp30) cc_final: 0.6722 (mp0) REVERT: A 937 LYS cc_start: 0.7237 (ttpt) cc_final: 0.6829 (tptp) REVERT: A 954 SER cc_start: 0.7638 (OUTLIER) cc_final: 0.7420 (t) REVERT: A 1077 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7514 (mmm) outliers start: 25 outliers final: 10 residues processed: 112 average time/residue: 1.1522 time to fit residues: 138.3765 Evaluate side-chains 108 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1077 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 100 optimal weight: 50.0000 chunk 62 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 46 optimal weight: 0.0970 chunk 40 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 GLN A 968 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8767 Z= 0.155 Angle : 0.571 11.281 12066 Z= 0.266 Chirality : 0.040 0.211 1441 Planarity : 0.004 0.040 1340 Dihedral : 11.003 173.053 3198 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.70 % Allowed : 10.69 % Favored : 86.61 % 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: 2.04 (0.28), residues: 921 helix: 1.98 (0.22), residues: 575 sheet: 0.57 (0.91), residues: 31 loop : 0.37 (0.37), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 650 HIS 0.002 0.001 HIS A 428 PHE 0.010 0.001 PHE A 608 TYR 0.016 0.001 TYR A 467 ARG 0.007 0.000 ARG A 382 *********************** 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 116 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.5960 (mtm) cc_final: 0.4915 (mmp) REVERT: A 421 ASN cc_start: 0.7989 (OUTLIER) cc_final: 0.7678 (m-40) REVERT: A 515 LEU cc_start: 0.7141 (mm) cc_final: 0.6552 (tp) REVERT: A 552 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6908 (mp0) REVERT: A 840 GLN cc_start: 0.7373 (mt0) cc_final: 0.6537 (mp10) REVERT: A 846 PHE cc_start: 0.7057 (m-80) cc_final: 0.6805 (m-10) REVERT: A 882 GLU cc_start: 0.6441 (pm20) cc_final: 0.5899 (mp0) REVERT: A 924 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7191 (tt0) REVERT: A 936 GLU cc_start: 0.6995 (tp30) cc_final: 0.6733 (mp0) REVERT: A 937 LYS cc_start: 0.7232 (ttpt) cc_final: 0.6826 (tptp) REVERT: A 954 SER cc_start: 0.7624 (OUTLIER) cc_final: 0.7412 (t) REVERT: A 1077 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7507 (mmm) outliers start: 21 outliers final: 9 residues processed: 109 average time/residue: 1.1816 time to fit residues: 137.6869 Evaluate side-chains 105 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1077 MET Chi-restraints excluded: chain A residue 1114 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 96 optimal weight: 30.0000 chunk 87 optimal weight: 0.6980 chunk 93 optimal weight: 9.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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: 0.7313 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8767 Z= 0.240 Angle : 0.634 8.620 12066 Z= 0.302 Chirality : 0.043 0.230 1441 Planarity : 0.004 0.039 1340 Dihedral : 11.263 171.681 3198 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.58 % Allowed : 11.18 % Favored : 86.24 % 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: 1.79 (0.28), residues: 921 helix: 1.83 (0.22), residues: 570 sheet: 0.35 (0.89), residues: 31 loop : 0.19 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 650 HIS 0.004 0.001 HIS A 332 PHE 0.015 0.002 PHE A 608 TYR 0.018 0.002 TYR A 545 ARG 0.006 0.001 ARG A 382 *********************** 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 113 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.5998 (mtm) cc_final: 0.4988 (mmp) REVERT: A 421 ASN cc_start: 0.8054 (OUTLIER) cc_final: 0.7680 (m-40) REVERT: A 515 LEU cc_start: 0.7258 (mm) cc_final: 0.6602 (tp) REVERT: A 552 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6864 (mp0) REVERT: A 840 GLN cc_start: 0.7468 (mt0) cc_final: 0.6660 (mp10) REVERT: A 846 PHE cc_start: 0.7171 (m-80) cc_final: 0.6948 (m-10) REVERT: A 882 GLU cc_start: 0.6499 (pm20) cc_final: 0.5919 (mp0) REVERT: A 924 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7245 (tt0) REVERT: A 936 GLU cc_start: 0.6978 (tp30) cc_final: 0.6697 (mp0) REVERT: A 937 LYS cc_start: 0.7251 (ttpt) cc_final: 0.6812 (tptp) REVERT: A 954 SER cc_start: 0.7641 (OUTLIER) cc_final: 0.7411 (t) REVERT: A 1077 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7557 (mmm) outliers start: 20 outliers final: 11 residues processed: 104 average time/residue: 1.1919 time to fit residues: 133.1939 Evaluate side-chains 106 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1077 MET Chi-restraints excluded: chain A residue 1114 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 40.0000 chunk 56 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 98 optimal weight: 50.0000 chunk 60 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 GLN A 968 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8767 Z= 0.174 Angle : 0.585 9.980 12066 Z= 0.275 Chirality : 0.041 0.213 1441 Planarity : 0.004 0.039 1340 Dihedral : 10.896 170.885 3198 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.70 % Allowed : 11.18 % Favored : 86.12 % 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: 1.87 (0.28), residues: 921 helix: 1.93 (0.22), residues: 571 sheet: 0.50 (0.90), residues: 31 loop : 0.15 (0.37), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 650 HIS 0.003 0.001 HIS A 332 PHE 0.012 0.001 PHE A 608 TYR 0.016 0.002 TYR A 256 ARG 0.006 0.000 ARG A 382 *********************** 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 109 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.5975 (mtm) cc_final: 0.4954 (mmp) REVERT: A 421 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7696 (m-40) REVERT: A 472 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.6768 (tm-30) REVERT: A 515 LEU cc_start: 0.7175 (mm) cc_final: 0.6531 (tp) REVERT: A 552 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.6881 (mp0) REVERT: A 774 ARG cc_start: 0.6704 (mtp85) cc_final: 0.6178 (mtp85) REVERT: A 840 GLN cc_start: 0.7405 (mt0) cc_final: 0.6578 (mp10) REVERT: A 846 PHE cc_start: 0.7131 (m-80) cc_final: 0.6915 (m-10) REVERT: A 882 GLU cc_start: 0.6415 (pm20) cc_final: 0.5866 (mp0) REVERT: A 924 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7220 (tt0) REVERT: A 936 GLU cc_start: 0.6997 (tp30) cc_final: 0.6730 (mp0) REVERT: A 937 LYS cc_start: 0.7238 (ttpt) cc_final: 0.6835 (tptp) REVERT: A 954 SER cc_start: 0.7685 (OUTLIER) cc_final: 0.7458 (t) REVERT: A 1077 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.7516 (mmm) outliers start: 21 outliers final: 11 residues processed: 101 average time/residue: 1.2599 time to fit residues: 135.8615 Evaluate side-chains 105 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1077 MET Chi-restraints excluded: chain A residue 1114 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 103 optimal weight: 50.0000 chunk 95 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 65 optimal weight: 0.0370 chunk 87 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- 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: 0.7299 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8767 Z= 0.204 Angle : 0.622 12.037 12066 Z= 0.292 Chirality : 0.041 0.214 1441 Planarity : 0.004 0.039 1340 Dihedral : 10.951 170.155 3198 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.58 % Allowed : 11.43 % Favored : 86.00 % 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: 1.78 (0.28), residues: 921 helix: 1.87 (0.22), residues: 571 sheet: 0.29 (0.88), residues: 31 loop : 0.11 (0.37), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 857 HIS 0.003 0.001 HIS A 332 PHE 0.014 0.001 PHE A 608 TYR 0.017 0.002 TYR A 545 ARG 0.006 0.000 ARG A 382 ********************** 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 107 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 87 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.5972 (mtm) cc_final: 0.4976 (mmp) REVERT: A 421 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7695 (m-40) REVERT: A 472 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.6769 (tm-30) REVERT: A 515 LEU cc_start: 0.7204 (mm) cc_final: 0.6552 (tp) REVERT: A 552 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: A 774 ARG cc_start: 0.6720 (mtp85) cc_final: 0.6191 (mtp85) REVERT: A 840 GLN cc_start: 0.7462 (mt0) cc_final: 0.6648 (mp10) REVERT: A 846 PHE cc_start: 0.7184 (m-80) cc_final: 0.6971 (m-10) REVERT: A 882 GLU cc_start: 0.6413 (pm20) cc_final: 0.5867 (mp0) REVERT: A 924 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7291 (tt0) REVERT: A 936 GLU cc_start: 0.6981 (tp30) cc_final: 0.6689 (mp0) REVERT: A 937 LYS cc_start: 0.7245 (ttpt) cc_final: 0.6840 (tptp) REVERT: A 954 SER cc_start: 0.7688 (OUTLIER) cc_final: 0.7458 (t) REVERT: A 1077 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7570 (mmm) outliers start: 20 outliers final: 11 residues processed: 99 average time/residue: 1.1736 time to fit residues: 124.2066 Evaluate side-chains 103 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 915 ASN Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain A residue 954 SER Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1077 MET Chi-restraints excluded: chain A residue 1114 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 0.0370 chunk 72 optimal weight: 0.0980 chunk 4 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.183941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.137709 restraints weight = 17128.577| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.12 r_work: 0.3402 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3379 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 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 = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8767 Z= 0.137 Angle : 0.570 12.652 12066 Z= 0.264 Chirality : 0.039 0.209 1441 Planarity : 0.004 0.039 1340 Dihedral : 10.624 169.827 3198 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.21 % Allowed : 11.92 % Favored : 85.87 % 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: 2.00 (0.28), residues: 921 helix: 2.04 (0.22), residues: 572 sheet: 0.43 (0.90), residues: 31 loop : 0.18 (0.37), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 650 HIS 0.002 0.000 HIS A 428 PHE 0.007 0.001 PHE A 454 TYR 0.017 0.001 TYR A 256 ARG 0.006 0.000 ARG A 382 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3192.23 seconds wall clock time: 57 minutes 32.36 seconds (3452.36 seconds total)