Starting phenix.real_space_refine (version: dev) on Fri Feb 24 14:14:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq2_32083/02_2023/7vq2_32083.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq2_32083/02_2023/7vq2_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_32083/02_2023/7vq2_32083.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq2_32083/02_2023/7vq2_32083.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq2_32083/02_2023/7vq2_32083.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq2_32083/02_2023/7vq2_32083.pdb" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.000 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 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 10.73, per 1000 atoms: 0.46 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: 18.75 Conformation dependent library (CDL) restraints added in 1.8 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: 0.44 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: 8.38 Time building geometry restraints manager: 19.63 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: 9073 16.93 - 33.87: 363 33.87 - 50.80: 120 50.80 - 67.73: 52 67.73 - 84.66: 12 Dihedral angle restraints: 9620 sinusoidal: 4304 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 9617 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 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. 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: 3.500 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: 1.120 Extract box with map and model: 14.890 Check model and map are aligned: 0.370 Process input model: 71.910 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.210 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3605 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 % 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 *********************** 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 : 2.047 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: 0.6303 time to fit residues: 246.7853 Evaluate side-chains 174 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 162 time to evaluate : 1.925 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 12 average time/residue: 0.3795 time to fit residues: 9.7180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 58 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 746 GLN ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.3891 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 11936 Z= 0.350 Angle : 0.695 6.031 16260 Z= 0.381 Chirality : 0.040 0.196 1828 Planarity : 0.005 0.052 2020 Dihedral : 6.086 74.753 1536 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 1.35 % 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: -1.53 (0.21), residues: 1408 helix: -0.33 (0.16), residues: 964 sheet: None (None), residues: 0 loop : -2.42 (0.27), residues: 444 *********************** 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 173 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 156 time to evaluate : 1.910 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: 17 outliers final: 13 residues processed: 170 average time/residue: 0.6242 time to fit residues: 144.3812 Evaluate side-chains 145 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 132 time to evaluate : 1.851 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 13 average time/residue: 0.2767 time to fit residues: 8.6395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 105 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 127 optimal weight: 30.0000 chunk 137 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 126 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 D1053 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3834 moved from start: 0.5242 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= 0.179 Angle : 0.563 6.158 16260 Z= 0.289 Chirality : 0.035 0.119 1828 Planarity : 0.004 0.038 2020 Dihedral : 5.547 73.151 1536 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer Outliers : 0.71 % 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: -0.32 (0.22), residues: 1408 helix: 0.66 (0.16), residues: 964 sheet: None (None), residues: 0 loop : -2.13 (0.29), residues: 444 *********************** 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 155 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 146 time to evaluate : 1.888 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 outliers start: 9 outliers final: 8 residues processed: 153 average time/residue: 0.5951 time to fit residues: 125.8513 Evaluate side-chains 136 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 1.880 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 8 average time/residue: 0.2911 time to fit residues: 6.3455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 66 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 127 optimal weight: 20.0000 chunk 135 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 973 HIS ** A1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1091 GLN ** B 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1091 GLN D1091 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4016 moved from start: 0.6173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 11936 Z= 0.296 Angle : 0.648 6.830 16260 Z= 0.350 Chirality : 0.037 0.172 1828 Planarity : 0.005 0.049 2020 Dihedral : 5.722 78.856 1536 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer Outliers : 1.83 % 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: -0.49 (0.22), residues: 1408 helix: 0.55 (0.16), residues: 952 sheet: None (None), residues: 0 loop : -2.17 (0.28), residues: 456 *********************** 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 148 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 125 time to evaluate : 1.828 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 outliers start: 23 outliers final: 19 residues processed: 143 average time/residue: 0.5695 time to fit residues: 115.9681 Evaluate side-chains 140 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 1.851 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 3 residues processed: 19 average time/residue: 0.2667 time to fit residues: 11.4934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 B1091 GLN ** C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4025 moved from start: 0.6703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 11936 Z= 0.264 Angle : 0.601 6.053 16260 Z= 0.319 Chirality : 0.037 0.158 1828 Planarity : 0.005 0.037 2020 Dihedral : 5.676 83.877 1536 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer Outliers : 2.22 % 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: -0.34 (0.22), residues: 1408 helix: 0.72 (0.16), residues: 956 sheet: None (None), residues: 0 loop : -2.31 (0.28), residues: 452 *********************** 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 157 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 129 time to evaluate : 1.926 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 outliers start: 28 outliers final: 21 residues processed: 146 average time/residue: 0.5610 time to fit residues: 116.6628 Evaluate side-chains 145 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 2.036 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 6 residues processed: 21 average time/residue: 0.2760 time to fit residues: 12.7702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 79 optimal weight: 0.6980 chunk 33 optimal weight: 0.0370 chunk 135 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 62 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 overall best weight: 1.5464 ------------------------------------------------------------------------------- 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 912 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3985 moved from start: 0.6924 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= 0.203 Angle : 0.554 6.108 16260 Z= 0.288 Chirality : 0.035 0.131 1828 Planarity : 0.004 0.044 2020 Dihedral : 5.494 83.266 1536 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer Outliers : 1.35 % 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: 0.01 (0.22), residues: 1408 helix: 1.04 (0.16), residues: 956 sheet: None (None), residues: 0 loop : -2.30 (0.27), residues: 452 *********************** 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 144 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 1.989 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 outliers start: 17 outliers final: 12 residues processed: 137 average time/residue: 0.5475 time to fit residues: 107.1945 Evaluate side-chains 133 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 1.951 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 12 average time/residue: 0.2795 time to fit residues: 8.2054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 134 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4064 moved from start: 0.7268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 11936 Z= 0.295 Angle : 0.619 6.226 16260 Z= 0.335 Chirality : 0.037 0.176 1828 Planarity : 0.005 0.038 2020 Dihedral : 5.709 88.206 1536 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer Outliers : 2.06 % 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: -0.17 (0.22), residues: 1408 helix: 0.94 (0.16), residues: 940 sheet: None (None), residues: 0 loop : -2.35 (0.27), residues: 468 *********************** 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 146 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 1.869 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 outliers start: 26 outliers final: 17 residues processed: 135 average time/residue: 0.5227 time to fit residues: 101.8563 Evaluate side-chains 135 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 1.821 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 17 average time/residue: 0.2656 time to fit residues: 10.4174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 40 optimal weight: 0.1980 chunk 26 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 129 optimal weight: 0.3980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3984 moved from start: 0.7407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 11936 Z= 0.193 Angle : 0.559 6.508 16260 Z= 0.287 Chirality : 0.036 0.126 1828 Planarity : 0.004 0.044 2020 Dihedral : 5.500 86.004 1536 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer Outliers : 1.27 % 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: 0.28 (0.22), residues: 1408 helix: 1.28 (0.16), residues: 956 sheet: None (None), residues: 0 loop : -2.29 (0.28), residues: 452 *********************** 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 145 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 2.008 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 outliers start: 16 outliers final: 12 residues processed: 139 average time/residue: 0.5498 time to fit residues: 109.5541 Evaluate side-chains 137 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 2.048 Switching outliers to nearest non-outliers 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: 7 residues processed: 12 average time/residue: 0.3191 time to fit residues: 8.8159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 129 optimal weight: 9.9990 chunk 75 optimal weight: 0.0980 chunk 54 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3931 moved from start: 0.7460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 11936 Z= 0.154 Angle : 0.543 7.737 16260 Z= 0.270 Chirality : 0.035 0.127 1828 Planarity : 0.004 0.037 2020 Dihedral : 5.287 82.156 1536 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer Outliers : 1.03 % 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: 0.72 (0.23), residues: 1408 helix: 1.64 (0.16), residues: 952 sheet: None (None), residues: 0 loop : -2.15 (0.28), residues: 456 *********************** 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 146 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 133 time to evaluate : 1.940 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 outliers start: 13 outliers final: 9 residues processed: 140 average time/residue: 0.5634 time to fit residues: 114.0418 Evaluate side-chains 139 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 130 time to evaluate : 1.619 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 9 average time/residue: 0.2936 time to fit residues: 6.9966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 92 optimal weight: 20.0000 chunk 139 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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** D1037 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3987 moved from start: 0.7651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 11936 Z= 0.197 Angle : 0.571 7.600 16260 Z= 0.291 Chirality : 0.036 0.139 1828 Planarity : 0.004 0.041 2020 Dihedral : 5.351 83.326 1536 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer Outliers : 0.56 % 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: 0.60 (0.22), residues: 1408 helix: 1.56 (0.16), residues: 952 sheet: None (None), residues: 0 loop : -2.23 (0.28), residues: 456 ********************** 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 130 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 123 time to evaluate : 2.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 126 average time/residue: 0.5854 time to fit residues: 106.9620 Evaluate side-chains 124 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 1.934 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 7 average time/residue: 0.2920 time to fit residues: 5.8427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.2980 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.4689 r_free = 0.4689 target = 0.139734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.113567 restraints weight = 121976.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.118516 restraints weight = 57489.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.121464 restraints weight = 37281.991| |-----------------------------------------------------------------------------| r_work (final): 0.4393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.7692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 11936 Z= 0.170 Angle : 0.565 7.928 16260 Z= 0.280 Chirality : 0.036 0.125 1828 Planarity : 0.004 0.038 2020 Dihedral : 5.257 82.351 1536 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer Outliers : 0.56 % 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: 0.80 (0.23), residues: 1408 helix: 1.75 (0.16), residues: 948 sheet: None (None), residues: 0 loop : -2.21 (0.28), residues: 460 =============================================================================== Job complete usr+sys time: 4231.27 seconds wall clock time: 75 minutes 57.92 seconds (4557.92 seconds total)