Starting phenix.real_space_refine on Sun Dec 10 21:30:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6td6_10464/12_2023/6td6_10464_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6td6_10464/12_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_10464/12_2023/6td6_10464.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6td6_10464/12_2023/6td6_10464.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6td6_10464/12_2023/6td6_10464_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6td6_10464/12_2023/6td6_10464_trim.pdb" } resolution = 4.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.014 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-1.21rc1-5172/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 dihedrals: 6 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.67, per 1000 atoms: 0.43 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: 12.51 Conformation dependent library (CDL) restraints added in 1.4 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: 1.06 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: 5.39 Time building geometry restraints manager: 13.07 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 - 25.21: 6856 25.21 - 50.43: 509 50.43 - 75.64: 73 75.64 - 100.86: 15 100.86 - 126.07: 10 Dihedral angle restraints: 7463 sinusoidal: 3832 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 7460 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: 0.010 Normalize map: mean=0, sd=1: 2.040 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: 0.240 Extract box with map and model: 6.880 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 49.050 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.530 ------------------------------------------------------------------------------- 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 : 17.681 126.071 2890 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 % Allowed : 11.83 % Favored : 87.82 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 617 HIS 0.008 0.002 HIS A 701 PHE 0.035 0.003 PHE A 521 TYR 0.037 0.003 TYR A 487 ARG 0.009 0.001 ARG A 812 *********************** 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 : 1.310 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: 0.4170 time to fit residues: 97.6667 Evaluate side-chains 125 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 123 time to evaluate : 1.228 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1749 time to fit residues: 2.2093 ------------------------------------------------------------------------------- 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: 0.9990 chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 25 optimal weight: 7.9990 chunk 50 optimal weight: 0.2980 chunk 39 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 88 optimal weight: 20.0000 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN A 503 ASN A 561 ASN A 838 HIS ** A 846 GLN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8124 Z= 0.258 Angle : 0.785 11.885 11048 Z= 0.413 Chirality : 0.044 0.289 1262 Planarity : 0.006 0.059 1365 Dihedral : 11.871 107.108 1114 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 24.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.34 % Favored : 87.55 % Rotamer: Outliers : 0.12 % Allowed : 4.87 % Favored : 95.01 % 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: -4.92 (0.21), residues: 956 helix: -2.98 (0.16), residues: 551 sheet: -2.77 (0.79), residues: 36 loop : -3.60 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 617 HIS 0.006 0.002 HIS A 838 PHE 0.018 0.002 PHE A 739 TYR 0.027 0.002 TYR A 586 ARG 0.007 0.001 ARG B 238 *********************** 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 174 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 173 time to evaluate : 1.087 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: 173 average time/residue: 0.3591 time to fit residues: 87.9959 Evaluate side-chains 129 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.106 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4085 ------------------------------------------------------------------------------- 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: 6.9990 chunk 27 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.6946 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8124 Z= 0.308 Angle : 0.766 8.800 11048 Z= 0.416 Chirality : 0.043 0.271 1262 Planarity : 0.005 0.056 1365 Dihedral : 9.146 85.940 1114 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 26.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.60 % Favored : 86.30 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % 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: -4.06 (0.23), residues: 956 helix: -2.24 (0.18), residues: 553 sheet: -2.66 (0.73), residues: 42 loop : -3.25 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 463 HIS 0.013 0.001 HIS A 838 PHE 0.021 0.002 PHE A 922 TYR 0.030 0.002 TYR A 291 ARG 0.005 0.001 ARG A 292 *********************** 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 159 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.289 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: 159 average time/residue: 0.3423 time to fit residues: 79.4767 Evaluate side-chains 122 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.365 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5614 ------------------------------------------------------------------------------- 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: 10.0000 chunk 67 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 846 GLN ** 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** ** 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: 0.7061 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8124 Z= 0.354 Angle : 0.794 8.110 11048 Z= 0.434 Chirality : 0.044 0.309 1262 Planarity : 0.005 0.057 1365 Dihedral : 8.519 60.817 1114 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 29.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.64 % Favored : 85.36 % Rotamer: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % 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: -3.58 (0.24), residues: 956 helix: -1.89 (0.19), residues: 552 sheet: -2.11 (0.85), residues: 30 loop : -3.02 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 463 HIS 0.008 0.002 HIS A 335 PHE 0.023 0.002 PHE A 400 TYR 0.038 0.002 TYR A 487 ARG 0.003 0.000 ARG A1047 *********************** 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 145 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.430 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 outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.3705 time to fit residues: 78.7850 Evaluate side-chains 111 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.348 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6990 ------------------------------------------------------------------------------- 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: 2.9990 chunk 1 optimal weight: 0.7980 chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 GLN ** A 668 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8124 Z= 0.214 Angle : 0.664 7.796 11048 Z= 0.356 Chirality : 0.042 0.299 1262 Planarity : 0.004 0.050 1365 Dihedral : 7.646 47.946 1114 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % 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: -2.73 (0.26), residues: 956 helix: -1.13 (0.20), residues: 555 sheet: -2.43 (0.76), residues: 37 loop : -2.71 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 617 HIS 0.004 0.001 HIS A1038 PHE 0.022 0.002 PHE A 922 TYR 0.021 0.001 TYR A 291 ARG 0.005 0.001 ARG A 408 *********************** 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 162 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.233 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 outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.3750 time to fit residues: 86.8309 Evaluate side-chains 120 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.286 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7064 ------------------------------------------------------------------------------- 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: 0.6980 chunk 18 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 23 optimal weight: 0.2980 chunk 94 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 7 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 921 GLN A 954 ASN A1080 ASN B 194 HIS B 200 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.5477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8124 Z= 0.226 Angle : 0.645 7.346 11048 Z= 0.346 Chirality : 0.040 0.279 1262 Planarity : 0.004 0.050 1365 Dihedral : 7.271 53.163 1114 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.61 % Favored : 88.39 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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 (0.26), residues: 956 helix: -0.80 (0.20), residues: 556 sheet: -2.21 (0.76), residues: 43 loop : -2.55 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 463 HIS 0.003 0.001 HIS A 736 PHE 0.015 0.002 PHE A 400 TYR 0.019 0.001 TYR B 100 ARG 0.002 0.000 ARG A1047 *********************** 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 158 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.315 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: 158 average time/residue: 0.3707 time to fit residues: 83.5648 Evaluate side-chains 122 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.326 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5551 ------------------------------------------------------------------------------- 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: 9.9990 chunk 54 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 79 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1080 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.5761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8124 Z= 0.255 Angle : 0.669 7.011 11048 Z= 0.364 Chirality : 0.041 0.298 1262 Planarity : 0.005 0.048 1365 Dihedral : 7.191 56.772 1114 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.34 % Favored : 87.66 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % 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: -2.25 (0.26), residues: 956 helix: -0.74 (0.20), residues: 558 sheet: -2.25 (0.77), residues: 43 loop : -2.51 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 617 HIS 0.005 0.001 HIS A1038 PHE 0.025 0.002 PHE A 470 TYR 0.017 0.001 TYR A 291 ARG 0.003 0.000 ARG A1047 *********************** 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 154 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.192 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 outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.3640 time to fit residues: 80.5208 Evaluate side-chains 121 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.303 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6341 ------------------------------------------------------------------------------- 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: 1.9990 chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 60 optimal weight: 0.0370 chunk 64 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.6078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8124 Z= 0.185 Angle : 0.602 5.683 11048 Z= 0.320 Chirality : 0.040 0.245 1262 Planarity : 0.004 0.052 1365 Dihedral : 6.841 59.633 1114 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % 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: -1.66 (0.27), residues: 956 helix: -0.24 (0.21), residues: 559 sheet: -2.00 (0.74), residues: 45 loop : -2.32 (0.36), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 617 HIS 0.004 0.001 HIS A 335 PHE 0.017 0.001 PHE A 470 TYR 0.016 0.001 TYR A 12 ARG 0.003 0.000 ARG A 785 *********************** 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 161 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.317 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: 161 average time/residue: 0.3631 time to fit residues: 84.1826 Evaluate side-chains 127 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.216 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4906 ------------------------------------------------------------------------------- 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: 3.9990 chunk 88 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 83 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.6205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8124 Z= 0.242 Angle : 0.646 5.397 11048 Z= 0.350 Chirality : 0.040 0.271 1262 Planarity : 0.004 0.053 1365 Dihedral : 6.847 55.772 1114 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.92 % Favored : 88.08 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -1.73 (0.27), residues: 956 helix: -0.28 (0.21), residues: 560 sheet: -2.10 (0.74), residues: 45 loop : -2.39 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 617 HIS 0.007 0.001 HIS A 335 PHE 0.019 0.002 PHE A 470 TYR 0.038 0.002 TYR A 852 ARG 0.003 0.000 ARG A1047 *********************** 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 158 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.315 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: 158 average time/residue: 0.3609 time to fit residues: 81.6738 Evaluate side-chains 128 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.261 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5614 ------------------------------------------------------------------------------- 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: 30.0000 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.6342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8124 Z= 0.214 Angle : 0.623 5.225 11048 Z= 0.334 Chirality : 0.040 0.242 1262 Planarity : 0.004 0.048 1365 Dihedral : 6.778 56.995 1114 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: -1.58 (0.27), residues: 956 helix: -0.17 (0.21), residues: 561 sheet: -2.04 (0.74), residues: 45 loop : -2.30 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 617 HIS 0.006 0.001 HIS A1038 PHE 0.019 0.002 PHE A 470 TYR 0.015 0.001 TYR A 12 ARG 0.003 0.000 ARG A 260 ********************** 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 158 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.227 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 outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.3607 time to fit residues: 82.1756 Evaluate side-chains 128 residues out of total 868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.196 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6474 ------------------------------------------------------------------------------- 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: 8.9990 chunk 71 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1080 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.119376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.094295 restraints weight = 105183.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.097647 restraints weight = 64831.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.099621 restraints weight = 44768.835| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.6458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8124 Z= 0.211 Angle : 0.618 5.267 11048 Z= 0.330 Chirality : 0.039 0.222 1262 Planarity : 0.004 0.049 1365 Dihedral : 6.340 49.794 1114 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: -1.49 (0.27), residues: 956 helix: -0.08 (0.21), residues: 561 sheet: -2.13 (0.73), residues: 45 loop : -2.27 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 617 HIS 0.005 0.001 HIS A 335 PHE 0.015 0.001 PHE A 470 TYR 0.025 0.001 TYR A 852 ARG 0.003 0.000 ARG A1047 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3386.95 seconds wall clock time: 61 minutes 7.58 seconds (3667.58 seconds total)