Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 16:58:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x21_32954/04_2023/7x21_32954_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x21_32954/04_2023/7x21_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_32954/04_2023/7x21_32954.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x21_32954/04_2023/7x21_32954.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x21_32954/04_2023/7x21_32954_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x21_32954/04_2023/7x21_32954_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-1.21rc1-4938/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: 8 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: 5.90, per 1000 atoms: 0.58 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: 4.42 Conformation dependent library (CDL) restraints added in 1.5 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: 1.54 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: 3.72 Time building geometry restraints manager: 4.73 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: 6064 32.98 - 65.96: 128 65.96 - 98.94: 22 98.94 - 131.92: 3 131.92 - 164.91: 1 Dihedral angle restraints: 6218 sinusoidal: 2560 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 6215 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.410 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 30.330 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.020 ------------------------------------------------------------------------------- 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 : 14.804 164.905 3859 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 % 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 *********************** 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 : 1.241 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 1.2488 time to fit residues: 204.2708 Evaluate side-chains 117 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.229 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7844 ------------------------------------------------------------------------------- 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: 4.9990 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: 0.7595 moved from start: 0.0889 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= 0.139 Angle : 0.761 30.624 14013 Z= 0.323 Chirality : 0.041 0.262 1597 Planarity : 0.004 0.046 1760 Dihedral : 9.599 157.905 1477 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 1.93 % 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: -0.13 (0.40), residues: 148 loop : -0.58 (0.25), residues: 584 *********************** 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 156 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 135 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 4 residues processed: 146 average time/residue: 1.3332 time to fit residues: 210.6534 Evaluate side-chains 125 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 1.218 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.6709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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: 0.7693 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.080 10349 Z= 0.459 Angle : 0.922 31.610 14013 Z= 0.419 Chirality : 0.051 0.278 1597 Planarity : 0.006 0.058 1760 Dihedral : 10.708 176.229 1477 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 3.22 % 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: 0.02 (0.23), residues: 1259 helix: 0.87 (0.22), residues: 528 sheet: -0.07 (0.42), residues: 129 loop : -0.69 (0.24), residues: 602 *********************** 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 159 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 124 time to evaluate : 1.274 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 13 residues processed: 144 average time/residue: 1.1442 time to fit residues: 178.9514 Evaluate side-chains 133 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 120 time to evaluate : 1.320 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 5 average time/residue: 0.9537 time to fit residues: 6.9520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.5980 chunk 85 optimal weight: 0.0770 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- 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: 0.7637 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 10349 Z= 0.174 Angle : 0.781 30.010 14013 Z= 0.337 Chirality : 0.042 0.273 1597 Planarity : 0.004 0.047 1760 Dihedral : 10.187 178.388 1477 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 2.48 % 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: 1.46 (0.23), residues: 524 sheet: -0.10 (0.41), residues: 135 loop : -0.62 (0.25), residues: 600 *********************** 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 157 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 130 time to evaluate : 1.261 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 12 residues processed: 144 average time/residue: 1.1278 time to fit residues: 176.7306 Evaluate side-chains 126 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 1.251 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 0.7151 time to fit residues: 4.1521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0470 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 0.4980 chunk 108 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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: 0.7616 moved from start: 0.1304 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= 0.147 Angle : 0.762 29.910 14013 Z= 0.323 Chirality : 0.041 0.255 1597 Planarity : 0.004 0.045 1760 Dihedral : 9.618 167.349 1477 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 3.04 % 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: 1.73 (0.23), residues: 524 sheet: -0.04 (0.41), residues: 136 loop : -0.57 (0.25), residues: 599 *********************** 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 165 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 132 time to evaluate : 1.252 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 14 residues processed: 150 average time/residue: 1.1331 time to fit residues: 184.7934 Evaluate side-chains 135 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 1.120 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.1049 time to fit residues: 2.1983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 ASN 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: 0.7642 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 10349 Z= 0.206 Angle : 0.794 30.129 14013 Z= 0.342 Chirality : 0.043 0.265 1597 Planarity : 0.004 0.047 1760 Dihedral : 9.747 161.235 1477 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 3.04 % 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: 0.57 (0.23), residues: 1259 helix: 1.56 (0.23), residues: 522 sheet: -0.06 (0.41), residues: 135 loop : -0.54 (0.25), residues: 602 *********************** 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 165 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 132 time to evaluate : 1.242 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 18 residues processed: 154 average time/residue: 1.0583 time to fit residues: 178.6310 Evaluate side-chains 138 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 1.252 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 13 residues processed: 5 average time/residue: 0.5090 time to fit residues: 4.6787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 0.1980 chunk 68 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 101 optimal weight: 0.0370 chunk 67 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 55 optimal weight: 0.0670 chunk 74 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- 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: 0.7590 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 10349 Z= 0.131 Angle : 0.755 29.776 14013 Z= 0.318 Chirality : 0.041 0.249 1597 Planarity : 0.004 0.044 1760 Dihedral : 9.136 157.622 1477 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 2.39 % 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: 0.80 (0.23), residues: 1259 helix: 1.86 (0.23), residues: 524 sheet: -0.07 (0.40), residues: 138 loop : -0.49 (0.25), residues: 597 *********************** 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 157 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 1.319 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 15 residues processed: 149 average time/residue: 1.1203 time to fit residues: 182.1824 Evaluate side-chains 136 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 1.239 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 3 average time/residue: 0.1516 time to fit residues: 2.3971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 chunk 82 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 10349 Z= 0.217 Angle : 0.797 30.138 14013 Z= 0.344 Chirality : 0.043 0.263 1597 Planarity : 0.004 0.045 1760 Dihedral : 9.513 153.522 1477 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 2.48 % 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: 0.61 (0.23), residues: 1259 helix: 1.61 (0.23), residues: 525 sheet: 0.02 (0.41), residues: 134 loop : -0.57 (0.24), residues: 600 *********************** 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 151 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 124 time to evaluate : 1.237 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 18 residues processed: 140 average time/residue: 1.0716 time to fit residues: 164.0865 Evaluate side-chains 139 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 1.307 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 12 residues processed: 6 average time/residue: 0.7418 time to fit residues: 6.7260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 67 optimal weight: 0.9980 chunk 48 optimal weight: 0.0040 chunk 88 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 chunk 101 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 B 213 GLN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1499 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= 0.145 Angle : 0.765 29.853 14013 Z= 0.323 Chirality : 0.041 0.148 1597 Planarity : 0.004 0.043 1760 Dihedral : 9.150 150.856 1477 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 1.56 % 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: 0.74 (0.23), residues: 1259 helix: 1.77 (0.23), residues: 525 sheet: -0.03 (0.41), residues: 138 loop : -0.51 (0.25), residues: 596 *********************** 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 140 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 15 residues processed: 136 average time/residue: 1.1421 time to fit residues: 170.0675 Evaluate side-chains 134 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 1.289 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 3 average time/residue: 0.6984 time to fit residues: 4.0456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 124 optimal weight: 0.0870 chunk 114 optimal weight: 0.4980 chunk 99 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 76 optimal weight: 0.0570 chunk 60 optimal weight: 0.0870 chunk 78 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 overall best weight: 0.3054 ------------------------------------------------------------------------------- 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 B 263 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 10349 Z= 0.125 Angle : 0.763 29.800 14013 Z= 0.320 Chirality : 0.040 0.211 1597 Planarity : 0.004 0.042 1760 Dihedral : 8.678 147.316 1477 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 1.38 % 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: 0.87 (0.23), residues: 1259 helix: 1.91 (0.23), residues: 525 sheet: 0.05 (0.40), residues: 138 loop : -0.48 (0.25), residues: 596 ********************** 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: 15 poor density : 132 time to evaluate : 1.248 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 13 residues processed: 144 average time/residue: 1.0309 time to fit residues: 163.4890 Evaluate side-chains 141 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 1.211 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.0941 time to fit residues: 1.9505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0870 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.176171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.117713 restraints weight = 10929.816| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.92 r_work: 0.2996 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 10349 Z= 0.146 Angle : 0.771 29.907 14013 Z= 0.326 Chirality : 0.041 0.181 1597 Planarity : 0.004 0.043 1760 Dihedral : 8.718 145.895 1477 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 1.93 % 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: 0.85 (0.23), residues: 1259 helix: 1.84 (0.23), residues: 525 sheet: 0.08 (0.40), residues: 138 loop : -0.45 (0.25), residues: 596 =============================================================================== Job complete usr+sys time: 3881.42 seconds wall clock time: 69 minutes 52.53 seconds (4192.53 seconds total)