Starting phenix.real_space_refine on Fri Mar 15 00:31:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x21_32954/03_2024/7x21_32954_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x21_32954/03_2024/7x21_32954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x21_32954/03_2024/7x21_32954.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x21_32954/03_2024/7x21_32954.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x21_32954/03_2024/7x21_32954_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x21_32954/03_2024/7x21_32954_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 9 Type Number sf(0) Gaussians K 2 8.98 5 Al 1 5.89 5 P 3 5.49 5 Mg 1 5.21 5 S 49 5.16 5 C 6558 2.51 5 N 1651 2.21 5 O 1898 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 63": "OE1" <-> "OE2" Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 201": "OD1" <-> "OD2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A GLU 242": "OE1" <-> "OE2" Residue "A TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 377": "OE1" <-> "OE2" Residue "A PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 562": "OE1" <-> "OE2" Residue "A GLU 692": "OE1" <-> "OE2" Residue "A PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 775": "OE1" <-> "OE2" Residue "A GLU 798": "OE1" <-> "OE2" Residue "A PHE 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 125": "OD1" <-> "OD2" Residue "B ASP 221": "OD1" <-> "OD2" Residue "B PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10167 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7662 Classifications: {'peptide': 986} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 35, 'TRANS': 950} Chain: "B" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2255 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 257} Chain: "A" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 118 Unusual residues: {' K': 2, ' MG': 1, 'ALF': 1, 'CLR': 2, 'PCW': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 114 Unusual residues: {'NAG': 1, 'PCW': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Time building chain proxies: 6.00, per 1000 atoms: 0.59 Number of scatterers: 10167 At special positions: 0 Unit cell: (122.84, 97.11, 173.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) K 2 19.00 S 49 16.00 P 3 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1898 8.00 N 1651 7.00 C 6558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 277 " distance=2.03 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 B 401 " - " ASN B 158 " Time building additional restraints: 4.24 Conformation dependent library (CDL) restraints added in 1.6 seconds 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2350 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 10 sheets defined 43.0% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 61 through 68 Processing helix chain 'A' and resid 78 through 88 removed outlier: 3.816A pdb=" N GLU A 83 " --> pdb=" O VAL A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 110 removed outlier: 3.685A pdb=" N GLN A 108 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N MET A 109 " --> pdb=" O PHE A 105 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 133 Processing helix chain 'A' and resid 140 through 162 Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 228 through 231 No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 278 through 288 Processing helix chain 'A' and resid 295 through 324 Processing helix chain 'A' and resid 329 through 343 Processing helix chain 'A' and resid 348 through 366 removed outlier: 3.803A pdb=" N LYS A 366 " --> pdb=" O ARG A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 378 Processing helix chain 'A' and resid 431 through 439 Processing helix chain 'A' and resid 463 through 475 Processing helix chain 'A' and resid 479 through 485 Processing helix chain 'A' and resid 523 through 529 removed outlier: 3.530A pdb=" N LYS A 529 " --> pdb=" O ARG A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 560 removed outlier: 3.781A pdb=" N LEU A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 620 Processing helix chain 'A' and resid 633 through 643 Processing helix chain 'A' and resid 653 through 659 Processing helix chain 'A' and resid 679 through 683 Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 707 through 720 removed outlier: 3.589A pdb=" N LEU A 711 " --> pdb=" O PRO A 707 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN A 720 " --> pdb=" O GLY A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 739 Proline residue: A 735 - end of helix Processing helix chain 'A' and resid 752 through 757 Processing helix chain 'A' and resid 768 through 808 removed outlier: 3.652A pdb=" N ALA A 794 " --> pdb=" O TYR A 790 " (cutoff:3.500A) Proline residue: A 801 - end of helix Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.686A pdb=" N LEU A 820 " --> pdb=" O THR A 816 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 821 " --> pdb=" O ILE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 836 Proline residue: A 830 - end of helix removed outlier: 3.817A pdb=" N ALA A 835 " --> pdb=" O SER A 831 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR A 836 " --> pdb=" O ILE A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 867 Processing helix chain 'A' and resid 869 through 888 removed outlier: 3.830A pdb=" N GLN A 888 " --> pdb=" O VAL A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 895 Processing helix chain 'A' and resid 899 through 902 No H-bonds generated for 'chain 'A' and resid 899 through 902' Processing helix chain 'A' and resid 920 through 950 Processing helix chain 'A' and resid 956 through 959 No H-bonds generated for 'chain 'A' and resid 956 through 959' Processing helix chain 'A' and resid 965 through 983 Processing helix chain 'A' and resid 998 through 1001 Processing helix chain 'A' and resid 1005 through 1024 Processing helix chain 'A' and resid 1030 through 1033 No H-bonds generated for 'chain 'A' and resid 1030 through 1033' Processing helix chain 'B' and resid 29 through 58 removed outlier: 3.596A pdb=" N TYR B 39 " --> pdb=" O ILE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 112 removed outlier: 4.601A pdb=" N ALA B 100 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N TYR B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LYS B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TYR B 112 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 153 through 156 Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 219 through 222 No H-bonds generated for 'chain 'B' and resid 219 through 222' Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing sheet with id= A, first strand: chain 'A' and resid 188 through 193 removed outlier: 11.892A pdb=" N GLN A 180 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N LYS A 206 " --> pdb=" O GLN A 180 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU A 182 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL A 202 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 237 through 239 removed outlier: 4.093A pdb=" N CYS A 223 " --> pdb=" O ARG A 239 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU A 263 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASP A 226 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N CYS A 261 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 368 through 370 removed outlier: 3.799A pdb=" N ILE A 742 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE A 384 " --> pdb=" O ALA A 725 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N THR A 727 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N CYS A 386 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS A 624 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N SER A 387 " --> pdb=" O LYS A 624 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE A 626 " --> pdb=" O SER A 387 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 408 through 411 removed outlier: 6.688A pdb=" N SER A 602 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU A 403 " --> pdb=" O LEU A 600 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU A 600 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N PHE A 405 " --> pdb=" O VAL A 598 " (cutoff:3.500A) removed outlier: 9.475A pdb=" N VAL A 598 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N PHE A 567 " --> pdb=" O VAL A 598 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU A 600 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU A 565 " --> pdb=" O LEU A 600 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER A 602 " --> pdb=" O ARG A 563 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ARG A 563 " --> pdb=" O SER A 602 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 538 through 541 removed outlier: 7.309A pdb=" N PHE A 595 " --> pdb=" O SER A 531 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ILE A 533 " --> pdb=" O PHE A 595 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N PHE A 597 " --> pdb=" O ILE A 533 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ILE A 535 " --> pdb=" O PHE A 597 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 674 through 678 removed outlier: 6.786A pdb=" N GLU A 699 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N VAL A 677 " --> pdb=" O GLU A 699 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL A 701 " --> pdb=" O VAL A 677 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 214 through 217 removed outlier: 3.567A pdb=" N ASP A 214 " --> pdb=" O ASN A 272 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ARG A 216 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N VAL A 270 " --> pdb=" O ARG A 216 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 77 through 79 Processing sheet with id= I, first strand: chain 'B' and resid 87 through 91 removed outlier: 6.475A pdb=" N LYS B 299 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N PHE B 90 " --> pdb=" O LYS B 299 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU B 301 " --> pdb=" O PHE B 90 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 209 through 211 406 hydrogen bonds defined for protein. 1158 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.29 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3164 1.34 - 1.46: 1518 1.46 - 1.58: 5579 1.58 - 1.70: 6 1.70 - 1.82: 82 Bond restraints: 10349 Sorted by residual: bond pdb=" C11 PCW B 403 " pdb=" O3 PCW B 403 " ideal model delta sigma weight residual 1.326 1.454 -0.128 2.00e-02 2.50e+03 4.11e+01 bond pdb=" C11 PCW B 402 " pdb=" O3 PCW B 402 " ideal model delta sigma weight residual 1.326 1.454 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C11 PCW A1106 " pdb=" O3 PCW A1106 " ideal model delta sigma weight residual 1.326 1.453 -0.127 2.00e-02 2.50e+03 4.06e+01 bond pdb=" C31 PCW B 403 " pdb=" O2 PCW B 403 " ideal model delta sigma weight residual 1.333 1.459 -0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C31 PCW B 402 " pdb=" O2 PCW B 402 " ideal model delta sigma weight residual 1.333 1.452 -0.119 2.00e-02 2.50e+03 3.55e+01 ... (remaining 10344 not shown) Histogram of bond angle deviations from ideal: 89.63 - 107.56: 360 107.56 - 125.49: 13519 125.49 - 143.43: 132 143.43 - 161.36: 0 161.36 - 179.29: 2 Bond angle restraints: 14013 Sorted by residual: angle pdb=" F1 ALF A1103 " pdb="AL ALF A1103 " pdb=" F2 ALF A1103 " ideal model delta sigma weight residual 108.68 179.29 -70.61 3.00e+00 1.11e-01 5.54e+02 angle pdb=" F3 ALF A1103 " pdb="AL ALF A1103 " pdb=" F4 ALF A1103 " ideal model delta sigma weight residual 109.63 179.11 -69.48 3.00e+00 1.11e-01 5.36e+02 angle pdb=" F2 ALF A1103 " pdb="AL ALF A1103 " pdb=" F4 ALF A1103 " ideal model delta sigma weight residual 110.21 89.63 20.58 3.00e+00 1.11e-01 4.71e+01 angle pdb=" F1 ALF A1103 " pdb="AL ALF A1103 " pdb=" F3 ALF A1103 " ideal model delta sigma weight residual 109.69 90.12 19.57 3.00e+00 1.11e-01 4.26e+01 angle pdb=" F2 ALF A1103 " pdb="AL ALF A1103 " pdb=" F3 ALF A1103 " ideal model delta sigma weight residual 109.59 90.09 19.50 3.00e+00 1.11e-01 4.23e+01 ... (remaining 14008 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.98: 6215 32.98 - 65.96: 140 65.96 - 98.94: 22 98.94 - 131.92: 3 131.92 - 164.91: 1 Dihedral angle restraints: 6381 sinusoidal: 2723 harmonic: 3658 Sorted by residual: dihedral pdb=" CB CYS B 159 " pdb=" SG CYS B 159 " pdb=" SG CYS B 175 " pdb=" CB CYS B 175 " ideal model delta sinusoidal sigma weight residual 93.00 139.15 -46.15 1 1.00e+01 1.00e-02 2.95e+01 dihedral pdb=" N PCW B 403 " pdb=" C4 PCW B 403 " pdb=" C5 PCW B 403 " pdb=" O4P PCW B 403 " ideal model delta sinusoidal sigma weight residual -66.66 98.25 -164.91 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" CA PHE B 296 " pdb=" C PHE B 296 " pdb=" N ASP B 297 " pdb=" CA ASP B 297 " ideal model delta harmonic sigma weight residual 180.00 158.30 21.70 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 6378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1386 0.064 - 0.129: 200 0.129 - 0.193: 5 0.193 - 0.257: 3 0.257 - 0.321: 3 Chirality restraints: 1597 Sorted by residual: chirality pdb=" C2 PCW A1106 " pdb=" C1 PCW A1106 " pdb=" C3 PCW A1106 " pdb=" O2 PCW A1106 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" C1 NAG B 401 " pdb=" ND2 ASN B 158 " pdb=" C2 NAG B 401 " pdb=" O5 NAG B 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C2 PCW B 402 " pdb=" C1 PCW B 402 " pdb=" C3 PCW B 402 " pdb=" O2 PCW B 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.60 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 1594 not shown) Planarity restraints: 1761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 401 " -0.277 2.00e-02 2.50e+03 2.32e-01 6.75e+02 pdb=" C7 NAG B 401 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG B 401 " -0.180 2.00e-02 2.50e+03 pdb=" N2 NAG B 401 " 0.395 2.00e-02 2.50e+03 pdb=" O7 NAG B 401 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A1029 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.66e+00 pdb=" C TRP A1029 " 0.041 2.00e-02 2.50e+03 pdb=" O TRP A1029 " -0.015 2.00e-02 2.50e+03 pdb=" N TRP A1030 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 891 " -0.035 5.00e-02 4.00e+02 5.41e-02 4.67e+00 pdb=" N PRO A 892 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 892 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 892 " -0.030 5.00e-02 4.00e+02 ... (remaining 1758 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.58: 74 2.58 - 3.22: 9771 3.22 - 3.86: 20163 3.86 - 4.50: 27812 4.50 - 5.14: 43959 Nonbonded interactions: 101779 Sorted by model distance: nonbonded pdb=" F3 ALF A1103 " pdb="MG MG A1104 " model vdw 1.943 2.120 nonbonded pdb=" OD1 ASP A 729 " pdb="MG MG A1104 " model vdw 2.066 2.170 nonbonded pdb=" O THR A 390 " pdb="MG MG A1104 " model vdw 2.077 2.170 nonbonded pdb=" OD2 ASP A 823 " pdb=" O HOH A1201 " model vdw 2.142 2.440 nonbonded pdb=" OG SER A 955 " pdb=" OE1 GLU A1016 " model vdw 2.171 2.440 ... (remaining 101774 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 3.930 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 30.610 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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 : 0.005 0.128 10349 Z= 0.363 Angle : 1.153 70.615 14013 Z= 0.451 Chirality : 0.046 0.321 1597 Planarity : 0.007 0.232 1760 Dihedral : 14.862 164.905 4022 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.45 (0.23), residues: 1259 helix: 1.48 (0.22), residues: 527 sheet: -0.06 (0.41), residues: 140 loop : -0.67 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 968 HIS 0.002 0.001 HIS A 487 PHE 0.020 0.002 PHE B 236 TYR 0.017 0.002 TYR A 257 ARG 0.009 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.0606 (tmm) cc_final: 0.0140 (mpp) REVERT: A 71 ASN cc_start: 0.6290 (t0) cc_final: 0.5696 (t0) REVERT: A 195 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6393 (mt-10) REVERT: A 366 LYS cc_start: 0.6567 (mtmt) cc_final: 0.6322 (mtpt) REVERT: A 500 PHE cc_start: 0.5418 (p90) cc_final: 0.4792 (p90) REVERT: A 911 GLU cc_start: 0.7372 (tt0) cc_final: 0.7160 (tt0) REVERT: B 36 LEU cc_start: 0.7676 (mt) cc_final: 0.7475 (mt) REVERT: B 63 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7337 (mt-10) REVERT: B 114 ASP cc_start: 0.6179 (m-30) cc_final: 0.5694 (m-30) REVERT: B 203 MET cc_start: 0.3649 (tpt) cc_final: 0.2479 (mpp) REVERT: B 223 ASP cc_start: 0.6622 (m-30) cc_final: 0.6194 (m-30) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 1.2161 time to fit residues: 198.7360 Evaluate side-chains 120 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 97 optimal weight: 0.5980 chunk 37 optimal weight: 0.3980 chunk 59 optimal weight: 0.0470 chunk 72 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 732 ASN ** A 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10349 Z= 0.141 Angle : 0.759 30.243 14013 Z= 0.323 Chirality : 0.041 0.272 1597 Planarity : 0.004 0.046 1760 Dihedral : 10.014 163.411 1640 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.66 % Allowed : 7.73 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.68 (0.23), residues: 1259 helix: 1.76 (0.23), residues: 527 sheet: -0.14 (0.40), residues: 148 loop : -0.59 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 968 HIS 0.002 0.001 HIS A 505 PHE 0.012 0.001 PHE A 335 TYR 0.014 0.001 TYR A 257 ARG 0.003 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 137 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.0667 (tmm) cc_final: 0.0201 (mpp) REVERT: A 71 ASN cc_start: 0.6303 (t0) cc_final: 0.5661 (t0) REVERT: A 150 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7244 (tp) REVERT: A 151 VAL cc_start: 0.8012 (t) cc_final: 0.7798 (t) REVERT: A 182 LEU cc_start: 0.7364 (tp) cc_final: 0.7158 (tp) REVERT: A 195 GLU cc_start: 0.6815 (mt-10) cc_final: 0.6359 (mt-10) REVERT: A 366 LYS cc_start: 0.6394 (mtmt) cc_final: 0.6175 (mtpt) REVERT: A 410 PHE cc_start: 0.6509 (m-80) cc_final: 0.5839 (m-80) REVERT: A 465 GLU cc_start: 0.6160 (mm-30) cc_final: 0.5678 (mm-30) REVERT: A 500 PHE cc_start: 0.5284 (p90) cc_final: 0.4716 (p90) REVERT: A 534 MET cc_start: 0.5902 (tpp) cc_final: 0.5341 (tpp) REVERT: A 601 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6893 (mp) REVERT: A 651 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.5346 (tp30) REVERT: A 911 GLU cc_start: 0.7387 (tt0) cc_final: 0.7178 (tt0) REVERT: B 36 LEU cc_start: 0.7637 (mt) cc_final: 0.7369 (mt) REVERT: B 63 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7313 (mt-10) REVERT: B 114 ASP cc_start: 0.6079 (m-30) cc_final: 0.5606 (m-30) REVERT: B 173 LYS cc_start: 0.7193 (mmtp) cc_final: 0.6697 (mptp) REVERT: B 203 MET cc_start: 0.3883 (tpt) cc_final: 0.2652 (mpp) REVERT: B 223 ASP cc_start: 0.6632 (m-30) cc_final: 0.6178 (m-30) outliers start: 18 outliers final: 3 residues processed: 147 average time/residue: 1.1501 time to fit residues: 182.9461 Evaluate side-chains 137 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 131 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 846 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 91 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 449 GLN ** A 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 10349 Z= 0.342 Angle : 0.854 30.874 14013 Z= 0.380 Chirality : 0.047 0.272 1597 Planarity : 0.005 0.049 1760 Dihedral : 10.926 179.471 1640 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.58 % Allowed : 10.40 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.25 (0.23), residues: 1259 helix: 1.20 (0.22), residues: 525 sheet: -0.16 (0.40), residues: 145 loop : -0.64 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 968 HIS 0.004 0.001 HIS A 487 PHE 0.014 0.002 PHE A1021 TYR 0.024 0.002 TYR A 805 ARG 0.006 0.001 ARG A 846 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 133 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.0551 (tmm) cc_final: -0.0036 (mpp) REVERT: A 71 ASN cc_start: 0.6302 (t0) cc_final: 0.5631 (t0) REVERT: A 150 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7211 (tp) REVERT: A 182 LEU cc_start: 0.7363 (tp) cc_final: 0.7147 (tp) REVERT: A 195 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6480 (mt-10) REVERT: A 273 THR cc_start: 0.7675 (m) cc_final: 0.6999 (t) REVERT: A 465 GLU cc_start: 0.6239 (mm-30) cc_final: 0.5865 (mm-30) REVERT: A 534 MET cc_start: 0.5992 (tpp) cc_final: 0.5391 (tpp) REVERT: A 601 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6994 (mp) REVERT: A 651 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.5540 (tp30) REVERT: A 844 MET cc_start: 0.7776 (mmm) cc_final: 0.7541 (mmm) REVERT: A 911 GLU cc_start: 0.7550 (tt0) cc_final: 0.7310 (tt0) REVERT: B 63 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7360 (mt-10) REVERT: B 114 ASP cc_start: 0.6230 (m-30) cc_final: 0.5758 (m-30) REVERT: B 173 LYS cc_start: 0.7397 (mmtp) cc_final: 0.6857 (mptp) REVERT: B 203 MET cc_start: 0.3697 (tpt) cc_final: 0.2901 (pmm) REVERT: B 206 ASN cc_start: 0.5088 (OUTLIER) cc_final: 0.4841 (p0) REVERT: B 221 ASP cc_start: 0.6058 (m-30) cc_final: 0.5674 (m-30) REVERT: B 223 ASP cc_start: 0.6655 (m-30) cc_final: 0.6147 (m-30) outliers start: 28 outliers final: 14 residues processed: 146 average time/residue: 1.0861 time to fit residues: 172.3726 Evaluate side-chains 142 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 846 ARG Chi-restraints excluded: chain A residue 963 ARG Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 282 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 76 optimal weight: 0.4980 chunk 114 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 108 optimal weight: 0.0170 chunk 32 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 417 ASN ** A 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10349 Z= 0.141 Angle : 0.752 29.807 14013 Z= 0.319 Chirality : 0.041 0.267 1597 Planarity : 0.004 0.046 1760 Dihedral : 10.082 173.000 1640 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.39 % Allowed : 12.14 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.63 (0.23), residues: 1259 helix: 1.66 (0.23), residues: 526 sheet: -0.14 (0.40), residues: 145 loop : -0.55 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 968 HIS 0.002 0.001 HIS A 57 PHE 0.010 0.001 PHE B 236 TYR 0.015 0.001 TYR A1025 ARG 0.002 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 137 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.0239 (tmm) cc_final: -0.0259 (mpp) REVERT: A 71 ASN cc_start: 0.6347 (t0) cc_final: 0.5707 (t0) REVERT: A 107 LYS cc_start: 0.6887 (OUTLIER) cc_final: 0.6504 (mttp) REVERT: A 150 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7223 (tp) REVERT: A 182 LEU cc_start: 0.7403 (tp) cc_final: 0.7140 (tp) REVERT: A 195 GLU cc_start: 0.6802 (mt-10) cc_final: 0.6379 (mt-10) REVERT: A 366 LYS cc_start: 0.6581 (mtmt) cc_final: 0.6321 (mtpt) REVERT: A 500 PHE cc_start: 0.5191 (p90) cc_final: 0.4714 (p90) REVERT: A 502 LEU cc_start: 0.6040 (tp) cc_final: 0.5709 (tm) REVERT: A 534 MET cc_start: 0.5816 (tpp) cc_final: 0.5264 (tpp) REVERT: A 601 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6893 (mp) REVERT: A 603 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7064 (mtm) REVERT: A 651 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.5467 (tp30) REVERT: A 738 LYS cc_start: 0.8048 (mmmt) cc_final: 0.7805 (mmmt) REVERT: A 911 GLU cc_start: 0.7454 (tt0) cc_final: 0.7252 (tt0) REVERT: B 63 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7338 (mt-10) REVERT: B 87 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6764 (mt-10) REVERT: B 114 ASP cc_start: 0.6130 (m-30) cc_final: 0.5681 (m-30) REVERT: B 173 LYS cc_start: 0.7183 (mmtp) cc_final: 0.6805 (mptp) REVERT: B 203 MET cc_start: 0.3687 (tpt) cc_final: 0.2481 (mpp) REVERT: B 206 ASN cc_start: 0.4794 (OUTLIER) cc_final: 0.4430 (m110) REVERT: B 213 GLN cc_start: 0.7230 (mt0) cc_final: 0.6984 (mt0) REVERT: B 223 ASP cc_start: 0.6592 (m-30) cc_final: 0.6101 (m-30) outliers start: 26 outliers final: 5 residues processed: 151 average time/residue: 0.9963 time to fit residues: 164.0312 Evaluate side-chains 145 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 133 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 206 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 4.9990 chunk 1 optimal weight: 0.0870 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 417 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10349 Z= 0.232 Angle : 0.795 30.263 14013 Z= 0.345 Chirality : 0.044 0.268 1597 Planarity : 0.004 0.048 1760 Dihedral : 10.404 165.414 1640 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.30 % Allowed : 12.97 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.50 (0.23), residues: 1259 helix: 1.50 (0.23), residues: 522 sheet: -0.18 (0.40), residues: 145 loop : -0.56 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1029 HIS 0.003 0.001 HIS A 402 PHE 0.011 0.002 PHE A 318 TYR 0.019 0.002 TYR A 805 ARG 0.004 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 135 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.0164 (tmm) cc_final: -0.0293 (mpp) REVERT: A 71 ASN cc_start: 0.6373 (t0) cc_final: 0.5676 (t0) REVERT: A 150 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7171 (tp) REVERT: A 182 LEU cc_start: 0.7382 (tp) cc_final: 0.7146 (tp) REVERT: A 195 GLU cc_start: 0.6792 (mt-10) cc_final: 0.6374 (mt-10) REVERT: A 465 GLU cc_start: 0.6185 (mm-30) cc_final: 0.5707 (mt-10) REVERT: A 502 LEU cc_start: 0.6045 (tp) cc_final: 0.5753 (tm) REVERT: A 534 MET cc_start: 0.5875 (tpp) cc_final: 0.5297 (tpp) REVERT: A 601 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6999 (mp) REVERT: A 603 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7163 (mtt) REVERT: A 651 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.5534 (tp30) REVERT: A 844 MET cc_start: 0.7798 (mmm) cc_final: 0.7556 (mmm) REVERT: A 911 GLU cc_start: 0.7527 (tt0) cc_final: 0.7299 (tt0) REVERT: B 63 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7354 (mt-10) REVERT: B 87 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6756 (mt-10) REVERT: B 114 ASP cc_start: 0.6017 (m-30) cc_final: 0.5588 (m-30) REVERT: B 173 LYS cc_start: 0.7180 (mmtp) cc_final: 0.6786 (mptp) REVERT: B 203 MET cc_start: 0.3638 (tpt) cc_final: 0.2480 (mpp) REVERT: B 206 ASN cc_start: 0.4762 (OUTLIER) cc_final: 0.4377 (m110) REVERT: B 221 ASP cc_start: 0.6180 (m-30) cc_final: 0.5808 (m-30) REVERT: B 223 ASP cc_start: 0.6604 (m-30) cc_final: 0.6101 (m-30) REVERT: B 273 ILE cc_start: 0.7979 (mt) cc_final: 0.7701 (mp) outliers start: 25 outliers final: 10 residues processed: 148 average time/residue: 1.0477 time to fit residues: 168.6825 Evaluate side-chains 140 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 282 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 417 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10349 Z= 0.291 Angle : 0.830 30.514 14013 Z= 0.366 Chirality : 0.045 0.290 1597 Planarity : 0.005 0.050 1760 Dihedral : 10.732 157.030 1640 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.04 % Allowed : 13.62 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.27 (0.23), residues: 1259 helix: 1.24 (0.22), residues: 523 sheet: -0.21 (0.42), residues: 133 loop : -0.63 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 968 HIS 0.003 0.001 HIS A 402 PHE 0.015 0.002 PHE A 335 TYR 0.022 0.002 TYR A 805 ARG 0.005 0.001 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 131 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.0227 (tmm) cc_final: -0.0025 (pmt) REVERT: A 71 ASN cc_start: 0.6363 (t0) cc_final: 0.5660 (t0) REVERT: A 150 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7164 (tp) REVERT: A 182 LEU cc_start: 0.7368 (tp) cc_final: 0.7145 (tp) REVERT: A 195 GLU cc_start: 0.6719 (mt-10) cc_final: 0.6352 (mt-10) REVERT: A 216 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.5484 (tmm160) REVERT: A 273 THR cc_start: 0.7645 (m) cc_final: 0.7013 (t) REVERT: A 465 GLU cc_start: 0.6185 (mm-30) cc_final: 0.5723 (mt-10) REVERT: A 474 VAL cc_start: 0.6969 (OUTLIER) cc_final: 0.6493 (p) REVERT: A 500 PHE cc_start: 0.5257 (p90) cc_final: 0.4908 (p90) REVERT: A 502 LEU cc_start: 0.5946 (tp) cc_final: 0.5604 (tm) REVERT: A 534 MET cc_start: 0.5859 (tpp) cc_final: 0.5271 (tpp) REVERT: A 601 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7028 (mp) REVERT: A 603 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7168 (mtt) REVERT: A 651 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.5617 (tp30) REVERT: A 911 GLU cc_start: 0.7531 (tt0) cc_final: 0.7297 (tt0) REVERT: B 63 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7361 (mt-10) REVERT: B 87 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6838 (mt-10) REVERT: B 114 ASP cc_start: 0.6071 (m-30) cc_final: 0.5650 (m-30) REVERT: B 173 LYS cc_start: 0.7219 (mmtp) cc_final: 0.6784 (mptp) REVERT: B 203 MET cc_start: 0.3757 (tpt) cc_final: 0.2562 (mpp) REVERT: B 206 ASN cc_start: 0.4889 (OUTLIER) cc_final: 0.4482 (m110) REVERT: B 213 GLN cc_start: 0.7329 (mt0) cc_final: 0.7027 (mm-40) REVERT: B 223 ASP cc_start: 0.6577 (m-30) cc_final: 0.6081 (m-30) REVERT: B 273 ILE cc_start: 0.7979 (mt) cc_final: 0.7650 (mp) outliers start: 33 outliers final: 13 residues processed: 151 average time/residue: 1.0090 time to fit residues: 166.5002 Evaluate side-chains 151 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 282 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 67 optimal weight: 0.2980 chunk 120 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 417 ASN B 208 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10349 Z= 0.160 Angle : 0.761 29.895 14013 Z= 0.325 Chirality : 0.042 0.270 1597 Planarity : 0.004 0.047 1760 Dihedral : 10.087 154.095 1640 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.30 % Allowed : 14.35 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.23), residues: 1259 helix: 1.63 (0.23), residues: 524 sheet: -0.07 (0.41), residues: 132 loop : -0.56 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 968 HIS 0.002 0.001 HIS A 57 PHE 0.013 0.001 PHE A 335 TYR 0.014 0.001 TYR A 805 ARG 0.004 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.0185 (tmm) cc_final: -0.0302 (mpp) REVERT: A 71 ASN cc_start: 0.6398 (t0) cc_final: 0.5701 (t0) REVERT: A 107 LYS cc_start: 0.6839 (mptp) cc_final: 0.6524 (mptm) REVERT: A 150 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7124 (tp) REVERT: A 182 LEU cc_start: 0.7376 (tp) cc_final: 0.7135 (tp) REVERT: A 195 GLU cc_start: 0.6680 (mt-10) cc_final: 0.6326 (mt-10) REVERT: A 366 LYS cc_start: 0.6606 (mtpt) cc_final: 0.6081 (ptmt) REVERT: A 465 GLU cc_start: 0.6182 (mm-30) cc_final: 0.5668 (mt-10) REVERT: A 500 PHE cc_start: 0.5192 (p90) cc_final: 0.4848 (p90) REVERT: A 502 LEU cc_start: 0.6033 (tp) cc_final: 0.5679 (tm) REVERT: A 534 MET cc_start: 0.5860 (tpp) cc_final: 0.5336 (tpp) REVERT: A 601 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6909 (mp) REVERT: A 603 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7012 (mtm) REVERT: A 651 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.5506 (tp30) REVERT: A 911 GLU cc_start: 0.7468 (tt0) cc_final: 0.7239 (tt0) REVERT: B 63 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7379 (mt-10) REVERT: B 114 ASP cc_start: 0.6037 (m-30) cc_final: 0.5623 (m-30) REVERT: B 173 LYS cc_start: 0.7097 (mmtp) cc_final: 0.6687 (mptp) REVERT: B 203 MET cc_start: 0.3790 (tpt) cc_final: 0.2590 (mpp) REVERT: B 206 ASN cc_start: 0.4902 (OUTLIER) cc_final: 0.4501 (m110) REVERT: B 213 GLN cc_start: 0.7237 (mt0) cc_final: 0.6943 (mt0) REVERT: B 221 ASP cc_start: 0.6228 (m-30) cc_final: 0.5874 (m-30) REVERT: B 223 ASP cc_start: 0.6631 (m-30) cc_final: 0.6106 (m-30) outliers start: 25 outliers final: 12 residues processed: 143 average time/residue: 1.0071 time to fit residues: 157.4538 Evaluate side-chains 140 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 767 PHE Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 206 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 0.7980 chunk 36 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 109 optimal weight: 0.0980 chunk 115 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN B 208 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10349 Z= 0.149 Angle : 0.754 29.924 14013 Z= 0.320 Chirality : 0.041 0.256 1597 Planarity : 0.004 0.046 1760 Dihedral : 9.761 150.603 1640 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.21 % Allowed : 14.90 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.23), residues: 1259 helix: 1.73 (0.23), residues: 524 sheet: -0.09 (0.40), residues: 135 loop : -0.54 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 968 HIS 0.002 0.001 HIS A 57 PHE 0.013 0.001 PHE A 335 TYR 0.017 0.001 TYR A1025 ARG 0.004 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 1.158 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.0130 (tmm) cc_final: -0.0303 (mpp) REVERT: A 71 ASN cc_start: 0.6337 (t0) cc_final: 0.5650 (t0) REVERT: A 107 LYS cc_start: 0.6863 (mptp) cc_final: 0.6646 (mptp) REVERT: A 150 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7114 (tp) REVERT: A 182 LEU cc_start: 0.7362 (tp) cc_final: 0.7106 (tp) REVERT: A 195 GLU cc_start: 0.6704 (mt-10) cc_final: 0.6251 (mt-10) REVERT: A 366 LYS cc_start: 0.6611 (mtpt) cc_final: 0.6111 (ptmt) REVERT: A 465 GLU cc_start: 0.6169 (mm-30) cc_final: 0.5643 (mt-10) REVERT: A 500 PHE cc_start: 0.5220 (p90) cc_final: 0.4846 (p90) REVERT: A 502 LEU cc_start: 0.6031 (tp) cc_final: 0.5687 (tm) REVERT: A 534 MET cc_start: 0.5900 (tpp) cc_final: 0.5369 (tpp) REVERT: A 601 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.6845 (mp) REVERT: A 603 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7627 (mpp) REVERT: A 651 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.5484 (tp30) REVERT: A 911 GLU cc_start: 0.7465 (tt0) cc_final: 0.7242 (tt0) REVERT: B 63 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7417 (mt-10) REVERT: B 114 ASP cc_start: 0.6014 (m-30) cc_final: 0.5605 (m-30) REVERT: B 203 MET cc_start: 0.3640 (tpt) cc_final: 0.2510 (mpp) REVERT: B 206 ASN cc_start: 0.4710 (OUTLIER) cc_final: 0.4354 (m110) REVERT: B 213 GLN cc_start: 0.7130 (mt0) cc_final: 0.6844 (mt0) REVERT: B 223 ASP cc_start: 0.6626 (m-30) cc_final: 0.6113 (m-30) outliers start: 24 outliers final: 11 residues processed: 141 average time/residue: 1.0456 time to fit residues: 160.9868 Evaluate side-chains 143 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 767 PHE Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 206 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 101 optimal weight: 0.0770 chunk 106 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN B 208 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10349 Z= 0.149 Angle : 0.757 29.925 14013 Z= 0.321 Chirality : 0.041 0.172 1597 Planarity : 0.004 0.045 1760 Dihedral : 9.648 148.345 1640 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.21 % Allowed : 15.18 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.23), residues: 1259 helix: 1.75 (0.23), residues: 524 sheet: -0.04 (0.40), residues: 135 loop : -0.51 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 968 HIS 0.002 0.001 HIS A 57 PHE 0.011 0.001 PHE A 335 TYR 0.016 0.001 TYR A1025 ARG 0.004 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 128 time to evaluate : 1.312 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.0134 (tmm) cc_final: -0.0313 (mpp) REVERT: A 71 ASN cc_start: 0.6329 (t0) cc_final: 0.5639 (t0) REVERT: A 107 LYS cc_start: 0.6863 (OUTLIER) cc_final: 0.6627 (mptp) REVERT: A 150 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7127 (tp) REVERT: A 182 LEU cc_start: 0.7380 (tp) cc_final: 0.7114 (tp) REVERT: A 195 GLU cc_start: 0.6664 (mt-10) cc_final: 0.6217 (mt-10) REVERT: A 366 LYS cc_start: 0.6634 (mtpt) cc_final: 0.6150 (ptmt) REVERT: A 465 GLU cc_start: 0.6201 (mm-30) cc_final: 0.5749 (mt-10) REVERT: A 500 PHE cc_start: 0.5200 (p90) cc_final: 0.4795 (p90) REVERT: A 502 LEU cc_start: 0.6036 (tp) cc_final: 0.5696 (tm) REVERT: A 534 MET cc_start: 0.5854 (tpp) cc_final: 0.5335 (tpp) REVERT: A 601 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6883 (mp) REVERT: A 603 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.6918 (mtm) REVERT: A 651 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.5490 (tp30) REVERT: A 911 GLU cc_start: 0.7469 (tt0) cc_final: 0.7246 (tt0) REVERT: B 114 ASP cc_start: 0.5989 (m-30) cc_final: 0.5585 (m-30) REVERT: B 203 MET cc_start: 0.3677 (tpt) cc_final: 0.2515 (mpp) REVERT: B 206 ASN cc_start: 0.4804 (OUTLIER) cc_final: 0.4407 (m110) REVERT: B 213 GLN cc_start: 0.7122 (mt0) cc_final: 0.6853 (mt0) REVERT: B 221 ASP cc_start: 0.6232 (m-30) cc_final: 0.5888 (m-30) REVERT: B 223 ASP cc_start: 0.6622 (m-30) cc_final: 0.6116 (m-30) outliers start: 24 outliers final: 13 residues processed: 141 average time/residue: 1.0051 time to fit residues: 154.7726 Evaluate side-chains 142 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 767 PHE Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 206 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 124 optimal weight: 0.0170 chunk 114 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 78 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN B 208 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10349 Z= 0.150 Angle : 0.760 29.917 14013 Z= 0.323 Chirality : 0.041 0.145 1597 Planarity : 0.004 0.045 1760 Dihedral : 9.602 144.980 1640 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.84 % Allowed : 15.82 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.71 (0.23), residues: 1259 helix: 1.74 (0.23), residues: 524 sheet: -0.12 (0.40), residues: 138 loop : -0.50 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 968 HIS 0.002 0.001 HIS A 57 PHE 0.011 0.001 PHE A 445 TYR 0.016 0.001 TYR A1025 ARG 0.004 0.000 ARG A 397 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 1.154 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.0111 (tmm) cc_final: -0.0328 (mpp) REVERT: A 71 ASN cc_start: 0.6292 (t0) cc_final: 0.5610 (t0) REVERT: A 150 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7123 (tp) REVERT: A 182 LEU cc_start: 0.7399 (tp) cc_final: 0.7161 (tp) REVERT: A 195 GLU cc_start: 0.6649 (mt-10) cc_final: 0.6202 (mt-10) REVERT: A 366 LYS cc_start: 0.6611 (mtpt) cc_final: 0.6160 (ptmt) REVERT: A 465 GLU cc_start: 0.6157 (mm-30) cc_final: 0.5651 (mt-10) REVERT: A 474 VAL cc_start: 0.7013 (OUTLIER) cc_final: 0.6566 (p) REVERT: A 500 PHE cc_start: 0.5180 (p90) cc_final: 0.4786 (p90) REVERT: A 502 LEU cc_start: 0.6052 (tp) cc_final: 0.5724 (tm) REVERT: A 534 MET cc_start: 0.5901 (tpp) cc_final: 0.5372 (tpp) REVERT: A 601 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6903 (mp) REVERT: A 603 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.6973 (mtm) REVERT: A 651 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.5487 (tp30) REVERT: A 911 GLU cc_start: 0.7475 (tt0) cc_final: 0.7247 (tt0) REVERT: B 114 ASP cc_start: 0.5993 (m-30) cc_final: 0.5586 (m-30) REVERT: B 203 MET cc_start: 0.3701 (tpt) cc_final: 0.2542 (mpp) REVERT: B 206 ASN cc_start: 0.4661 (OUTLIER) cc_final: 0.4296 (m110) REVERT: B 213 GLN cc_start: 0.7106 (mt0) cc_final: 0.6845 (mt0) REVERT: B 221 ASP cc_start: 0.6228 (m-30) cc_final: 0.5882 (m-30) REVERT: B 223 ASP cc_start: 0.6558 (m-30) cc_final: 0.6060 (m-30) outliers start: 20 outliers final: 12 residues processed: 138 average time/residue: 1.0059 time to fit residues: 152.4920 Evaluate side-chains 144 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 767 PHE Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 206 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN B 208 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.173917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.117979 restraints weight = 10977.364| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.68 r_work: 0.2992 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10349 Z= 0.193 Angle : 0.790 30.085 14013 Z= 0.340 Chirality : 0.042 0.146 1597 Planarity : 0.004 0.046 1760 Dihedral : 9.938 145.946 1640 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.84 % Allowed : 16.01 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.23), residues: 1259 helix: 1.59 (0.23), residues: 524 sheet: -0.08 (0.40), residues: 135 loop : -0.53 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 968 HIS 0.002 0.001 HIS A 402 PHE 0.011 0.001 PHE A 318 TYR 0.017 0.002 TYR A 805 ARG 0.005 0.000 ARG A 397 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3631.70 seconds wall clock time: 64 minutes 53.04 seconds (3893.04 seconds total)