Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 18:48:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6td6_10464/04_2023/6td6_10464_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6td6_10464/04_2023/6td6_10464.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6td6_10464/04_2023/6td6_10464.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6td6_10464/04_2023/6td6_10464.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6td6_10464/04_2023/6td6_10464_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6td6_10464/04_2023/6td6_10464_trim.pdb" } resolution = 4.76 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= -0.014 sd= 0.473 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 55 5.16 5 C 5186 2.51 5 N 1259 2.21 5 O 1414 1.98 5 H 7766 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 46": "OD1" <-> "OD2" Residue "A PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 49": "OD1" <-> "OD2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A ASP 267": "OD1" <-> "OD2" Residue "A ARG 292": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 497": "OE1" <-> "OE2" Residue "A PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 723": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 731": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 750": "OD1" <-> "OD2" Residue "A TYR 757": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 762": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 785": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 804": "OE1" <-> "OE2" Residue "A TYR 809": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 812": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 835": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 857": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 916": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 920": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 949": "OD1" <-> "OD2" Residue "A TYR 953": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 964": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 981": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1030": "OD1" <-> "OD2" Residue "A ARG 1040": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 1100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1121": "OE1" <-> "OE2" Residue "B TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 129": "OD1" <-> "OD2" Residue "B PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 164": "OE1" <-> "OE2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B ASP 231": "OD1" <-> "OD2" Residue "B TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 15680 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 842, 13378 Classifications: {'peptide': 842} Link IDs: {'PTRANS': 34, 'TRANS': 807} Chain breaks: 10 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2260 Classifications: {'peptide': 140} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 133} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.86, per 1000 atoms: 0.44 Number of scatterers: 15680 At special positions: 0 Unit cell: (117.04, 83.6, 95.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 O 1414 8.00 N 1259 7.00 C 5186 6.00 H 7766 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 323 " distance=2.02 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 304 " distance=2.03 Simple disulfide: pdb=" SG CYS A 781 " - pdb=" SG CYS A 801 " distance=2.03 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 829 " distance=2.03 Simple disulfide: pdb=" SG CYS A 828 " - pdb=" SG CYS A 843 " 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 BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A1301 " - " ASN A 319 " " NAG C 1 " - " ASN A 767 " Time building additional restraints: 13.84 Conformation dependent library (CDL) restraints added in 1.3 seconds 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1878 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 5 sheets defined 62.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 6 through 19 Processing helix chain 'A' and resid 19 through 41 removed outlier: 4.509A pdb=" N VAL A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 73 Processing helix chain 'A' and resid 84 through 89 removed outlier: 3.636A pdb=" N TRP A 89 " --> pdb=" O PRO A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 286 Processing helix chain 'A' and resid 288 through 295 Processing helix chain 'A' and resid 309 through 318 Processing helix chain 'A' and resid 326 through 341 removed outlier: 4.790A pdb=" N THR A 332 " --> pdb=" O THR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 380 removed outlier: 3.590A pdb=" N THR A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 419 removed outlier: 3.957A pdb=" N VAL A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 467 removed outlier: 3.564A pdb=" N LEU A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TRP A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A 453 " --> pdb=" O TRP A 449 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLY A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 492 removed outlier: 3.877A pdb=" N THR A 472 " --> pdb=" O SER A 468 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 473 " --> pdb=" O ALA A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 504 Processing helix chain 'A' and resid 505 through 511 Processing helix chain 'A' and resid 515 through 531 removed outlier: 4.229A pdb=" N PHE A 519 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 523 " --> pdb=" O PHE A 519 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 588 removed outlier: 5.216A pdb=" N ALA A 572 " --> pdb=" O ARG A 568 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N SER A 573 " --> pdb=" O HIS A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 591 No H-bonds generated for 'chain 'A' and resid 589 through 591' Processing helix chain 'A' and resid 593 through 628 removed outlier: 3.708A pdb=" N LYS A 597 " --> pdb=" O ILE A 593 " (cutoff:3.500A) Proline residue: A 619 - end of helix Processing helix chain 'A' and resid 649 through 669 removed outlier: 3.831A pdb=" N TYR A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 690 removed outlier: 3.568A pdb=" N TRP A 690 " --> pdb=" O VAL A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 718 removed outlier: 3.537A pdb=" N SER A 715 " --> pdb=" O PHE A 711 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU A 717 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LYS A 718 " --> pdb=" O TYR A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 721 No H-bonds generated for 'chain 'A' and resid 719 through 721' Processing helix chain 'A' and resid 770 through 785 Processing helix chain 'A' and resid 802 through 812 Processing helix chain 'A' and resid 837 through 854 Proline residue: A 845 - end of helix Processing helix chain 'A' and resid 916 through 935 Processing helix chain 'A' and resid 936 through 937 No H-bonds generated for 'chain 'A' and resid 936 through 937' Processing helix chain 'A' and resid 938 through 942 Processing helix chain 'A' and resid 950 through 982 removed outlier: 5.190A pdb=" N SER A 960 " --> pdb=" O GLN A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 1010 removed outlier: 4.291A pdb=" N SER A 988 " --> pdb=" O ASN A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1042 removed outlier: 3.680A pdb=" N SER A1018 " --> pdb=" O ASN A1014 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE A1025 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLY A1026 " --> pdb=" O SER A1022 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ASP A1030 " --> pdb=" O GLY A1026 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N PHE A1031 " --> pdb=" O LEU A1027 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER A1032 " --> pdb=" O ALA A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1076 removed outlier: 6.447A pdb=" N GLY A1060 " --> pdb=" O SER A1056 " (cutoff:3.500A) Proline residue: A1061 - end of helix Processing helix chain 'A' and resid 1081 through 1113 removed outlier: 4.399A pdb=" N LEU A1106 " --> pdb=" O ALA A1102 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N MET A1107 " --> pdb=" O THR A1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 135 Processing helix chain 'B' and resid 159 through 177 removed outlier: 4.524A pdb=" N TYR B 171 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER B 172 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 214 through 216 No H-bonds generated for 'chain 'B' and resid 214 through 216' Processing helix chain 'B' and resid 217 through 228 Processing sheet with id=AA1, first strand: chain 'A' and resid 398 through 400 Processing sheet with id=AA2, first strand: chain 'A' and resid 790 through 791 removed outlier: 3.625A pdb=" N GLU A 907 " --> pdb=" O LYS A 791 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LYS A 865 " --> pdb=" O LYS A 900 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU A 902 " --> pdb=" O GLY A 863 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLY A 863 " --> pdb=" O LEU A 902 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 790 through 791 removed outlier: 3.625A pdb=" N GLU A 907 " --> pdb=" O LYS A 791 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N PHE A 906 " --> pdb=" O PHE A 739 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N PHE A 739 " --> pdb=" O PHE A 906 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N SER A 908 " --> pdb=" O MET A 737 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N MET A 737 " --> pdb=" O SER A 908 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N VAL A 910 " --> pdb=" O MET A 735 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 137 through 138 Processing sheet with id=AA5, first strand: chain 'B' and resid 144 through 145 removed outlier: 6.100A pdb=" N LEU B 145 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU B 186 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL B 184 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA B 209 " --> pdb=" O VAL B 184 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1281 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: 5.55 Time building geometry restraints manager: 14.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 7752 1.03 - 1.23: 20 1.23 - 1.42: 3523 1.42 - 1.62: 4509 1.62 - 1.82: 86 Bond restraints: 15890 Sorted by residual: bond pdb=" CB TRP A1011 " pdb=" CG TRP A1011 " ideal model delta sigma weight residual 1.498 1.415 0.083 3.10e-02 1.04e+03 7.09e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.37e+00 bond pdb=" CG1 ILE A1058 " pdb=" CD1 ILE A1058 " ideal model delta sigma weight residual 1.513 1.418 0.095 3.90e-02 6.57e+02 5.91e+00 bond pdb=" C PHE A 894 " pdb=" N THR A 895 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.37e-02 5.33e+03 5.62e+00 bond pdb=" C SER A 247 " pdb=" N SER A 248 " ideal model delta sigma weight residual 1.331 1.378 -0.047 2.07e-02 2.33e+03 5.13e+00 ... (remaining 15885 not shown) Histogram of bond angle deviations from ideal: 73.03 - 87.89: 2 87.89 - 102.76: 60 102.76 - 117.63: 20784 117.63 - 132.49: 7752 132.49 - 147.36: 22 Bond angle restraints: 28620 Sorted by residual: angle pdb="HD21 ASN A 319 " pdb=" ND2 ASN A 319 " pdb="HD22 ASN A 319 " ideal model delta sigma weight residual 120.00 73.03 46.97 3.00e+00 1.11e-01 2.45e+02 angle pdb=" CG ASN A 319 " pdb=" ND2 ASN A 319 " pdb="HD22 ASN A 319 " ideal model delta sigma weight residual 120.00 74.36 45.64 3.00e+00 1.11e-01 2.31e+02 angle pdb=" CG ASN A 319 " pdb=" ND2 ASN A 319 " pdb="HD21 ASN A 319 " ideal model delta sigma weight residual 120.00 147.36 -27.36 3.00e+00 1.11e-01 8.32e+01 angle pdb=" CA LEU A 409 " pdb=" C LEU A 409 " pdb=" N LEU A 410 " ideal model delta sigma weight residual 118.27 113.05 5.22 1.30e+00 5.92e-01 1.61e+01 angle pdb=" C VAL A 688 " pdb=" CA VAL A 688 " pdb=" CB VAL A 688 " ideal model delta sigma weight residual 112.24 107.17 5.07 1.34e+00 5.57e-01 1.43e+01 ... (remaining 28615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 5516 17.86 - 35.71: 766 35.71 - 53.57: 144 53.57 - 71.43: 43 71.43 - 89.28: 10 Dihedral angle restraints: 6479 sinusoidal: 2848 harmonic: 3631 Sorted by residual: dihedral pdb=" CA LEU A 369 " pdb=" C LEU A 369 " pdb=" N ASN A 370 " pdb=" CA ASN A 370 " ideal model delta harmonic sigma weight residual -180.00 -135.06 -44.94 0 5.00e+00 4.00e-02 8.08e+01 dihedral pdb=" CA LYS A 699 " pdb=" C LYS A 699 " pdb=" N SER A 700 " pdb=" CA SER A 700 " ideal model delta harmonic sigma weight residual -180.00 -139.38 -40.62 0 5.00e+00 4.00e-02 6.60e+01 dihedral pdb=" CB CYS A 295 " pdb=" SG CYS A 295 " pdb=" SG CYS A 304 " pdb=" CB CYS A 304 " ideal model delta sinusoidal sigma weight residual 93.00 147.48 -54.48 1 1.00e+01 1.00e-02 4.02e+01 ... (remaining 6476 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 1260 0.329 - 0.658: 1 0.658 - 0.986: 0 0.986 - 1.315: 0 1.315 - 1.644: 1 Chirality restraints: 1262 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.76 -1.64 2.00e-02 2.50e+03 6.75e+03 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 319 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" CB VAL A 518 " pdb=" CA VAL A 518 " pdb=" CG1 VAL A 518 " pdb=" CG2 VAL A 518 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1259 not shown) Planarity restraints: 2297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 771 " -0.044 5.00e-02 4.00e+02 6.74e-02 7.28e+00 pdb=" N PRO A 772 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 772 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 772 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 310 " -0.044 5.00e-02 4.00e+02 6.66e-02 7.10e+00 pdb=" N PRO A 311 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 311 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 311 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A 614 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.20e+00 pdb=" C MET A 614 " 0.043 2.00e-02 2.50e+03 pdb=" O MET A 614 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE A 615 " -0.014 2.00e-02 2.50e+03 ... (remaining 2294 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.03: 524 2.03 - 2.67: 26008 2.67 - 3.31: 49332 3.31 - 3.96: 58801 3.96 - 4.60: 89778 Nonbonded interactions: 224443 Sorted by model distance: nonbonded pdb=" O VAL A 606 " pdb=" HG1 THR A 609 " model vdw 1.385 1.850 nonbonded pdb=" O SER A 783 " pdb="HE21 GLN A 787 " model vdw 1.426 1.850 nonbonded pdb=" O GLN A 782 " pdb="HE21 GLN A 786 " model vdw 1.431 1.850 nonbonded pdb=" O THR A 66 " pdb="HD21 ASN A 70 " model vdw 1.444 1.850 nonbonded pdb=" O GLU A 626 " pdb=" H PHE A 629 " model vdw 1.445 1.850 ... (remaining 224438 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 group one per residue 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: 1.510 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: 0.260 Extract box with map and model: 7.820 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 51.090 Find NCS groups from input model: 0.280 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 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 : 0.010 0.095 8124 Z= 0.629 Angle : 1.112 13.160 11048 Z= 0.639 Chirality : 0.071 1.644 1262 Planarity : 0.007 0.067 1365 Dihedral : 15.727 82.944 2827 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 55.96 Ramachandran Plot: Outliers : 0.42 % Allowed : 22.80 % Favored : 76.78 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.65 % 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: -6.33 (0.19), residues: 956 helix: -4.18 (0.13), residues: 517 sheet: -4.06 (0.80), residues: 26 loop : -4.15 (0.25), residues: 413 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 327 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 169 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 171 average time/residue: 0.4201 time to fit residues: 98.2328 Evaluate side-chains 125 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 123 time to evaluate : 1.251 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1493 time to fit residues: 2.1238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 50 optimal weight: 0.0980 chunk 39 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN A 561 ASN A 668 ASN ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 HIS B 106 GLN ** B 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 8124 Z= 0.270 Angle : 0.771 8.003 11048 Z= 0.413 Chirality : 0.044 0.280 1262 Planarity : 0.006 0.058 1365 Dihedral : 7.430 41.946 1051 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 23.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.34 % Favored : 87.66 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -4.84 (0.22), residues: 956 helix: -2.91 (0.16), residues: 549 sheet: -2.61 (0.82), residues: 36 loop : -3.58 (0.29), residues: 371 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 327 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 175 average time/residue: 0.3812 time to fit residues: 94.1539 Evaluate side-chains 129 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.343 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 60 optimal weight: 0.5980 chunk 24 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 96 optimal weight: 20.0000 chunk 79 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1080 ASN ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.062 8124 Z= 0.367 Angle : 0.797 9.543 11048 Z= 0.439 Chirality : 0.043 0.262 1262 Planarity : 0.006 0.051 1365 Dihedral : 7.222 41.672 1051 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 31.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.75 % Favored : 85.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -4.12 (0.23), residues: 956 helix: -2.35 (0.18), residues: 547 sheet: -2.85 (0.71), residues: 42 loop : -3.16 (0.31), residues: 367 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 327 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.3587 time to fit residues: 81.1763 Evaluate side-chains 118 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.274 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 918 ASN A1080 ASN ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 8124 Z= 0.250 Angle : 0.699 6.684 11048 Z= 0.378 Chirality : 0.042 0.278 1262 Planarity : 0.005 0.051 1365 Dihedral : 6.667 41.080 1051 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 22.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.25), residues: 956 helix: -1.64 (0.19), residues: 555 sheet: -2.58 (0.76), residues: 36 loop : -2.85 (0.33), residues: 365 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 327 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.4004 time to fit residues: 86.8551 Evaluate side-chains 115 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.332 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 5.9990 chunk 1 optimal weight: 0.4980 chunk 70 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 GLN A 954 ASN B 200 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 8124 Z= 0.192 Angle : 0.633 5.242 11048 Z= 0.340 Chirality : 0.041 0.313 1262 Planarity : 0.004 0.053 1365 Dihedral : 6.122 39.741 1051 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.27), residues: 956 helix: -0.80 (0.20), residues: 555 sheet: -2.41 (0.73), residues: 45 loop : -2.51 (0.35), residues: 356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 327 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.3686 time to fit residues: 87.9737 Evaluate side-chains 123 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.175 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 0.0980 chunk 31 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1080 ASN ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 8124 Z= 0.271 Angle : 0.666 5.822 11048 Z= 0.363 Chirality : 0.040 0.289 1262 Planarity : 0.004 0.051 1365 Dihedral : 6.091 38.922 1051 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 22.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.34 % Favored : 87.66 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.26), residues: 956 helix: -0.83 (0.20), residues: 555 sheet: -2.39 (0.74), residues: 43 loop : -2.48 (0.35), residues: 358 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 327 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.3753 time to fit residues: 82.3539 Evaluate side-chains 120 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.297 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 53 optimal weight: 0.5980 chunk 79 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 ASN A1080 ASN ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.5915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8124 Z= 0.180 Angle : 0.616 5.615 11048 Z= 0.328 Chirality : 0.040 0.293 1262 Planarity : 0.004 0.050 1365 Dihedral : 5.796 38.831 1051 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.27), residues: 956 helix: -0.40 (0.20), residues: 558 sheet: -2.38 (0.72), residues: 45 loop : -2.29 (0.36), residues: 353 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 327 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.3924 time to fit residues: 90.4603 Evaluate side-chains 123 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.298 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 46 optimal weight: 0.0980 chunk 8 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN A 954 ASN ** A1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.6179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 8124 Z= 0.177 Angle : 0.596 4.981 11048 Z= 0.316 Chirality : 0.039 0.246 1262 Planarity : 0.004 0.052 1365 Dihedral : 5.595 37.929 1051 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.27), residues: 956 helix: -0.11 (0.21), residues: 562 sheet: -2.32 (0.71), residues: 45 loop : -2.22 (0.36), residues: 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 327 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.3585 time to fit residues: 81.0124 Evaluate side-chains 123 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.236 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.6132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 8124 Z= 0.298 Angle : 0.692 6.139 11048 Z= 0.377 Chirality : 0.041 0.292 1262 Planarity : 0.005 0.054 1365 Dihedral : 5.953 37.588 1051 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 23.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.34 % Favored : 87.66 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.27), residues: 956 helix: -0.50 (0.20), residues: 561 sheet: -2.43 (0.69), residues: 45 loop : -2.36 (0.36), residues: 350 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 327 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.3800 time to fit residues: 85.5704 Evaluate side-chains 121 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.369 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 20.0000 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1080 ASN B 194 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.6321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 8124 Z= 0.232 Angle : 0.647 5.234 11048 Z= 0.347 Chirality : 0.040 0.261 1262 Planarity : 0.004 0.050 1365 Dihedral : 5.832 37.792 1051 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 20.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.27), residues: 956 helix: -0.34 (0.20), residues: 561 sheet: -2.48 (0.69), residues: 45 loop : -2.32 (0.36), residues: 350 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 327 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.3601 time to fit residues: 78.4977 Evaluate side-chains 120 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.259 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 79 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.120849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.096190 restraints weight = 104012.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.099554 restraints weight = 63139.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.101597 restraints weight = 43285.624| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.6600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8124 Z= 0.181 Angle : 0.611 8.227 11048 Z= 0.320 Chirality : 0.039 0.246 1262 Planarity : 0.004 0.048 1365 Dihedral : 5.529 37.051 1051 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.27), residues: 956 helix: 0.06 (0.21), residues: 563 sheet: -2.27 (0.70), residues: 45 loop : -2.18 (0.36), residues: 348 =============================================================================== Job complete usr+sys time: 3263.18 seconds wall clock time: 58 minutes 40.08 seconds (3520.08 seconds total)