Starting phenix.real_space_refine on Tue Mar 19 04:22:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq2_32083/03_2024/7vq2_32083.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq2_32083/03_2024/7vq2_32083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq2_32083/03_2024/7vq2_32083.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq2_32083/03_2024/7vq2_32083.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq2_32083/03_2024/7vq2_32083.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq2_32083/03_2024/7vq2_32083.pdb" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.000 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 76 5.16 5 C 7732 2.51 5 N 1872 2.21 5 O 1896 1.98 5 H 11764 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 809": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 815": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 821": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 848": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 863": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 893": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 936": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 975": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 994": "OE1" <-> "OE2" Residue "A TYR 1004": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1084": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 809": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 815": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 821": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 848": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 863": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 893": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 936": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 975": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 994": "OE1" <-> "OE2" Residue "B TYR 1004": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1084": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 809": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 815": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 821": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 848": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 863": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 893": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 936": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 975": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 994": "OE1" <-> "OE2" Residue "C TYR 1004": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1084": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 809": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 815": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 821": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 848": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 863": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 893": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 936": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 975": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 994": "OE1" <-> "OE2" Residue "D TYR 1004": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 1084": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23340 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5835 Classifications: {'peptide': 354} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 332} Chain: "B" Number of atoms: 5835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5835 Classifications: {'peptide': 354} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 332} Chain: "C" Number of atoms: 5835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5835 Classifications: {'peptide': 354} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 332} Chain: "D" Number of atoms: 5835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5835 Classifications: {'peptide': 354} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 332} Time building chain proxies: 9.97, per 1000 atoms: 0.43 Number of scatterers: 23340 At special positions: 0 Unit cell: (137.655, 137.655, 73.53, 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 76 16.00 O 1896 8.00 N 1872 7.00 C 7732 6.00 H 11764 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 996 " - pdb=" SG CYS A1008 " distance=2.03 Simple disulfide: pdb=" SG CYS B 996 " - pdb=" SG CYS B1008 " distance=2.03 Simple disulfide: pdb=" SG CYS C 996 " - pdb=" SG CYS C1008 " distance=2.03 Simple disulfide: pdb=" SG CYS D 996 " - pdb=" SG CYS D1008 " 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 Time building additional restraints: 18.38 Conformation dependent library (CDL) restraints added in 2.4 seconds 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2704 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 0 sheets defined 76.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 753 through 762 removed outlier: 3.527A pdb=" N LEU A 761 " --> pdb=" O THR A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 768 removed outlier: 3.842A pdb=" N LEU A 766 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU A 767 " --> pdb=" O PHE A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 780 removed outlier: 3.659A pdb=" N GLN A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 794 removed outlier: 3.572A pdb=" N ALA A 794 " --> pdb=" O ALA A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 819 Processing helix chain 'A' and resid 826 through 846 Processing helix chain 'A' and resid 855 through 866 Processing helix chain 'A' and resid 866 through 888 removed outlier: 3.881A pdb=" N THR A 884 " --> pdb=" O VAL A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 908 Processing helix chain 'A' and resid 909 through 917 removed outlier: 3.596A pdb=" N ILE A 916 " --> pdb=" O ILE A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 956 removed outlier: 4.741A pdb=" N LYS A 932 " --> pdb=" O LYS A 928 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ASP A 933 " --> pdb=" O ARG A 929 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 936 " --> pdb=" O LYS A 932 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 940 " --> pdb=" O PHE A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 978 removed outlier: 3.804A pdb=" N LEU A 966 " --> pdb=" O ARG A 962 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR A 972 " --> pdb=" O ARG A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1036 removed outlier: 3.558A pdb=" N PHE A1035 " --> pdb=" O LEU A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1056 removed outlier: 3.871A pdb=" N GLN A1053 " --> pdb=" O ASN A1049 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN A1054 " --> pdb=" O TYR A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1077 removed outlier: 4.371A pdb=" N HIS A1068 " --> pdb=" O LYS A1064 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ASP A1069 " --> pdb=" O PHE A1065 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU A1070 " --> pdb=" O GLN A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1098 removed outlier: 4.054A pdb=" N LEU A1086 " --> pdb=" O PRO A1082 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU A1087 " --> pdb=" O PRO A1083 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER A1088 " --> pdb=" O PHE A1084 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 762 removed outlier: 3.527A pdb=" N LEU B 761 " --> pdb=" O THR B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 768 removed outlier: 3.843A pdb=" N LEU B 766 " --> pdb=" O ALA B 762 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU B 767 " --> pdb=" O PHE B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 780 removed outlier: 3.659A pdb=" N GLN B 779 " --> pdb=" O GLU B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 794 removed outlier: 3.572A pdb=" N ALA B 794 " --> pdb=" O ALA B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 819 Processing helix chain 'B' and resid 826 through 846 Processing helix chain 'B' and resid 855 through 866 Processing helix chain 'B' and resid 866 through 888 removed outlier: 3.881A pdb=" N THR B 884 " --> pdb=" O VAL B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 908 Processing helix chain 'B' and resid 909 through 917 removed outlier: 3.596A pdb=" N ILE B 916 " --> pdb=" O ILE B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 956 removed outlier: 4.741A pdb=" N LYS B 932 " --> pdb=" O LYS B 928 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ASP B 933 " --> pdb=" O ARG B 929 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE B 936 " --> pdb=" O LYS B 932 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 940 " --> pdb=" O PHE B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 978 removed outlier: 3.804A pdb=" N LEU B 966 " --> pdb=" O ARG B 962 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR B 972 " --> pdb=" O ARG B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 1021 through 1036 removed outlier: 3.558A pdb=" N PHE B1035 " --> pdb=" O LEU B1031 " (cutoff:3.500A) Processing helix chain 'B' and resid 1038 through 1056 removed outlier: 3.871A pdb=" N GLN B1053 " --> pdb=" O ASN B1049 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN B1054 " --> pdb=" O TYR B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1077 removed outlier: 4.371A pdb=" N HIS B1068 " --> pdb=" O LYS B1064 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ASP B1069 " --> pdb=" O PHE B1065 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU B1070 " --> pdb=" O GLN B1066 " (cutoff:3.500A) Processing helix chain 'B' and resid 1081 through 1098 removed outlier: 4.055A pdb=" N LEU B1086 " --> pdb=" O PRO B1082 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU B1087 " --> pdb=" O PRO B1083 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER B1088 " --> pdb=" O PHE B1084 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 762 removed outlier: 3.527A pdb=" N LEU C 761 " --> pdb=" O THR C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 768 removed outlier: 3.841A pdb=" N LEU C 766 " --> pdb=" O ALA C 762 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU C 767 " --> pdb=" O PHE C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 775 through 780 removed outlier: 3.659A pdb=" N GLN C 779 " --> pdb=" O GLU C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 794 removed outlier: 3.573A pdb=" N ALA C 794 " --> pdb=" O ALA C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 819 Processing helix chain 'C' and resid 826 through 846 Processing helix chain 'C' and resid 855 through 866 Processing helix chain 'C' and resid 866 through 888 removed outlier: 3.881A pdb=" N THR C 884 " --> pdb=" O VAL C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 891 through 908 Processing helix chain 'C' and resid 909 through 917 removed outlier: 3.596A pdb=" N ILE C 916 " --> pdb=" O ILE C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 956 removed outlier: 4.741A pdb=" N LYS C 932 " --> pdb=" O LYS C 928 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ASP C 933 " --> pdb=" O ARG C 929 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE C 936 " --> pdb=" O LYS C 932 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 940 " --> pdb=" O PHE C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 978 removed outlier: 3.804A pdb=" N LEU C 966 " --> pdb=" O ARG C 962 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR C 972 " --> pdb=" O ARG C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 1021 through 1036 removed outlier: 3.558A pdb=" N PHE C1035 " --> pdb=" O LEU C1031 " (cutoff:3.500A) Processing helix chain 'C' and resid 1038 through 1056 removed outlier: 3.871A pdb=" N GLN C1053 " --> pdb=" O ASN C1049 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN C1054 " --> pdb=" O TYR C1050 " (cutoff:3.500A) Processing helix chain 'C' and resid 1058 through 1077 removed outlier: 4.372A pdb=" N HIS C1068 " --> pdb=" O LYS C1064 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ASP C1069 " --> pdb=" O PHE C1065 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU C1070 " --> pdb=" O GLN C1066 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1098 removed outlier: 4.054A pdb=" N LEU C1086 " --> pdb=" O PRO C1082 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU C1087 " --> pdb=" O PRO C1083 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER C1088 " --> pdb=" O PHE C1084 " (cutoff:3.500A) Processing helix chain 'D' and resid 753 through 762 removed outlier: 3.527A pdb=" N LEU D 761 " --> pdb=" O THR D 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 768 removed outlier: 3.842A pdb=" N LEU D 766 " --> pdb=" O ALA D 762 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU D 767 " --> pdb=" O PHE D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 775 through 780 removed outlier: 3.659A pdb=" N GLN D 779 " --> pdb=" O GLU D 775 " (cutoff:3.500A) Processing helix chain 'D' and resid 783 through 794 removed outlier: 3.572A pdb=" N ALA D 794 " --> pdb=" O ALA D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 819 Processing helix chain 'D' and resid 826 through 846 Processing helix chain 'D' and resid 855 through 866 Processing helix chain 'D' and resid 866 through 888 removed outlier: 3.880A pdb=" N THR D 884 " --> pdb=" O VAL D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 891 through 908 Processing helix chain 'D' and resid 909 through 917 removed outlier: 3.597A pdb=" N ILE D 916 " --> pdb=" O ILE D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 920 through 956 removed outlier: 4.741A pdb=" N LYS D 932 " --> pdb=" O LYS D 928 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ASP D 933 " --> pdb=" O ARG D 929 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE D 936 " --> pdb=" O LYS D 932 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 940 " --> pdb=" O PHE D 936 " (cutoff:3.500A) Processing helix chain 'D' and resid 962 through 978 removed outlier: 3.804A pdb=" N LEU D 966 " --> pdb=" O ARG D 962 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR D 972 " --> pdb=" O ARG D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 1021 through 1036 removed outlier: 3.559A pdb=" N PHE D1035 " --> pdb=" O LEU D1031 " (cutoff:3.500A) Processing helix chain 'D' and resid 1038 through 1056 removed outlier: 3.870A pdb=" N GLN D1053 " --> pdb=" O ASN D1049 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN D1054 " --> pdb=" O TYR D1050 " (cutoff:3.500A) Processing helix chain 'D' and resid 1058 through 1077 removed outlier: 4.371A pdb=" N HIS D1068 " --> pdb=" O LYS D1064 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ASP D1069 " --> pdb=" O PHE D1065 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU D1070 " --> pdb=" O GLN D1066 " (cutoff:3.500A) Processing helix chain 'D' and resid 1081 through 1098 removed outlier: 4.054A pdb=" N LEU D1086 " --> pdb=" O PRO D1082 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU D1087 " --> pdb=" O PRO D1083 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER D1088 " --> pdb=" O PHE D1084 " (cutoff:3.500A) 744 hydrogen bonds defined for protein. 2172 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: 7.44 Time building geometry restraints manager: 19.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 11728 1.13 - 1.30: 1736 1.30 - 1.47: 4966 1.47 - 1.64: 5162 1.64 - 1.81: 108 Bond restraints: 23700 Sorted by residual: bond pdb=" N PRO A1021 " pdb=" CD PRO A1021 " ideal model delta sigma weight residual 1.473 1.614 -0.141 1.40e-02 5.10e+03 1.02e+02 bond pdb=" N PRO C1021 " pdb=" CD PRO C1021 " ideal model delta sigma weight residual 1.473 1.614 -0.141 1.40e-02 5.10e+03 1.02e+02 bond pdb=" N PRO D1021 " pdb=" CD PRO D1021 " ideal model delta sigma weight residual 1.473 1.614 -0.141 1.40e-02 5.10e+03 1.01e+02 bond pdb=" N PRO B1021 " pdb=" CD PRO B1021 " ideal model delta sigma weight residual 1.473 1.613 -0.140 1.40e-02 5.10e+03 1.00e+02 bond pdb=" CE1 PHE A 809 " pdb=" HE1 PHE A 809 " ideal model delta sigma weight residual 0.930 1.094 -0.164 2.00e-02 2.50e+03 6.69e+01 ... (remaining 23695 not shown) Histogram of bond angle deviations from ideal: 95.85 - 103.45: 212 103.45 - 111.05: 25280 111.05 - 118.64: 5205 118.64 - 126.24: 11908 126.24 - 133.84: 335 Bond angle restraints: 42940 Sorted by residual: angle pdb=" CA ALA A1013 " pdb=" C ALA A1013 " pdb=" N THR A1014 " ideal model delta sigma weight residual 117.96 110.03 7.93 1.23e+00 6.61e-01 4.16e+01 angle pdb=" CA ALA C1013 " pdb=" C ALA C1013 " pdb=" N THR C1014 " ideal model delta sigma weight residual 117.96 110.05 7.91 1.23e+00 6.61e-01 4.13e+01 angle pdb=" CA ALA B1013 " pdb=" C ALA B1013 " pdb=" N THR B1014 " ideal model delta sigma weight residual 117.96 110.08 7.88 1.23e+00 6.61e-01 4.10e+01 angle pdb=" CA ALA D1013 " pdb=" C ALA D1013 " pdb=" N THR D1014 " ideal model delta sigma weight residual 117.96 110.10 7.86 1.23e+00 6.61e-01 4.09e+01 angle pdb=" N GLY B1000 " pdb=" CA GLY B1000 " pdb=" C GLY B1000 " ideal model delta sigma weight residual 115.08 110.03 5.05 1.19e+00 7.06e-01 1.80e+01 ... (remaining 42935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 10445 16.93 - 33.87: 427 33.87 - 50.80: 228 50.80 - 67.73: 84 67.73 - 84.66: 12 Dihedral angle restraints: 11196 sinusoidal: 5880 harmonic: 5316 Sorted by residual: dihedral pdb=" CA ALA C1013 " pdb=" C ALA C1013 " pdb=" N THR C1014 " pdb=" CA THR C1014 " ideal model delta harmonic sigma weight residual -180.00 -147.80 -32.20 0 5.00e+00 4.00e-02 4.15e+01 dihedral pdb=" CA ALA A1013 " pdb=" C ALA A1013 " pdb=" N THR A1014 " pdb=" CA THR A1014 " ideal model delta harmonic sigma weight residual -180.00 -147.81 -32.19 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" CA ALA D1013 " pdb=" C ALA D1013 " pdb=" N THR D1014 " pdb=" CA THR D1014 " ideal model delta harmonic sigma weight residual -180.00 -147.87 -32.13 0 5.00e+00 4.00e-02 4.13e+01 ... (remaining 11193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1203 0.036 - 0.072: 186 0.072 - 0.108: 376 0.108 - 0.144: 55 0.144 - 0.180: 8 Chirality restraints: 1828 Sorted by residual: chirality pdb=" CA VAL C 824 " pdb=" N VAL C 824 " pdb=" C VAL C 824 " pdb=" CB VAL C 824 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.14e-01 chirality pdb=" CA VAL A 824 " pdb=" N VAL A 824 " pdb=" C VAL A 824 " pdb=" CB VAL A 824 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.14e-01 chirality pdb=" CA VAL B 824 " pdb=" N VAL B 824 " pdb=" C VAL B 824 " pdb=" CB VAL B 824 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.13e-01 ... (remaining 1825 not shown) Planarity restraints: 3348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D1013 " 0.022 2.00e-02 2.50e+03 4.94e-02 2.44e+01 pdb=" C ALA D1013 " -0.085 2.00e-02 2.50e+03 pdb=" O ALA D1013 " 0.033 2.00e-02 2.50e+03 pdb=" N THR D1014 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B1013 " -0.022 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" C ALA B1013 " 0.085 2.00e-02 2.50e+03 pdb=" O ALA B1013 " -0.033 2.00e-02 2.50e+03 pdb=" N THR B1014 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C1013 " -0.022 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" C ALA C1013 " 0.085 2.00e-02 2.50e+03 pdb=" O ALA C1013 " -0.033 2.00e-02 2.50e+03 pdb=" N THR C1014 " -0.030 2.00e-02 2.50e+03 ... (remaining 3345 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 759 2.01 - 2.66: 29813 2.66 - 3.31: 71466 3.31 - 3.95: 87738 3.95 - 4.60: 130925 Nonbonded interactions: 320701 Sorted by model distance: nonbonded pdb="HE22 GLN C1056 " pdb="HE21 GLN D1054 " model vdw 1.364 2.100 nonbonded pdb="HE22 GLN A1056 " pdb="HE21 GLN B1054 " model vdw 1.364 2.100 nonbonded pdb="HE22 GLN B1056 " pdb="HE21 GLN C1054 " model vdw 1.364 2.100 nonbonded pdb="HE21 GLN A1054 " pdb="HE22 GLN D1056 " model vdw 1.364 2.100 nonbonded pdb=" H GLU B 994 " pdb=" H GLU B1022 " model vdw 1.402 2.100 ... (remaining 320696 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 3.770 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: 0.290 Extract box with map and model: 14.290 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 69.900 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.100 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3834 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 : 0.009 0.141 11936 Z= 0.577 Angle : 0.834 7.935 16260 Z= 0.541 Chirality : 0.051 0.180 1828 Planarity : 0.004 0.049 2020 Dihedral : 12.144 84.663 4256 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 1.42 % Allowed : 4.83 % Favored : 93.75 % Rotamer: Outliers : 1.27 % Allowed : 1.27 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -3.35 (0.18), residues: 1408 helix: -1.74 (0.14), residues: 968 sheet: None (None), residues: 0 loop : -3.04 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C1063 HIS 0.002 0.000 HIS B 958 PHE 0.002 0.001 PHE B 939 TYR 0.002 0.000 TYR D 893 ARG 0.002 0.000 ARG C1096 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 270 time to evaluate : 1.944 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 16 outliers final: 12 residues processed: 286 average time/residue: 0.5979 time to fit residues: 232.5443 Evaluate side-chains 174 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 162 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 893 TYR Chi-restraints excluded: chain A residue 979 PHE Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain B residue 893 TYR Chi-restraints excluded: chain B residue 979 PHE Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain C residue 893 TYR Chi-restraints excluded: chain C residue 979 PHE Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain D residue 893 TYR Chi-restraints excluded: chain D residue 979 PHE Chi-restraints excluded: chain D residue 1048 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 746 GLN ** A1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 746 GLN ** B1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 746 GLN ** C1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 746 GLN ** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4078 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11936 Z= 0.275 Angle : 0.644 5.720 16260 Z= 0.348 Chirality : 0.038 0.169 1828 Planarity : 0.005 0.054 2020 Dihedral : 7.066 71.406 1560 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.27 % Allowed : 7.38 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.21), residues: 1408 helix: -0.16 (0.16), residues: 964 sheet: None (None), residues: 0 loop : -2.28 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 944 HIS 0.008 0.002 HIS C1068 PHE 0.025 0.002 PHE C 809 TYR 0.017 0.001 TYR A 806 ARG 0.004 0.000 ARG B1077 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 161 time to evaluate : 1.961 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 16 outliers final: 11 residues processed: 174 average time/residue: 0.6049 time to fit residues: 143.9258 Evaluate side-chains 150 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 139 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain C residue 933 ASP Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1048 PHE Chi-restraints excluded: chain D residue 1049 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 137 optimal weight: 0.7980 chunk 113 optimal weight: 0.4980 chunk 126 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 102 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1053 GLN B1053 GLN C1053 GLN ** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1053 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4021 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11936 Z= 0.164 Angle : 0.542 5.586 16260 Z= 0.276 Chirality : 0.035 0.121 1828 Planarity : 0.005 0.062 2020 Dihedral : 6.040 66.468 1544 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.95 % Allowed : 9.60 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.22), residues: 1408 helix: 0.95 (0.16), residues: 956 sheet: None (None), residues: 0 loop : -2.24 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 944 HIS 0.004 0.001 HIS B1068 PHE 0.015 0.001 PHE C 939 TYR 0.009 0.001 TYR D 806 ARG 0.012 0.000 ARG D 777 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 153 time to evaluate : 1.895 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 12 outliers final: 8 residues processed: 159 average time/residue: 0.6312 time to fit residues: 135.6881 Evaluate side-chains 139 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 908 LEU Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 1048 PHE Chi-restraints excluded: chain D residue 1049 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 66 optimal weight: 0.0370 chunk 14 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 127 optimal weight: 40.0000 chunk 135 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 36 optimal weight: 0.0670 chunk 112 optimal weight: 1.9990 overall best weight: 1.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1037 ASN ** B 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1037 ASN ** C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4152 moved from start: 0.5803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11936 Z= 0.197 Angle : 0.556 6.159 16260 Z= 0.291 Chirality : 0.035 0.138 1828 Planarity : 0.005 0.050 2020 Dihedral : 5.839 60.982 1544 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.51 % Allowed : 9.76 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.22), residues: 1408 helix: 1.06 (0.17), residues: 956 sheet: None (None), residues: 0 loop : -2.01 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 944 HIS 0.007 0.001 HIS D1068 PHE 0.028 0.002 PHE B 813 TYR 0.020 0.001 TYR B 806 ARG 0.002 0.000 ARG D 777 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 1.856 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 19 outliers final: 17 residues processed: 149 average time/residue: 0.5127 time to fit residues: 109.5802 Evaluate side-chains 145 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain B residue 852 ASP Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 857 MET Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1040 LEU Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1048 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 121 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4126 moved from start: 0.6139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11936 Z= 0.160 Angle : 0.529 7.335 16260 Z= 0.269 Chirality : 0.035 0.142 1828 Planarity : 0.004 0.038 2020 Dihedral : 5.642 57.478 1544 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.06 % Allowed : 10.08 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.23), residues: 1408 helix: 1.35 (0.17), residues: 956 sheet: None (None), residues: 0 loop : -1.94 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 944 HIS 0.005 0.001 HIS B1068 PHE 0.019 0.001 PHE C1052 TYR 0.012 0.001 TYR A1074 ARG 0.003 0.000 ARG D 777 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 1.870 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 26 outliers final: 18 residues processed: 150 average time/residue: 0.5008 time to fit residues: 108.4125 Evaluate side-chains 139 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain B residue 852 ASP Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 907 CYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1040 LEU Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1048 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 33 optimal weight: 0.2980 chunk 135 optimal weight: 0.0040 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 overall best weight: 2.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 HIS A 973 HIS A1091 GLN ** B 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1091 GLN ** C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1091 GLN ** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 912 HIS D 958 HIS ** D1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1091 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4274 moved from start: 0.6751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11936 Z= 0.262 Angle : 0.606 6.602 16260 Z= 0.327 Chirality : 0.037 0.163 1828 Planarity : 0.005 0.053 2020 Dihedral : 5.854 59.124 1544 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.54 % Allowed : 10.08 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.22), residues: 1408 helix: 1.13 (0.17), residues: 944 sheet: None (None), residues: 0 loop : -2.20 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 868 HIS 0.006 0.001 HIS D1068 PHE 0.026 0.002 PHE A 809 TYR 0.026 0.002 TYR A 806 ARG 0.004 0.000 ARG A 961 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 124 time to evaluate : 1.707 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 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: 32 outliers final: 29 residues processed: 147 average time/residue: 0.4804 time to fit residues: 103.7760 Evaluate side-chains 148 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 119 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 835 TRP Chi-restraints excluded: chain B residue 852 ASP Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 907 CYS Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 933 ASP Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1040 LEU Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 857 MET Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 939 PHE Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1040 LEU Chi-restraints excluded: chain D residue 1048 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 76 optimal weight: 0.5980 chunk 114 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 134 optimal weight: 7.9990 chunk 84 optimal weight: 0.0570 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 chunk 83 optimal weight: 4.9990 overall best weight: 1.4502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4216 moved from start: 0.6905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11936 Z= 0.186 Angle : 0.541 6.360 16260 Z= 0.279 Chirality : 0.036 0.135 1828 Planarity : 0.004 0.044 2020 Dihedral : 5.685 59.568 1544 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.06 % Allowed : 10.63 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.22), residues: 1408 helix: 1.28 (0.16), residues: 972 sheet: None (None), residues: 0 loop : -1.98 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 944 HIS 0.006 0.001 HIS D1068 PHE 0.026 0.001 PHE A 813 TYR 0.014 0.001 TYR B1074 ARG 0.002 0.000 ARG D 777 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 1.727 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 26 outliers final: 22 residues processed: 148 average time/residue: 0.4836 time to fit residues: 104.1464 Evaluate side-chains 148 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 126 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain B residue 852 ASP Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 907 CYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 939 PHE Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1048 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.7980 chunk 80 optimal weight: 8.9990 chunk 40 optimal weight: 0.0970 chunk 26 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4220 moved from start: 0.7087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11936 Z= 0.181 Angle : 0.535 6.418 16260 Z= 0.276 Chirality : 0.035 0.126 1828 Planarity : 0.005 0.045 2020 Dihedral : 5.641 58.716 1544 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.90 % Allowed : 10.63 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.23), residues: 1408 helix: 1.38 (0.16), residues: 972 sheet: None (None), residues: 0 loop : -1.93 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 944 HIS 0.006 0.001 HIS A1068 PHE 0.024 0.001 PHE A 813 TYR 0.015 0.001 TYR B1074 ARG 0.003 0.000 ARG A 961 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 126 time to evaluate : 1.581 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 revert: symmetry clash revert: symmetry clash 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: 24 outliers final: 21 residues processed: 144 average time/residue: 0.4802 time to fit residues: 102.0266 Evaluate side-chains 143 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 852 ASP Chi-restraints excluded: chain B residue 907 CYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1040 LEU Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 939 PHE Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1040 LEU Chi-restraints excluded: chain D residue 1048 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 1.9990 chunk 125 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 75 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 132 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 869 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4179 moved from start: 0.7200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11936 Z= 0.152 Angle : 0.521 6.270 16260 Z= 0.263 Chirality : 0.035 0.126 1828 Planarity : 0.004 0.041 2020 Dihedral : 5.538 59.014 1544 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.90 % Allowed : 10.56 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.23), residues: 1408 helix: 1.63 (0.17), residues: 968 sheet: None (None), residues: 0 loop : -1.84 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 944 HIS 0.005 0.001 HIS A1068 PHE 0.028 0.001 PHE C 813 TYR 0.012 0.001 TYR B1074 ARG 0.002 0.000 ARG C 777 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 2.020 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 931 MET cc_start: 0.3920 (ppp) cc_final: 0.3624 (ppp) outliers start: 24 outliers final: 23 residues processed: 143 average time/residue: 0.4760 time to fit residues: 101.2999 Evaluate side-chains 149 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 852 ASP Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 907 CYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1040 LEU Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1040 LEU Chi-restraints excluded: chain D residue 1048 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 2.9990 chunk 63 optimal weight: 20.0000 chunk 92 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 111 optimal weight: 0.6980 chunk 11 optimal weight: 8.9990 chunk 85 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 118 optimal weight: 0.5980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4197 moved from start: 0.7328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11936 Z= 0.163 Angle : 0.528 6.571 16260 Z= 0.270 Chirality : 0.035 0.130 1828 Planarity : 0.005 0.042 2020 Dihedral : 5.537 59.425 1544 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.90 % Allowed : 10.63 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.23), residues: 1408 helix: 1.62 (0.17), residues: 976 sheet: None (None), residues: 0 loop : -1.77 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 944 HIS 0.005 0.001 HIS B1068 PHE 0.028 0.001 PHE C 813 TYR 0.012 0.001 TYR B1074 ARG 0.003 0.000 ARG C 929 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 127 time to evaluate : 1.886 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 931 MET cc_start: 0.3830 (ppp) cc_final: 0.3601 (ppp) outliers start: 24 outliers final: 23 residues processed: 141 average time/residue: 0.4501 time to fit residues: 94.8729 Evaluate side-chains 148 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 125 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 852 ASP Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 907 CYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1040 LEU Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1040 LEU Chi-restraints excluded: chain D residue 1048 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 114 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 6 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 869 ASN ** 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 = 0.4705 r_free = 0.4705 target = 0.140532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.111688 restraints weight = 120265.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.118089 restraints weight = 60480.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.122826 restraints weight = 38680.541| |-----------------------------------------------------------------------------| r_work (final): 0.4447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.7419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11936 Z= 0.144 Angle : 0.516 7.272 16260 Z= 0.260 Chirality : 0.035 0.126 1828 Planarity : 0.004 0.040 2020 Dihedral : 5.456 59.518 1544 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.06 % Allowed : 10.63 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.23), residues: 1408 helix: 1.86 (0.17), residues: 968 sheet: None (None), residues: 0 loop : -1.78 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 944 HIS 0.004 0.001 HIS A1068 PHE 0.023 0.001 PHE C 813 TYR 0.011 0.001 TYR B1074 ARG 0.002 0.000 ARG A 961 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4421.90 seconds wall clock time: 79 minutes 5.11 seconds (4745.11 seconds total)