Starting phenix.real_space_refine on Wed Mar 4 09:41:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d7h_27230/03_2026/8d7h_27230.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d7h_27230/03_2026/8d7h_27230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d7h_27230/03_2026/8d7h_27230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d7h_27230/03_2026/8d7h_27230.map" model { file = "/net/cci-nas-00/data/ceres_data/8d7h_27230/03_2026/8d7h_27230.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d7h_27230/03_2026/8d7h_27230.cif" } resolution = 3.4 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 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= 0.028 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: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 7970 2.51 5 N 2156 2.21 5 O 2368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 125 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12540 Number of models: 1 Model: "" Number of chains: 22 Chain: "C" Number of atoms: 2259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2259 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 24, 'TRANS': 257} Chain: "D" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1432 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 16, 'TRANS': 161} Chain: "A" Number of atoms: 2355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2355 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 280} Chain: "G" Number of atoms: 2259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2259 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 24, 'TRANS': 257} Chain: "H" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1432 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 16, 'TRANS': 161} Chain: "E" Number of atoms: 2355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2355 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 280} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.93, per 1000 atoms: 0.23 Number of scatterers: 12540 At special positions: 0 Unit cell: (196.94, 156.52, 101.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 2368 8.00 N 2156 7.00 C 7970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 127 " distance=2.04 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 143 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 116 " - pdb=" SG CYS G 127 " distance=2.04 Simple disulfide: pdb=" SG CYS G 154 " - pdb=" SG CYS G 164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 116 " distance=2.03 Simple disulfide: pdb=" SG CYS E 143 " - pdb=" SG CYS E 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 184 " - pdb=" SG CYS E 195 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG F 1 " - " NAG F 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 501 " - " ASN A 168 " " NAG A 502 " - " ASN A 292 " " NAG B 1 " - " ASN C 190 " " NAG E 501 " - " ASN E 168 " " NAG E 502 " - " ASN E 292 " " NAG F 1 " - " ASN C 70 " " NAG I 1 " - " ASN C 60 " " NAG J 1 " - " ASN C 142 " " NAG K 1 " - " ASN A 92 " " NAG L 1 " - " ASN A 104 " " NAG M 1 " - " ASN A 140 " " NAG N 1 " - " ASN G 190 " " NAG O 1 " - " ASN G 70 " " NAG P 1 " - " ASN G 60 " " NAG Q 1 " - " ASN G 142 " " NAG R 1 " - " ASN E 92 " " NAG S 1 " - " ASN E 104 " " NAG T 1 " - " ASN E 140 " Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 515.0 milliseconds 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2860 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 26 sheets defined 19.5% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.560A pdb=" N HIS C 83 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER C 84 " --> pdb=" O LEU C 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 80 through 84' Processing helix chain 'D' and resid 35 through 66 removed outlier: 4.252A pdb=" N SER D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE D 40 " --> pdb=" O PRO D 36 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 90 through 97 removed outlier: 3.625A pdb=" N LEU D 97 " --> pdb=" O VAL D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 120 Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 126 through 154 Processing helix chain 'D' and resid 176 through 208 Processing helix chain 'A' and resid 69 through 74 removed outlier: 3.819A pdb=" N LEU A 74 " --> pdb=" O THR A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'G' and resid 65 through 67 No H-bonds generated for 'chain 'G' and resid 65 through 67' Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.526A pdb=" N HIS G 83 " --> pdb=" O GLU G 80 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER G 84 " --> pdb=" O LEU G 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 80 through 84' Processing helix chain 'H' and resid 35 through 66 removed outlier: 4.251A pdb=" N SER H 39 " --> pdb=" O GLY H 35 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE H 40 " --> pdb=" O PRO H 36 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN H 41 " --> pdb=" O GLY H 37 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY H 66 " --> pdb=" O LEU H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 71 Processing helix chain 'H' and resid 90 through 97 removed outlier: 3.637A pdb=" N LEU H 97 " --> pdb=" O VAL H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 120 Processing helix chain 'H' and resid 121 through 123 No H-bonds generated for 'chain 'H' and resid 121 through 123' Processing helix chain 'H' and resid 126 through 154 Processing helix chain 'H' and resid 176 through 208 Processing helix chain 'E' and resid 69 through 74 removed outlier: 3.948A pdb=" N LEU E 74 " --> pdb=" O THR E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 231 Processing sheet with id=AA1, first strand: chain 'C' and resid 32 through 36 removed outlier: 6.379A pdb=" N HIS C 32 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N HIS C 104 " --> pdb=" O HIS C 32 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLN C 34 " --> pdb=" O HIS C 104 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU C 97 " --> pdb=" O HIS C 91 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N HIS C 91 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N HIS C 99 " --> pdb=" O CYS C 89 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS C 89 " --> pdb=" O HIS C 99 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 101 " --> pdb=" O TYR C 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 41 through 45 removed outlier: 3.602A pdb=" N VAL C 42 " --> pdb=" O LEU C 76 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 113 through 114 removed outlier: 3.758A pdb=" N HIS C 130 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 140 through 145 removed outlier: 3.684A pdb=" N THR C 144 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN C 190 " --> pdb=" O VAL C 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 211 through 214 removed outlier: 3.657A pdb=" N VAL C 224 " --> pdb=" O HIS C 265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 255 through 258 removed outlier: 3.544A pdb=" N GLN C 255 " --> pdb=" O TYR C 246 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR C 246 " --> pdb=" O GLN C 255 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE C 243 " --> pdb=" O ALA C 281 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 42 through 44 removed outlier: 3.589A pdb=" N VAL A 42 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 61 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 91 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 49 through 51 removed outlier: 3.665A pdb=" N GLY A 132 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A 125 " --> pdb=" O CYS A 116 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 186 through 187 removed outlier: 4.008A pdb=" N GLU A 186 " --> pdb=" O HIS A 196 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR A 156 " --> pdb=" O ASN A 140 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ASN A 140 " --> pdb=" O THR A 156 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N THR A 234 " --> pdb=" O CYS A 143 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER A 145 " --> pdb=" O THR A 234 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 182 through 183 Processing sheet with id=AB2, first strand: chain 'A' and resid 182 through 183 Processing sheet with id=AB3, first strand: chain 'A' and resid 242 through 244 Processing sheet with id=AB4, first strand: chain 'A' and resid 284 through 286 removed outlier: 3.540A pdb=" N PHE A 308 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 32 through 36 removed outlier: 6.402A pdb=" N HIS G 32 " --> pdb=" O LEU G 102 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N HIS G 104 " --> pdb=" O HIS G 32 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLN G 34 " --> pdb=" O HIS G 104 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LEU G 97 " --> pdb=" O HIS G 91 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N HIS G 91 " --> pdb=" O LEU G 97 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS G 99 " --> pdb=" O CYS G 89 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 41 through 45 removed outlier: 3.508A pdb=" N VAL G 42 " --> pdb=" O LEU G 76 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 113 through 114 removed outlier: 3.756A pdb=" N HIS G 130 " --> pdb=" O VAL G 113 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 140 through 145 removed outlier: 3.685A pdb=" N THR G 144 " --> pdb=" O SER G 180 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN G 190 " --> pdb=" O VAL G 183 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 211 through 214 removed outlier: 3.731A pdb=" N VAL G 224 " --> pdb=" O HIS G 265 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 255 through 258 removed outlier: 3.689A pdb=" N GLN G 255 " --> pdb=" O TYR G 246 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR G 246 " --> pdb=" O GLN G 255 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL G 257 " --> pdb=" O LEU G 244 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE G 243 " --> pdb=" O ALA G 281 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 42 through 44 removed outlier: 3.572A pdb=" N VAL E 42 " --> pdb=" O SER E 61 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER E 61 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N THR E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU E 91 " --> pdb=" O THR E 95 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 49 through 51 removed outlier: 3.665A pdb=" N GLY E 132 " --> pdb=" O LEU E 50 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA E 125 " --> pdb=" O CYS E 116 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 186 through 187 removed outlier: 4.002A pdb=" N GLU E 186 " --> pdb=" O HIS E 196 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR E 156 " --> pdb=" O ASN E 140 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ASN E 140 " --> pdb=" O THR E 156 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N THR E 234 " --> pdb=" O CYS E 143 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER E 145 " --> pdb=" O THR E 234 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 182 through 183 Processing sheet with id=AC6, first strand: chain 'E' and resid 182 through 183 Processing sheet with id=AC7, first strand: chain 'E' and resid 242 through 244 Processing sheet with id=AC8, first strand: chain 'E' and resid 284 through 286 removed outlier: 3.538A pdb=" N PHE E 308 " --> pdb=" O ARG E 277 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1167 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: 1.78 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4000 1.35 - 1.47: 3228 1.47 - 1.59: 5630 1.59 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 12916 Sorted by residual: bond pdb=" C1 NAG O 1 " pdb=" O5 NAG O 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.93e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.88e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.22e+00 ... (remaining 12911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 17046 1.38 - 2.76: 532 2.76 - 4.15: 68 4.15 - 5.53: 14 5.53 - 6.91: 4 Bond angle restraints: 17664 Sorted by residual: angle pdb=" C GLY H 164 " pdb=" N THR H 165 " pdb=" CA THR H 165 " ideal model delta sigma weight residual 121.54 126.74 -5.20 1.91e+00 2.74e-01 7.41e+00 angle pdb=" C GLY D 164 " pdb=" N THR D 165 " pdb=" CA THR D 165 " ideal model delta sigma weight residual 121.54 126.71 -5.17 1.91e+00 2.74e-01 7.33e+00 angle pdb=" C HIS C 25 " pdb=" N SER C 26 " pdb=" CA SER C 26 " ideal model delta sigma weight residual 120.51 123.74 -3.23 1.45e+00 4.76e-01 4.95e+00 angle pdb=" C LEU C 251 " pdb=" N ASP C 252 " pdb=" CA ASP C 252 " ideal model delta sigma weight residual 122.46 125.52 -3.06 1.41e+00 5.03e-01 4.70e+00 angle pdb=" C LEU G 251 " pdb=" N ASP G 252 " pdb=" CA ASP G 252 " ideal model delta sigma weight residual 121.54 125.27 -3.73 1.91e+00 2.74e-01 3.81e+00 ... (remaining 17659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 7488 17.59 - 35.18: 438 35.18 - 52.76: 116 52.76 - 70.35: 23 70.35 - 87.94: 15 Dihedral angle restraints: 8080 sinusoidal: 3642 harmonic: 4438 Sorted by residual: dihedral pdb=" CB CYS G 46 " pdb=" SG CYS G 46 " pdb=" SG CYS G 89 " pdb=" CB CYS G 89 " ideal model delta sinusoidal sigma weight residual 93.00 43.91 49.09 1 1.00e+01 1.00e-02 3.31e+01 dihedral pdb=" CB CYS C 46 " pdb=" SG CYS C 46 " pdb=" SG CYS C 89 " pdb=" CB CYS C 89 " ideal model delta sinusoidal sigma weight residual 93.00 45.65 47.35 1 1.00e+01 1.00e-02 3.10e+01 dihedral pdb=" CB CYS C 116 " pdb=" SG CYS C 116 " pdb=" SG CYS C 127 " pdb=" CB CYS C 127 " ideal model delta sinusoidal sigma weight residual 93.00 54.73 38.27 1 1.00e+01 1.00e-02 2.06e+01 ... (remaining 8077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1627 0.046 - 0.091: 254 0.091 - 0.137: 139 0.137 - 0.182: 0 0.182 - 0.228: 2 Chirality restraints: 2022 Sorted by residual: chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN E 104 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN A 104 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA VAL E 290 " pdb=" N VAL E 290 " pdb=" C VAL E 290 " pdb=" CB VAL E 290 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 2019 not shown) Planarity restraints: 2246 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 66 " 0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO D 67 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 66 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.38e+00 pdb=" N PRO H 67 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO H 67 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 67 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 66 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.07e+00 pdb=" N PRO E 67 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO E 67 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 67 " -0.020 5.00e-02 4.00e+02 ... (remaining 2243 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3481 2.81 - 3.33: 10249 3.33 - 3.86: 19416 3.86 - 4.38: 20534 4.38 - 4.90: 37340 Nonbonded interactions: 91020 Sorted by model distance: nonbonded pdb=" OD1 ASP A 120 " pdb=" OG SER A 122 " model vdw 2.291 3.040 nonbonded pdb=" OD1 ASP G 197 " pdb=" OG1 THR G 200 " model vdw 2.329 3.040 nonbonded pdb=" OD1 ASP E 120 " pdb=" OG SER E 122 " model vdw 2.334 3.040 nonbonded pdb=" NH2 ARG C 245 " pdb=" OE1 GLN C 279 " model vdw 2.359 3.120 nonbonded pdb=" NH2 ARG G 245 " pdb=" OE1 GLN G 279 " model vdw 2.360 3.120 ... (remaining 91015 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.540 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.990 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 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 : 0.003 0.044 12960 Z= 0.156 Angle : 0.531 6.910 17784 Z= 0.266 Chirality : 0.041 0.228 2022 Planarity : 0.004 0.047 2228 Dihedral : 12.375 87.938 5184 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.06 % Allowed : 8.45 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.21), residues: 1514 helix: 2.16 (0.30), residues: 250 sheet: -0.29 (0.25), residues: 456 loop : -2.42 (0.19), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 213 TYR 0.005 0.000 TYR C 136 PHE 0.004 0.000 PHE H 74 TRP 0.003 0.000 TRP G 254 HIS 0.004 0.000 HIS G 83 Details of bonding type rmsd covalent geometry : bond 0.00320 (12916) covalent geometry : angle 0.52760 (17664) SS BOND : bond 0.00293 ( 12) SS BOND : angle 0.85675 ( 24) hydrogen bonds : bond 0.21798 ( 419) hydrogen bonds : angle 7.12612 ( 1167) link_BETA1-4 : bond 0.00351 ( 14) link_BETA1-4 : angle 0.89759 ( 42) link_NAG-ASN : bond 0.00289 ( 18) link_NAG-ASN : angle 0.89087 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 206 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 83 HIS cc_start: 0.4518 (m-70) cc_final: 0.4266 (m-70) REVERT: C 104 HIS cc_start: 0.7099 (m-70) cc_final: 0.6777 (m-70) REVERT: C 226 TRP cc_start: 0.8826 (p90) cc_final: 0.8561 (p90) REVERT: D 117 LEU cc_start: 0.7648 (tt) cc_final: 0.7446 (tt) REVERT: D 209 MET cc_start: 0.5983 (tpp) cc_final: 0.5263 (mtt) REVERT: A 57 LEU cc_start: 0.7672 (tp) cc_final: 0.7432 (mp) REVERT: G 83 HIS cc_start: 0.4061 (m170) cc_final: 0.3807 (m-70) REVERT: G 226 TRP cc_start: 0.8708 (p90) cc_final: 0.8409 (p90) REVERT: H 209 MET cc_start: 0.6323 (tpp) cc_final: 0.5666 (mtt) REVERT: E 57 LEU cc_start: 0.7761 (tp) cc_final: 0.7393 (mp) outliers start: 14 outliers final: 6 residues processed: 217 average time/residue: 0.1272 time to fit residues: 38.0470 Evaluate side-chains 142 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 136 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 282 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.0050 chunk 149 optimal weight: 4.9990 overall best weight: 1.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN C 83 HIS D 105 GLN A 113 ASN A 196 HIS G 100 GLN G 265 HIS G 285 ASN H 105 GLN H 106 ASN H 175 HIS E 113 ASN E 196 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.189851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.140313 restraints weight = 17990.317| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 4.28 r_work: 0.3528 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12960 Z= 0.157 Angle : 0.653 12.788 17784 Z= 0.311 Chirality : 0.046 0.387 2022 Planarity : 0.005 0.051 2228 Dihedral : 5.441 56.489 2342 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.94 % Allowed : 13.42 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.22), residues: 1514 helix: 3.12 (0.32), residues: 246 sheet: 0.28 (0.25), residues: 458 loop : -1.92 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 297 TYR 0.017 0.002 TYR H 49 PHE 0.015 0.002 PHE H 185 TRP 0.017 0.001 TRP C 57 HIS 0.005 0.001 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00356 (12916) covalent geometry : angle 0.62466 (17664) SS BOND : bond 0.00393 ( 12) SS BOND : angle 1.57200 ( 24) hydrogen bonds : bond 0.05000 ( 419) hydrogen bonds : angle 4.92026 ( 1167) link_BETA1-4 : bond 0.00417 ( 14) link_BETA1-4 : angle 1.93462 ( 42) link_NAG-ASN : bond 0.00384 ( 18) link_NAG-ASN : angle 2.99774 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.7315 (m-70) cc_final: 0.6958 (m-70) REVERT: C 117 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7955 (ptt-90) REVERT: C 226 TRP cc_start: 0.8854 (p90) cc_final: 0.8412 (p90) REVERT: D 201 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7167 (m-30) REVERT: D 209 MET cc_start: 0.6102 (tpp) cc_final: 0.5443 (mtt) REVERT: A 57 LEU cc_start: 0.8112 (tp) cc_final: 0.7773 (mp) REVERT: A 340 ARG cc_start: 0.8148 (ptt90) cc_final: 0.7786 (ptt-90) REVERT: G 103 LEU cc_start: 0.5171 (pp) cc_final: 0.4706 (mm) REVERT: G 104 HIS cc_start: 0.7099 (m-70) cc_final: 0.6626 (m-70) REVERT: H 201 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7179 (m-30) REVERT: H 209 MET cc_start: 0.6371 (tpp) cc_final: 0.5935 (mtt) REVERT: E 57 LEU cc_start: 0.8187 (tp) cc_final: 0.7744 (mp) outliers start: 39 outliers final: 17 residues processed: 164 average time/residue: 0.0851 time to fit residues: 22.3506 Evaluate side-chains 139 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 175 HIS Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 189 HIS Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 285 ASN Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 282 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 147 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 106 ASN G 83 HIS H 53 GLN ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.180148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.128657 restraints weight = 17566.472| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 3.63 r_work: 0.3388 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12960 Z= 0.191 Angle : 0.692 13.349 17784 Z= 0.330 Chirality : 0.047 0.307 2022 Planarity : 0.005 0.065 2228 Dihedral : 5.567 59.980 2340 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.32 % Allowed : 14.78 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.22), residues: 1514 helix: 3.10 (0.31), residues: 244 sheet: 0.52 (0.25), residues: 450 loop : -1.63 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 297 TYR 0.014 0.002 TYR D 110 PHE 0.024 0.002 PHE A 266 TRP 0.008 0.001 TRP A 210 HIS 0.006 0.001 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00447 (12916) covalent geometry : angle 0.65770 (17664) SS BOND : bond 0.00308 ( 12) SS BOND : angle 1.28095 ( 24) hydrogen bonds : bond 0.07174 ( 419) hydrogen bonds : angle 4.83933 ( 1167) link_BETA1-4 : bond 0.00374 ( 14) link_BETA1-4 : angle 2.11920 ( 42) link_NAG-ASN : bond 0.00539 ( 18) link_NAG-ASN : angle 3.45810 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 111 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.7301 (m-70) cc_final: 0.7066 (m-70) REVERT: C 117 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7869 (ptt-90) REVERT: D 209 MET cc_start: 0.6437 (tpp) cc_final: 0.5983 (mtt) REVERT: A 57 LEU cc_start: 0.8320 (tp) cc_final: 0.8026 (mp) REVERT: A 268 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7774 (p90) REVERT: A 340 ARG cc_start: 0.8029 (ptt90) cc_final: 0.7725 (ptt-90) REVERT: G 44 LEU cc_start: 0.6045 (OUTLIER) cc_final: 0.5181 (mm) REVERT: G 74 LEU cc_start: 0.7172 (mt) cc_final: 0.6885 (mp) REVERT: G 190 ASN cc_start: 0.6810 (OUTLIER) cc_final: 0.6605 (m-40) REVERT: G 246 TYR cc_start: 0.6254 (p90) cc_final: 0.5822 (p90) REVERT: H 201 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.7822 (m-30) REVERT: H 209 MET cc_start: 0.6643 (tpp) cc_final: 0.6331 (mtt) REVERT: E 57 LEU cc_start: 0.8349 (tp) cc_final: 0.7953 (mp) REVERT: E 268 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7779 (p90) outliers start: 44 outliers final: 26 residues processed: 145 average time/residue: 0.0898 time to fit residues: 20.5151 Evaluate side-chains 134 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 190 ASN Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 268 PHE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 314 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 74 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 71 optimal weight: 0.0970 chunk 104 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 285 ASN G 83 HIS H 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.180801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.128652 restraints weight = 17655.629| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 3.81 r_work: 0.3388 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12960 Z= 0.139 Angle : 0.616 14.080 17784 Z= 0.295 Chirality : 0.045 0.521 2022 Planarity : 0.004 0.063 2228 Dihedral : 5.387 56.545 2340 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.87 % Allowed : 16.74 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.22), residues: 1514 helix: 3.37 (0.31), residues: 244 sheet: 0.63 (0.24), residues: 470 loop : -1.50 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 95 TYR 0.009 0.001 TYR D 110 PHE 0.020 0.002 PHE A 266 TRP 0.013 0.001 TRP D 196 HIS 0.004 0.001 HIS G 83 Details of bonding type rmsd covalent geometry : bond 0.00325 (12916) covalent geometry : angle 0.58344 (17664) SS BOND : bond 0.00337 ( 12) SS BOND : angle 1.20608 ( 24) hydrogen bonds : bond 0.06103 ( 419) hydrogen bonds : angle 4.54881 ( 1167) link_BETA1-4 : bond 0.00294 ( 14) link_BETA1-4 : angle 1.63231 ( 42) link_NAG-ASN : bond 0.00456 ( 18) link_NAG-ASN : angle 3.32306 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 108 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 HIS cc_start: 0.7254 (m-70) cc_final: 0.7020 (m-70) REVERT: C 117 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8377 (ttt-90) REVERT: D 201 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.7710 (m-30) REVERT: D 209 MET cc_start: 0.6399 (tpp) cc_final: 0.6009 (mtt) REVERT: A 57 LEU cc_start: 0.8332 (tp) cc_final: 0.7994 (mp) REVERT: A 340 ARG cc_start: 0.7971 (ptt90) cc_final: 0.7549 (ptt-90) REVERT: G 103 LEU cc_start: 0.4974 (pp) cc_final: 0.4409 (mm) REVERT: G 190 ASN cc_start: 0.6907 (OUTLIER) cc_final: 0.6626 (m-40) REVERT: G 246 TYR cc_start: 0.6200 (p90) cc_final: 0.5703 (p90) REVERT: H 201 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.7738 (m-30) REVERT: H 209 MET cc_start: 0.6682 (tpp) cc_final: 0.6326 (mtt) REVERT: E 57 LEU cc_start: 0.8413 (tp) cc_final: 0.7979 (mp) outliers start: 38 outliers final: 18 residues processed: 137 average time/residue: 0.0882 time to fit residues: 19.1123 Evaluate side-chains 123 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 190 ASN Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 282 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 14 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 56 optimal weight: 0.0770 chunk 133 optimal weight: 0.9980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 285 ASN G 83 HIS G 285 ASN H 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.181221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.129811 restraints weight = 17500.159| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 3.58 r_work: 0.3402 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12960 Z= 0.124 Angle : 0.603 18.360 17784 Z= 0.288 Chirality : 0.045 0.421 2022 Planarity : 0.004 0.060 2228 Dihedral : 5.256 52.900 2340 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 4.00 % Allowed : 16.37 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.22), residues: 1514 helix: 3.49 (0.31), residues: 244 sheet: 0.68 (0.25), residues: 452 loop : -1.37 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 297 TYR 0.013 0.001 TYR C 87 PHE 0.016 0.002 PHE A 266 TRP 0.014 0.001 TRP H 196 HIS 0.003 0.001 HIS D 52 Details of bonding type rmsd covalent geometry : bond 0.00287 (12916) covalent geometry : angle 0.56452 (17664) SS BOND : bond 0.00418 ( 12) SS BOND : angle 1.18296 ( 24) hydrogen bonds : bond 0.05615 ( 419) hydrogen bonds : angle 4.40559 ( 1167) link_BETA1-4 : bond 0.00406 ( 14) link_BETA1-4 : angle 1.44035 ( 42) link_NAG-ASN : bond 0.00609 ( 18) link_NAG-ASN : angle 3.65555 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 109 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 117 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8384 (ttt-90) REVERT: C 234 ASP cc_start: 0.7541 (t0) cc_final: 0.7335 (t0) REVERT: D 201 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.7664 (m-30) REVERT: D 209 MET cc_start: 0.6530 (tpp) cc_final: 0.6100 (mtt) REVERT: A 57 LEU cc_start: 0.8350 (tp) cc_final: 0.8000 (mp) REVERT: A 340 ARG cc_start: 0.7886 (ptt90) cc_final: 0.7551 (ptt-90) REVERT: G 44 LEU cc_start: 0.6078 (OUTLIER) cc_final: 0.5151 (mm) REVERT: G 103 LEU cc_start: 0.4986 (pp) cc_final: 0.4505 (mm) REVERT: G 190 ASN cc_start: 0.6933 (OUTLIER) cc_final: 0.6671 (m-40) REVERT: G 246 TYR cc_start: 0.6046 (p90) cc_final: 0.5686 (p90) REVERT: H 201 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.7719 (m-30) REVERT: H 209 MET cc_start: 0.6667 (tpp) cc_final: 0.6365 (mtt) REVERT: E 57 LEU cc_start: 0.8432 (tp) cc_final: 0.7993 (mp) outliers start: 53 outliers final: 29 residues processed: 153 average time/residue: 0.0840 time to fit residues: 20.6713 Evaluate side-chains 137 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 190 ASN Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 285 ASN Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 314 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 30 optimal weight: 0.4980 chunk 29 optimal weight: 0.5980 chunk 125 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 2 optimal weight: 0.0970 chunk 142 optimal weight: 0.1980 chunk 28 optimal weight: 0.8980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 285 ASN G 83 HIS H 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.182060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.130883 restraints weight = 17349.798| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 3.64 r_work: 0.3419 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12960 Z= 0.111 Angle : 0.601 14.887 17784 Z= 0.285 Chirality : 0.045 0.463 2022 Planarity : 0.004 0.057 2228 Dihedral : 5.154 48.472 2340 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.32 % Allowed : 17.35 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.22), residues: 1514 helix: 3.62 (0.31), residues: 244 sheet: 0.75 (0.25), residues: 452 loop : -1.28 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 95 TYR 0.013 0.001 TYR C 87 PHE 0.013 0.001 PHE A 266 TRP 0.017 0.001 TRP H 196 HIS 0.002 0.000 HIS D 52 Details of bonding type rmsd covalent geometry : bond 0.00251 (12916) covalent geometry : angle 0.55708 (17664) SS BOND : bond 0.00351 ( 12) SS BOND : angle 1.03018 ( 24) hydrogen bonds : bond 0.04999 ( 419) hydrogen bonds : angle 4.22946 ( 1167) link_BETA1-4 : bond 0.00348 ( 14) link_BETA1-4 : angle 1.33583 ( 42) link_NAG-ASN : bond 0.00406 ( 18) link_NAG-ASN : angle 3.94674 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 109 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 117 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8409 (ttt-90) REVERT: C 234 ASP cc_start: 0.7586 (t0) cc_final: 0.7331 (t0) REVERT: D 201 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.7637 (m-30) REVERT: D 209 MET cc_start: 0.6522 (tpp) cc_final: 0.5596 (mtt) REVERT: A 57 LEU cc_start: 0.8348 (tp) cc_final: 0.7995 (mp) REVERT: A 340 ARG cc_start: 0.7865 (ptt90) cc_final: 0.7535 (ptt-90) REVERT: G 44 LEU cc_start: 0.6167 (OUTLIER) cc_final: 0.5260 (mm) REVERT: G 103 LEU cc_start: 0.5244 (pp) cc_final: 0.4734 (mm) REVERT: G 246 TYR cc_start: 0.6040 (p90) cc_final: 0.5677 (p90) REVERT: H 201 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.7656 (m-30) REVERT: H 209 MET cc_start: 0.6625 (tpp) cc_final: 0.6290 (mtt) REVERT: E 57 LEU cc_start: 0.8406 (tp) cc_final: 0.7954 (mp) outliers start: 44 outliers final: 25 residues processed: 143 average time/residue: 0.0845 time to fit residues: 19.2481 Evaluate side-chains 132 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 314 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 112 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 139 optimal weight: 0.4980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 83 HIS ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 256 HIS G 285 ASN H 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.180269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.129287 restraints weight = 17282.656| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 3.40 r_work: 0.3394 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12960 Z= 0.135 Angle : 0.614 13.355 17784 Z= 0.294 Chirality : 0.046 0.567 2022 Planarity : 0.004 0.059 2228 Dihedral : 5.158 51.761 2340 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.02 % Allowed : 17.42 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.22), residues: 1514 helix: 3.19 (0.32), residues: 256 sheet: 0.76 (0.25), residues: 448 loop : -1.26 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 95 TYR 0.011 0.001 TYR C 87 PHE 0.013 0.002 PHE A 266 TRP 0.019 0.001 TRP H 196 HIS 0.003 0.001 HIS D 52 Details of bonding type rmsd covalent geometry : bond 0.00319 (12916) covalent geometry : angle 0.57269 (17664) SS BOND : bond 0.00386 ( 12) SS BOND : angle 1.21405 ( 24) hydrogen bonds : bond 0.05563 ( 419) hydrogen bonds : angle 4.24358 ( 1167) link_BETA1-4 : bond 0.00437 ( 14) link_BETA1-4 : angle 1.30681 ( 42) link_NAG-ASN : bond 0.00464 ( 18) link_NAG-ASN : angle 3.85434 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 114 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 117 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7981 (ptt-90) REVERT: C 234 ASP cc_start: 0.7693 (t0) cc_final: 0.7437 (t0) REVERT: D 201 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.7667 (m-30) REVERT: D 209 MET cc_start: 0.6583 (tpp) cc_final: 0.5687 (mtt) REVERT: A 57 LEU cc_start: 0.8355 (tp) cc_final: 0.7998 (mp) REVERT: A 150 ASP cc_start: 0.8820 (p0) cc_final: 0.8561 (p0) REVERT: A 340 ARG cc_start: 0.7847 (ptt90) cc_final: 0.7524 (ptt-90) REVERT: G 44 LEU cc_start: 0.6103 (OUTLIER) cc_final: 0.5182 (mm) REVERT: G 103 LEU cc_start: 0.5330 (pp) cc_final: 0.4787 (mm) REVERT: G 246 TYR cc_start: 0.6055 (p90) cc_final: 0.5660 (p90) REVERT: H 201 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.7676 (m-30) REVERT: H 209 MET cc_start: 0.6622 (tpp) cc_final: 0.6322 (mtt) REVERT: E 57 LEU cc_start: 0.8432 (tp) cc_final: 0.7990 (mp) outliers start: 40 outliers final: 28 residues processed: 145 average time/residue: 0.0815 time to fit residues: 19.0138 Evaluate side-chains 136 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 87 TYR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 314 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 49 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 21 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 142 optimal weight: 0.0170 chunk 113 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 285 ASN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 ASN H 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.178656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.126780 restraints weight = 17479.875| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.57 r_work: 0.3382 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12960 Z= 0.136 Angle : 0.630 13.247 17784 Z= 0.302 Chirality : 0.047 0.499 2022 Planarity : 0.004 0.058 2228 Dihedral : 5.227 52.146 2340 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.39 % Allowed : 17.57 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.22), residues: 1514 helix: 3.17 (0.32), residues: 256 sheet: 0.74 (0.25), residues: 446 loop : -1.23 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 95 TYR 0.009 0.001 TYR H 110 PHE 0.016 0.002 PHE A 266 TRP 0.021 0.001 TRP H 196 HIS 0.003 0.001 HIS D 52 Details of bonding type rmsd covalent geometry : bond 0.00322 (12916) covalent geometry : angle 0.59091 (17664) SS BOND : bond 0.00388 ( 12) SS BOND : angle 1.19993 ( 24) hydrogen bonds : bond 0.05634 ( 419) hydrogen bonds : angle 4.22112 ( 1167) link_BETA1-4 : bond 0.00455 ( 14) link_BETA1-4 : angle 1.35909 ( 42) link_NAG-ASN : bond 0.00484 ( 18) link_NAG-ASN : angle 3.80493 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 112 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 117 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8044 (ptt-90) REVERT: C 234 ASP cc_start: 0.7834 (t0) cc_final: 0.7518 (t0) REVERT: D 201 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.7851 (m-30) REVERT: D 209 MET cc_start: 0.6567 (tpp) cc_final: 0.5615 (mtt) REVERT: A 57 LEU cc_start: 0.8405 (tp) cc_final: 0.8055 (mp) REVERT: A 150 ASP cc_start: 0.8942 (p0) cc_final: 0.8693 (p0) REVERT: G 44 LEU cc_start: 0.6307 (OUTLIER) cc_final: 0.5465 (mm) REVERT: G 103 LEU cc_start: 0.5370 (pp) cc_final: 0.4811 (mm) REVERT: G 246 TYR cc_start: 0.6051 (p90) cc_final: 0.5708 (p90) REVERT: H 201 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.7829 (m-30) REVERT: H 209 MET cc_start: 0.6634 (tpp) cc_final: 0.6308 (mtt) REVERT: E 57 LEU cc_start: 0.8473 (tp) cc_final: 0.8011 (mp) outliers start: 45 outliers final: 31 residues processed: 149 average time/residue: 0.0820 time to fit residues: 19.5765 Evaluate side-chains 136 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 285 ASN Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 314 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 149 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 33 optimal weight: 0.0570 chunk 78 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 21 optimal weight: 0.0770 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN H 175 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.180799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.129516 restraints weight = 17365.012| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 3.50 r_work: 0.3404 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12960 Z= 0.117 Angle : 0.620 16.216 17784 Z= 0.296 Chirality : 0.048 0.761 2022 Planarity : 0.004 0.055 2228 Dihedral : 5.255 58.827 2340 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.87 % Allowed : 18.25 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.22), residues: 1514 helix: 3.27 (0.32), residues: 256 sheet: 0.80 (0.25), residues: 446 loop : -1.15 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 95 TYR 0.009 0.001 TYR G 276 PHE 0.012 0.001 PHE A 266 TRP 0.024 0.001 TRP H 196 HIS 0.003 0.000 HIS D 52 Details of bonding type rmsd covalent geometry : bond 0.00268 (12916) covalent geometry : angle 0.58353 (17664) SS BOND : bond 0.00382 ( 12) SS BOND : angle 1.07809 ( 24) hydrogen bonds : bond 0.05079 ( 419) hydrogen bonds : angle 4.13228 ( 1167) link_BETA1-4 : bond 0.00416 ( 14) link_BETA1-4 : angle 1.17330 ( 42) link_NAG-ASN : bond 0.00369 ( 18) link_NAG-ASN : angle 3.70608 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 107 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 234 ASP cc_start: 0.7699 (t0) cc_final: 0.7367 (t0) REVERT: D 201 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.7610 (m-30) REVERT: D 209 MET cc_start: 0.6612 (tpp) cc_final: 0.5648 (mtt) REVERT: A 57 LEU cc_start: 0.8352 (tp) cc_final: 0.8009 (mp) REVERT: A 150 ASP cc_start: 0.8770 (p0) cc_final: 0.8504 (p0) REVERT: G 44 LEU cc_start: 0.6032 (OUTLIER) cc_final: 0.5208 (mm) REVERT: G 103 LEU cc_start: 0.5309 (pp) cc_final: 0.4761 (mm) REVERT: G 246 TYR cc_start: 0.5918 (p90) cc_final: 0.5594 (p90) REVERT: H 201 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.7648 (m-30) REVERT: H 209 MET cc_start: 0.6588 (tpp) cc_final: 0.6273 (mtt) REVERT: E 57 LEU cc_start: 0.8404 (tp) cc_final: 0.7936 (mp) outliers start: 38 outliers final: 29 residues processed: 141 average time/residue: 0.0790 time to fit residues: 18.1280 Evaluate side-chains 134 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 87 TYR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 314 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 68 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 88 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 285 ASN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.174980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.122927 restraints weight = 17480.948| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 3.62 r_work: 0.3329 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12960 Z= 0.177 Angle : 0.696 16.182 17784 Z= 0.335 Chirality : 0.052 0.757 2022 Planarity : 0.005 0.064 2228 Dihedral : 5.667 56.526 2340 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.87 % Allowed : 18.33 % Favored : 78.81 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.22), residues: 1514 helix: 3.01 (0.32), residues: 256 sheet: 0.70 (0.24), residues: 474 loop : -1.40 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 95 TYR 0.015 0.002 TYR H 110 PHE 0.017 0.002 PHE A 266 TRP 0.022 0.001 TRP H 196 HIS 0.004 0.001 HIS H 52 Details of bonding type rmsd covalent geometry : bond 0.00423 (12916) covalent geometry : angle 0.65396 (17664) SS BOND : bond 0.00380 ( 12) SS BOND : angle 1.35109 ( 24) hydrogen bonds : bond 0.06873 ( 419) hydrogen bonds : angle 4.38939 ( 1167) link_BETA1-4 : bond 0.00491 ( 14) link_BETA1-4 : angle 1.36979 ( 42) link_NAG-ASN : bond 0.00680 ( 18) link_NAG-ASN : angle 4.16383 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3028 Ramachandran restraints generated. 1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 101 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 234 ASP cc_start: 0.7903 (t0) cc_final: 0.7556 (t0) REVERT: C 260 SER cc_start: 0.8401 (p) cc_final: 0.8123 (t) REVERT: D 209 MET cc_start: 0.6618 (tpp) cc_final: 0.6181 (mtt) REVERT: A 57 LEU cc_start: 0.8410 (tp) cc_final: 0.8083 (mp) REVERT: A 150 ASP cc_start: 0.8962 (p0) cc_final: 0.8733 (p0) REVERT: G 44 LEU cc_start: 0.6253 (OUTLIER) cc_final: 0.5528 (mm) REVERT: G 208 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7445 (mp0) REVERT: G 246 TYR cc_start: 0.5932 (p90) cc_final: 0.5570 (p90) REVERT: H 201 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.7954 (m-30) REVERT: H 209 MET cc_start: 0.6694 (tpp) cc_final: 0.6390 (mtt) REVERT: E 57 LEU cc_start: 0.8483 (tp) cc_final: 0.8073 (mp) outliers start: 38 outliers final: 31 residues processed: 136 average time/residue: 0.0824 time to fit residues: 18.3360 Evaluate side-chains 130 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 87 TYR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 190 ASN Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 285 ASN Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 201 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 195 CYS Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 314 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 129 optimal weight: 0.7980 chunk 67 optimal weight: 0.3980 chunk 57 optimal weight: 0.0040 chunk 98 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 100 GLN ** 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 = 0.4120 r_free = 0.4120 target = 0.176289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.124815 restraints weight = 17336.390| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 3.50 r_work: 0.3328 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 12960 Z= 0.202 Angle : 1.103 59.157 17784 Z= 0.643 Chirality : 0.053 0.751 2022 Planarity : 0.005 0.064 2228 Dihedral : 5.719 56.317 2340 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 2.64 % Allowed : 18.55 % Favored : 78.81 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.22), residues: 1514 helix: 2.99 (0.31), residues: 256 sheet: 0.68 (0.24), residues: 474 loop : -1.41 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 89 TYR 0.013 0.001 TYR H 110 PHE 0.014 0.002 PHE G 243 TRP 0.019 0.001 TRP H 196 HIS 0.004 0.001 HIS H 52 Details of bonding type rmsd covalent geometry : bond 0.00414 (12916) covalent geometry : angle 1.07845 (17664) SS BOND : bond 0.00389 ( 12) SS BOND : angle 1.28720 ( 24) hydrogen bonds : bond 0.06707 ( 419) hydrogen bonds : angle 4.38317 ( 1167) link_BETA1-4 : bond 0.00477 ( 14) link_BETA1-4 : angle 1.31651 ( 42) link_NAG-ASN : bond 0.00480 ( 18) link_NAG-ASN : angle 4.25273 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3392.01 seconds wall clock time: 58 minutes 35.44 seconds (3515.44 seconds total)