Starting phenix.real_space_refine on Thu Sep 18 02:22:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zui_60484/09_2025/8zui_60484.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zui_60484/09_2025/8zui_60484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zui_60484/09_2025/8zui_60484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zui_60484/09_2025/8zui_60484.map" model { file = "/net/cci-nas-00/data/ceres_data/8zui_60484/09_2025/8zui_60484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zui_60484/09_2025/8zui_60484.cif" } resolution = 2.56 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= 0.001 sd= 0.023 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 144 5.16 5 C 8318 2.51 5 N 2392 2.21 5 O 2524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13378 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1145 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 9, 'TRANS': 136} Chain breaks: 1 Chain: "B" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1145 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 9, 'TRANS': 136} Chain breaks: 1 Chain: "C" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1145 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 9, 'TRANS': 136} Chain breaks: 1 Chain: "D" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1080 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1080 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1094 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1145 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 9, 'TRANS': 136} Chain breaks: 1 Chain: "H" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1145 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 9, 'TRANS': 136} Chain breaks: 1 Chain: "I" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1145 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 9, 'TRANS': 136} Chain breaks: 1 Chain: "J" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1080 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "K" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1080 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "L" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1094 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 2.85, per 1000 atoms: 0.21 Number of scatterers: 13378 At special positions: 0 Unit cell: (148.42, 117.26, 100.04, 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 144 16.00 O 2524 8.00 N 2392 7.00 C 8318 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=66, symmetry=0 Simple disulfide: pdb=" SG CYS A 145 " - pdb=" SG CYS A 177 " distance=2.03 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 177 " distance=2.03 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 177 " distance=2.03 Simple disulfide: pdb=" SG CYS D 44 " - pdb=" SG CYS D 58 " distance=2.03 Simple disulfide: pdb=" SG CYS D 59 " - pdb=" SG CYS D 72 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 81 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 102 " - pdb=" SG CYS D 117 " distance=2.03 Simple disulfide: pdb=" SG CYS D 105 " - pdb=" SG CYS D 125 " distance=2.03 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 143 " distance=2.03 Simple disulfide: pdb=" SG CYS D 146 " - pdb=" SG CYS D 158 " distance=2.03 Simple disulfide: pdb=" SG CYS D 149 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 168 " - pdb=" SG CYS D 179 " distance=2.03 Simple disulfide: pdb=" SG CYS E 44 " - pdb=" SG CYS E 58 " distance=2.03 Simple disulfide: pdb=" SG CYS E 59 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 81 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 102 " - pdb=" SG CYS E 117 " distance=2.03 Simple disulfide: pdb=" SG CYS E 105 " - pdb=" SG CYS E 125 " distance=2.03 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 143 " distance=2.03 Simple disulfide: pdb=" SG CYS E 146 " - pdb=" SG CYS E 158 " distance=2.03 Simple disulfide: pdb=" SG CYS E 149 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 168 " - pdb=" SG CYS E 179 " distance=2.03 Simple disulfide: pdb=" SG CYS F 44 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS F 59 " - pdb=" SG CYS F 72 " distance=2.03 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 81 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 99 " distance=2.03 Simple disulfide: pdb=" SG CYS F 102 " - pdb=" SG CYS F 117 " distance=2.03 Simple disulfide: pdb=" SG CYS F 105 " - pdb=" SG CYS F 125 " distance=2.03 Simple disulfide: pdb=" SG CYS F 127 " - pdb=" SG CYS F 143 " distance=2.03 Simple disulfide: pdb=" SG CYS F 146 " - pdb=" SG CYS F 158 " distance=2.03 Simple disulfide: pdb=" SG CYS F 149 " - pdb=" SG CYS F 166 " distance=2.03 Simple disulfide: pdb=" SG CYS F 168 " - pdb=" SG CYS F 179 " distance=2.03 Simple disulfide: pdb=" SG CYS G 145 " - pdb=" SG CYS G 177 " distance=2.03 Simple disulfide: pdb=" SG CYS H 145 " - pdb=" SG CYS H 177 " distance=2.03 Simple disulfide: pdb=" SG CYS I 145 " - pdb=" SG CYS I 177 " distance=2.03 Simple disulfide: pdb=" SG CYS J 44 " - pdb=" SG CYS J 58 " distance=2.03 Simple disulfide: pdb=" SG CYS J 59 " - pdb=" SG CYS J 72 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 81 " distance=2.03 Simple disulfide: pdb=" SG CYS J 84 " - pdb=" SG CYS J 99 " distance=2.03 Simple disulfide: pdb=" SG CYS J 102 " - pdb=" SG CYS J 117 " distance=2.03 Simple disulfide: pdb=" SG CYS J 105 " - pdb=" SG CYS J 125 " distance=2.03 Simple disulfide: pdb=" SG CYS J 127 " - pdb=" SG CYS J 143 " distance=2.03 Simple disulfide: pdb=" SG CYS J 146 " - pdb=" SG CYS J 158 " distance=2.03 Simple disulfide: pdb=" SG CYS J 149 " - pdb=" SG CYS J 166 " distance=2.03 Simple disulfide: pdb=" SG CYS J 168 " - pdb=" SG CYS J 179 " distance=2.03 Simple disulfide: pdb=" SG CYS K 44 " - pdb=" SG CYS K 58 " distance=2.03 Simple disulfide: pdb=" SG CYS K 59 " - pdb=" SG CYS K 72 " distance=2.03 Simple disulfide: pdb=" SG CYS K 62 " - pdb=" SG CYS K 81 " distance=2.03 Simple disulfide: pdb=" SG CYS K 84 " - pdb=" SG CYS K 99 " distance=2.03 Simple disulfide: pdb=" SG CYS K 102 " - pdb=" SG CYS K 117 " distance=2.03 Simple disulfide: pdb=" SG CYS K 105 " - pdb=" SG CYS K 125 " distance=2.03 Simple disulfide: pdb=" SG CYS K 127 " - pdb=" SG CYS K 143 " distance=2.03 Simple disulfide: pdb=" SG CYS K 146 " - pdb=" SG CYS K 158 " distance=2.03 Simple disulfide: pdb=" SG CYS K 149 " - pdb=" SG CYS K 166 " distance=2.03 Simple disulfide: pdb=" SG CYS K 168 " - pdb=" SG CYS K 179 " distance=2.03 Simple disulfide: pdb=" SG CYS L 44 " - pdb=" SG CYS L 58 " distance=2.03 Simple disulfide: pdb=" SG CYS L 59 " - pdb=" SG CYS L 72 " distance=2.03 Simple disulfide: pdb=" SG CYS L 62 " - pdb=" SG CYS L 81 " distance=2.03 Simple disulfide: pdb=" SG CYS L 84 " - pdb=" SG CYS L 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 102 " - pdb=" SG CYS L 117 " distance=2.03 Simple disulfide: pdb=" SG CYS L 105 " - pdb=" SG CYS L 125 " distance=2.03 Simple disulfide: pdb=" SG CYS L 127 " - pdb=" SG CYS L 143 " distance=2.03 Simple disulfide: pdb=" SG CYS L 146 " - pdb=" SG CYS L 158 " distance=2.03 Simple disulfide: pdb=" SG CYS L 149 " - pdb=" SG CYS L 166 " distance=2.03 Simple disulfide: pdb=" SG CYS L 168 " - pdb=" SG CYS L 179 " 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 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 553.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3216 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 60 sheets defined 1.7% alpha, 37.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'B' and resid 214 through 218 Processing helix chain 'C' and resid 214 through 218 Processing helix chain 'G' and resid 214 through 218 Processing helix chain 'H' and resid 214 through 218 Processing helix chain 'I' and resid 214 through 218 Processing sheet with id=AA1, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 120 removed outlier: 6.550A pdb=" N LEU A 152 " --> pdb=" O ILE A 173 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE A 173 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N HIS A 154 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER A 171 " --> pdb=" O HIS A 154 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 156 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AA6, first strand: chain 'B' and resid 118 through 120 removed outlier: 6.550A pdb=" N LEU B 152 " --> pdb=" O ILE B 173 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE B 173 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N HIS B 154 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER B 171 " --> pdb=" O HIS B 154 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE B 156 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AA8, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AA9, first strand: chain 'C' and resid 118 through 120 removed outlier: 6.550A pdb=" N LEU C 152 " --> pdb=" O ILE C 173 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE C 173 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N HIS C 154 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER C 171 " --> pdb=" O HIS C 154 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE C 156 " --> pdb=" O LEU C 169 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 48 through 50 Processing sheet with id=AB2, first strand: chain 'D' and resid 66 through 70 removed outlier: 7.249A pdb=" N ASP D 80 " --> pdb=" O TYR D 69 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AB4, first strand: chain 'D' and resid 112 through 115 removed outlier: 6.623A pdb=" N VAL D 124 " --> pdb=" O ILE D 114 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 131 through 135 Processing sheet with id=AB6, first strand: chain 'D' and resid 152 through 156 removed outlier: 6.809A pdb=" N VAL D 165 " --> pdb=" O HIS D 155 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 172 through 175 Processing sheet with id=AB8, first strand: chain 'E' and resid 48 through 50 Processing sheet with id=AB9, first strand: chain 'E' and resid 66 through 70 removed outlier: 7.241A pdb=" N ASP E 80 " --> pdb=" O TYR E 69 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 88 through 89 Processing sheet with id=AC2, first strand: chain 'E' and resid 112 through 115 removed outlier: 6.640A pdb=" N VAL E 124 " --> pdb=" O ILE E 114 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 131 through 135 Processing sheet with id=AC4, first strand: chain 'E' and resid 152 through 156 removed outlier: 6.795A pdb=" N VAL E 165 " --> pdb=" O HIS E 155 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 172 through 175 Processing sheet with id=AC6, first strand: chain 'F' and resid 48 through 50 Processing sheet with id=AC7, first strand: chain 'F' and resid 66 through 70 removed outlier: 7.211A pdb=" N ASP F 80 " --> pdb=" O TYR F 69 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 88 through 89 Processing sheet with id=AC9, first strand: chain 'F' and resid 112 through 115 removed outlier: 6.627A pdb=" N VAL F 124 " --> pdb=" O ILE F 114 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 131 through 135 Processing sheet with id=AD2, first strand: chain 'F' and resid 152 through 156 removed outlier: 6.802A pdb=" N VAL F 165 " --> pdb=" O HIS F 155 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 172 through 175 Processing sheet with id=AD4, first strand: chain 'G' and resid 104 through 105 Processing sheet with id=AD5, first strand: chain 'G' and resid 104 through 105 Processing sheet with id=AD6, first strand: chain 'G' and resid 118 through 120 removed outlier: 6.550A pdb=" N LEU G 152 " --> pdb=" O ILE G 173 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE G 173 " --> pdb=" O LEU G 152 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N HIS G 154 " --> pdb=" O SER G 171 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER G 171 " --> pdb=" O HIS G 154 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE G 156 " --> pdb=" O LEU G 169 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AD8, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AD9, first strand: chain 'H' and resid 118 through 120 removed outlier: 6.550A pdb=" N LEU H 152 " --> pdb=" O ILE H 173 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE H 173 " --> pdb=" O LEU H 152 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N HIS H 154 " --> pdb=" O SER H 171 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER H 171 " --> pdb=" O HIS H 154 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE H 156 " --> pdb=" O LEU H 169 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 104 through 105 Processing sheet with id=AE2, first strand: chain 'I' and resid 104 through 105 Processing sheet with id=AE3, first strand: chain 'I' and resid 118 through 120 removed outlier: 6.550A pdb=" N LEU I 152 " --> pdb=" O ILE I 173 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE I 173 " --> pdb=" O LEU I 152 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N HIS I 154 " --> pdb=" O SER I 171 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER I 171 " --> pdb=" O HIS I 154 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE I 156 " --> pdb=" O LEU I 169 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 48 through 50 Processing sheet with id=AE5, first strand: chain 'J' and resid 66 through 70 removed outlier: 7.249A pdb=" N ASP J 80 " --> pdb=" O TYR J 69 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 88 through 89 Processing sheet with id=AE7, first strand: chain 'J' and resid 112 through 115 removed outlier: 6.623A pdb=" N VAL J 124 " --> pdb=" O ILE J 114 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 131 through 135 Processing sheet with id=AE9, first strand: chain 'J' and resid 152 through 156 removed outlier: 6.819A pdb=" N VAL J 165 " --> pdb=" O HIS J 155 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 172 through 175 Processing sheet with id=AF2, first strand: chain 'K' and resid 48 through 50 Processing sheet with id=AF3, first strand: chain 'K' and resid 66 through 70 removed outlier: 7.244A pdb=" N ASP K 80 " --> pdb=" O TYR K 69 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 88 through 89 Processing sheet with id=AF5, first strand: chain 'K' and resid 112 through 115 removed outlier: 6.641A pdb=" N VAL K 124 " --> pdb=" O ILE K 114 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 131 through 135 Processing sheet with id=AF7, first strand: chain 'K' and resid 152 through 156 removed outlier: 6.794A pdb=" N VAL K 165 " --> pdb=" O HIS K 155 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 172 through 175 Processing sheet with id=AF9, first strand: chain 'L' and resid 48 through 50 Processing sheet with id=AG1, first strand: chain 'L' and resid 66 through 70 removed outlier: 7.208A pdb=" N ASP L 80 " --> pdb=" O TYR L 69 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 88 through 89 Processing sheet with id=AG3, first strand: chain 'L' and resid 112 through 115 removed outlier: 6.635A pdb=" N VAL L 124 " --> pdb=" O ILE L 114 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 131 through 135 Processing sheet with id=AG5, first strand: chain 'L' and resid 152 through 156 removed outlier: 6.807A pdb=" N VAL L 165 " --> pdb=" O HIS L 155 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 172 through 175 420 hydrogen bonds defined for protein. 1044 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: 2.33 Time building geometry restraints manager: 1.36 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: 4517 1.35 - 1.46: 3061 1.46 - 1.58: 5932 1.58 - 1.70: 0 1.70 - 1.81: 150 Bond restraints: 13660 Sorted by residual: bond pdb=" C CYS L 44 " pdb=" N PRO L 45 " ideal model delta sigma weight residual 1.331 1.346 -0.015 1.21e-02 6.83e+03 1.48e+00 bond pdb=" C CYS F 44 " pdb=" N PRO F 45 " ideal model delta sigma weight residual 1.331 1.345 -0.014 1.21e-02 6.83e+03 1.31e+00 bond pdb=" CB PRO I 193 " pdb=" CG PRO I 193 " ideal model delta sigma weight residual 1.492 1.531 -0.039 5.00e-02 4.00e+02 5.95e-01 bond pdb=" CB PRO C 193 " pdb=" CG PRO C 193 " ideal model delta sigma weight residual 1.492 1.531 -0.039 5.00e-02 4.00e+02 5.95e-01 bond pdb=" CB PRO A 193 " pdb=" CG PRO A 193 " ideal model delta sigma weight residual 1.492 1.530 -0.038 5.00e-02 4.00e+02 5.74e-01 ... (remaining 13655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.72: 16937 0.72 - 1.44: 1271 1.44 - 2.17: 212 2.17 - 2.89: 66 2.89 - 3.61: 18 Bond angle restraints: 18504 Sorted by residual: angle pdb=" C ALA H 114 " pdb=" N ASN H 115 " pdb=" CA ASN H 115 " ideal model delta sigma weight residual 122.63 124.80 -2.17 1.44e+00 4.82e-01 2.27e+00 angle pdb=" C ALA B 114 " pdb=" N ASN B 115 " pdb=" CA ASN B 115 " ideal model delta sigma weight residual 122.63 124.80 -2.17 1.44e+00 4.82e-01 2.27e+00 angle pdb=" C ALA I 114 " pdb=" N ASN I 115 " pdb=" CA ASN I 115 " ideal model delta sigma weight residual 122.63 124.78 -2.15 1.44e+00 4.82e-01 2.22e+00 angle pdb=" C ALA C 114 " pdb=" N ASN C 115 " pdb=" CA ASN C 115 " ideal model delta sigma weight residual 122.63 124.78 -2.15 1.44e+00 4.82e-01 2.22e+00 angle pdb=" C ALA G 114 " pdb=" N ASN G 115 " pdb=" CA ASN G 115 " ideal model delta sigma weight residual 122.63 124.77 -2.14 1.44e+00 4.82e-01 2.20e+00 ... (remaining 18499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 7834 16.97 - 33.93: 416 33.93 - 50.90: 122 50.90 - 67.86: 30 67.86 - 84.83: 6 Dihedral angle restraints: 8408 sinusoidal: 3416 harmonic: 4992 Sorted by residual: dihedral pdb=" CB CYS F 149 " pdb=" SG CYS F 149 " pdb=" SG CYS F 166 " pdb=" CB CYS F 166 " ideal model delta sinusoidal sigma weight residual 93.00 150.93 -57.93 1 1.00e+01 1.00e-02 4.50e+01 dihedral pdb=" CB CYS L 149 " pdb=" SG CYS L 149 " pdb=" SG CYS L 166 " pdb=" CB CYS L 166 " ideal model delta sinusoidal sigma weight residual 93.00 150.90 -57.90 1 1.00e+01 1.00e-02 4.50e+01 dihedral pdb=" CB CYS D 149 " pdb=" SG CYS D 149 " pdb=" SG CYS D 166 " pdb=" CB CYS D 166 " ideal model delta sinusoidal sigma weight residual 93.00 148.21 -55.21 1 1.00e+01 1.00e-02 4.12e+01 ... (remaining 8405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1312 0.027 - 0.054: 373 0.054 - 0.080: 173 0.080 - 0.107: 97 0.107 - 0.134: 69 Chirality restraints: 2024 Sorted by residual: chirality pdb=" CA ILE L 57 " pdb=" N ILE L 57 " pdb=" C ILE L 57 " pdb=" CB ILE L 57 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA ILE B 156 " pdb=" N ILE B 156 " pdb=" C ILE B 156 " pdb=" CB ILE B 156 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA ILE H 156 " pdb=" N ILE H 156 " pdb=" C ILE H 156 " pdb=" CB ILE H 156 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 2021 not shown) Planarity restraints: 2430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS E 44 " -0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO E 45 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO E 45 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 45 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS K 44 " 0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO K 45 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO K 45 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO K 45 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS D 44 " 0.018 5.00e-02 4.00e+02 2.81e-02 1.26e+00 pdb=" N PRO D 45 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO D 45 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 45 " 0.016 5.00e-02 4.00e+02 ... (remaining 2427 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 865 2.74 - 3.28: 12076 3.28 - 3.82: 22130 3.82 - 4.36: 26447 4.36 - 4.90: 45647 Nonbonded interactions: 107165 Sorted by model distance: nonbonded pdb=" OH TYR B 191 " pdb=" OE2 GLU E 108 " model vdw 2.203 3.040 nonbonded pdb=" OH TYR H 191 " pdb=" OE2 GLU K 108 " model vdw 2.208 3.040 nonbonded pdb=" OH TYR C 191 " pdb=" OE2 GLU D 108 " model vdw 2.224 3.040 nonbonded pdb=" OH TYR G 191 " pdb=" OE2 GLU L 108 " model vdw 2.227 3.040 nonbonded pdb=" OH TYR I 191 " pdb=" OE2 GLU J 108 " model vdw 2.235 3.040 ... (remaining 107160 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.520 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.680 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:7.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 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 : 0.002 0.039 13726 Z= 0.087 Angle : 0.439 3.612 18636 Z= 0.241 Chirality : 0.041 0.134 2024 Planarity : 0.003 0.028 2430 Dihedral : 11.317 84.828 4994 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.80 % Allowed : 7.04 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.88 (0.21), residues: 1686 helix: None (None), residues: 0 sheet: 1.17 (0.24), residues: 468 loop : 0.43 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 106 TYR 0.006 0.001 TYR F 67 PHE 0.006 0.001 PHE L 141 TRP 0.005 0.001 TRP A 190 HIS 0.002 0.001 HIS H 154 Details of bonding type rmsd covalent geometry : bond 0.00193 (13660) covalent geometry : angle 0.43972 (18504) SS BOND : bond 0.00118 ( 66) SS BOND : angle 0.30047 ( 132) hydrogen bonds : bond 0.10956 ( 408) hydrogen bonds : angle 4.93191 ( 1044) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 207 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 TYR cc_start: 0.8070 (m-10) cc_final: 0.7850 (m-10) REVERT: J 105 CYS cc_start: 0.5962 (m) cc_final: 0.5574 (m) outliers start: 12 outliers final: 2 residues processed: 216 average time/residue: 0.3690 time to fit residues: 91.0952 Evaluate side-chains 188 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 186 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain G residue 139 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.0970 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 103 GLN A 123 GLN A 137 GLN A 149 HIS B 101 GLN B 103 GLN B 115 ASN B 123 GLN B 149 HIS B 168 ASN C 103 GLN C 115 ASN C 123 GLN D 111 GLN D 162 GLN D 177 ASN E 111 GLN E 162 GLN F 46 GLN F 111 GLN F 134 HIS F 169 HIS ** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 GLN G 103 GLN G 123 GLN G 149 HIS H 101 GLN H 103 GLN H 115 ASN H 123 GLN H 149 HIS H 168 ASN I 101 GLN I 103 GLN I 115 ASN I 123 GLN I 149 HIS J 111 GLN J 162 GLN J 177 ASN K 111 GLN K 162 GLN L 46 GLN L 111 GLN L 177 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.176795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.146195 restraints weight = 16390.187| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.41 r_work: 0.3851 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 13726 Z= 0.323 Angle : 0.660 9.418 18636 Z= 0.348 Chirality : 0.046 0.179 2024 Planarity : 0.005 0.044 2430 Dihedral : 4.843 36.810 1864 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.68 % Allowed : 10.39 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.36 (0.20), residues: 1686 helix: None (None), residues: 0 sheet: 0.83 (0.23), residues: 534 loop : 0.00 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 179 TYR 0.019 0.002 TYR C 191 PHE 0.018 0.002 PHE L 141 TRP 0.015 0.002 TRP B 190 HIS 0.010 0.001 HIS L 134 Details of bonding type rmsd covalent geometry : bond 0.00732 (13660) covalent geometry : angle 0.64347 (18504) SS BOND : bond 0.00502 ( 66) SS BOND : angle 1.85281 ( 132) hydrogen bonds : bond 0.03512 ( 408) hydrogen bonds : angle 5.20193 ( 1044) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 219 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 93 VAL cc_start: 0.8651 (OUTLIER) cc_final: 0.8432 (m) REVERT: B 129 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6941 (tm-30) REVERT: B 179 ARG cc_start: 0.7710 (mtm-85) cc_final: 0.7454 (ttm-80) REVERT: B 222 GLU cc_start: 0.7652 (mp0) cc_final: 0.7327 (mp0) REVERT: C 129 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6861 (tm-30) REVERT: D 177 ASN cc_start: 0.5999 (OUTLIER) cc_final: 0.5771 (t0) REVERT: E 159 GLN cc_start: 0.8636 (mt0) cc_final: 0.8212 (mt0) REVERT: E 162 GLN cc_start: 0.8401 (tt0) cc_final: 0.8073 (tt0) REVERT: G 105 LEU cc_start: 0.8259 (mt) cc_final: 0.7955 (mp) REVERT: H 113 LEU cc_start: 0.8001 (mt) cc_final: 0.7799 (mt) REVERT: H 129 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6911 (tm-30) REVERT: I 129 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6711 (tm-30) REVERT: J 177 ASN cc_start: 0.6997 (OUTLIER) cc_final: 0.6711 (t160) REVERT: L 103 SER cc_start: 0.8418 (m) cc_final: 0.8138 (p) REVERT: L 133 ARG cc_start: 0.8246 (ptp-170) cc_final: 0.8001 (ptp-170) outliers start: 40 outliers final: 13 residues processed: 241 average time/residue: 0.3684 time to fit residues: 101.6942 Evaluate side-chains 218 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain F residue 99 CYS Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 134 HIS Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain I residue 129 GLU Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain J residue 177 ASN Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 159 GLN Chi-restraints excluded: chain L residue 167 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 165 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 126 optimal weight: 0.0170 chunk 7 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 chunk 154 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS B 149 HIS B 168 ASN C 149 HIS C 164 GLN F 134 HIS ** F 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 HIS G 115 ASN ** H 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 HIS H 168 ASN I 137 GLN I 149 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.178965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.148582 restraints weight = 16519.821| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 2.42 r_work: 0.3882 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13726 Z= 0.147 Angle : 0.536 6.274 18636 Z= 0.286 Chirality : 0.042 0.166 2024 Planarity : 0.004 0.039 2430 Dihedral : 4.498 19.882 1860 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.68 % Allowed : 13.81 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.37 (0.20), residues: 1686 helix: None (None), residues: 0 sheet: 0.85 (0.24), residues: 498 loop : 0.03 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 179 TYR 0.011 0.001 TYR G 191 PHE 0.017 0.001 PHE L 141 TRP 0.009 0.001 TRP B 190 HIS 0.007 0.001 HIS F 134 Details of bonding type rmsd covalent geometry : bond 0.00335 (13660) covalent geometry : angle 0.52314 (18504) SS BOND : bond 0.00279 ( 66) SS BOND : angle 1.45849 ( 132) hydrogen bonds : bond 0.02904 ( 408) hydrogen bonds : angle 5.11833 ( 1044) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 186 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8359 (m) REVERT: B 129 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6748 (tm-30) REVERT: B 222 GLU cc_start: 0.7621 (mp0) cc_final: 0.7268 (mp0) REVERT: C 129 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6813 (tm-30) REVERT: E 162 GLN cc_start: 0.8390 (tt0) cc_final: 0.7875 (tt0) REVERT: F 46 GLN cc_start: 0.8748 (tt0) cc_final: 0.8433 (tp40) REVERT: G 105 LEU cc_start: 0.8262 (mt) cc_final: 0.7972 (mp) REVERT: H 113 LEU cc_start: 0.8039 (mt) cc_final: 0.7808 (mt) REVERT: H 167 VAL cc_start: 0.8121 (t) cc_final: 0.7865 (m) REVERT: H 174 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8256 (tttt) REVERT: I 129 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6664 (tm-30) REVERT: L 103 SER cc_start: 0.8223 (m) cc_final: 0.7951 (p) REVERT: L 128 ARG cc_start: 0.8440 (ptp90) cc_final: 0.8187 (mtt90) outliers start: 40 outliers final: 18 residues processed: 209 average time/residue: 0.3718 time to fit residues: 88.6108 Evaluate side-chains 206 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain F residue 99 CYS Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 174 LYS Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 129 GLU Chi-restraints excluded: chain J residue 104 LYS Chi-restraints excluded: chain L residue 99 CYS Chi-restraints excluded: chain L residue 167 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 156 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS B 137 GLN B 149 HIS C 164 GLN D 177 ASN F 134 HIS F 177 ASN G 149 HIS ** H 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 ASN H 149 HIS H 168 ASN I 149 HIS J 177 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.177411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.146766 restraints weight = 16397.348| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 2.39 r_work: 0.3862 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13726 Z= 0.200 Angle : 0.557 8.111 18636 Z= 0.297 Chirality : 0.043 0.166 2024 Planarity : 0.004 0.040 2430 Dihedral : 4.618 20.954 1860 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.08 % Allowed : 14.28 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.21 (0.20), residues: 1686 helix: None (None), residues: 0 sheet: 0.71 (0.23), residues: 522 loop : -0.09 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 82 TYR 0.013 0.001 TYR C 191 PHE 0.017 0.002 PHE A 228 TRP 0.011 0.001 TRP B 190 HIS 0.006 0.001 HIS L 134 Details of bonding type rmsd covalent geometry : bond 0.00453 (13660) covalent geometry : angle 0.54489 (18504) SS BOND : bond 0.00352 ( 66) SS BOND : angle 1.45735 ( 132) hydrogen bonds : bond 0.03089 ( 408) hydrogen bonds : angle 5.15876 ( 1044) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 194 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6820 (tm-30) REVERT: B 222 GLU cc_start: 0.7630 (mp0) cc_final: 0.7302 (mp0) REVERT: C 129 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6817 (tm-30) REVERT: D 177 ASN cc_start: 0.6054 (OUTLIER) cc_final: 0.5771 (t0) REVERT: F 133 ARG cc_start: 0.8151 (ptp-170) cc_final: 0.7862 (mtm180) REVERT: F 147 SER cc_start: 0.8048 (m) cc_final: 0.7600 (m) REVERT: G 105 LEU cc_start: 0.8319 (mt) cc_final: 0.8036 (mp) REVERT: H 167 VAL cc_start: 0.8146 (t) cc_final: 0.7911 (m) REVERT: H 222 GLU cc_start: 0.7548 (mp0) cc_final: 0.7074 (mp0) REVERT: I 129 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6673 (tm-30) REVERT: J 105 CYS cc_start: 0.6641 (m) cc_final: 0.6306 (m) REVERT: J 177 ASN cc_start: 0.6920 (OUTLIER) cc_final: 0.6579 (t0) REVERT: L 133 ARG cc_start: 0.8170 (ptp-170) cc_final: 0.7831 (ptp-170) outliers start: 46 outliers final: 23 residues processed: 218 average time/residue: 0.3922 time to fit residues: 96.8452 Evaluate side-chains 216 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain F residue 99 CYS Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 141 LYS Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 129 GLU Chi-restraints excluded: chain J residue 177 ASN Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 99 CYS Chi-restraints excluded: chain L residue 127 CYS Chi-restraints excluded: chain L residue 165 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 21 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 120 optimal weight: 0.0170 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 GLN B 149 HIS B 201 GLN C 164 GLN F 134 HIS F 177 ASN H 149 HIS I 149 HIS L 162 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.177591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.146898 restraints weight = 16419.880| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.39 r_work: 0.3865 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13726 Z= 0.169 Angle : 0.533 7.344 18636 Z= 0.285 Chirality : 0.042 0.140 2024 Planarity : 0.004 0.035 2430 Dihedral : 4.574 23.891 1860 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.28 % Allowed : 14.28 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.20), residues: 1686 helix: None (None), residues: 0 sheet: 0.73 (0.24), residues: 492 loop : -0.06 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 82 TYR 0.010 0.001 TYR G 191 PHE 0.015 0.001 PHE L 141 TRP 0.010 0.001 TRP B 190 HIS 0.005 0.001 HIS L 134 Details of bonding type rmsd covalent geometry : bond 0.00386 (13660) covalent geometry : angle 0.52248 (18504) SS BOND : bond 0.00282 ( 66) SS BOND : angle 1.37223 ( 132) hydrogen bonds : bond 0.02957 ( 408) hydrogen bonds : angle 5.08555 ( 1044) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 191 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7444 (mm-30) REVERT: B 222 GLU cc_start: 0.7675 (mp0) cc_final: 0.7351 (mp0) REVERT: C 129 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6847 (tm-30) REVERT: E 109 MET cc_start: 0.7887 (mmm) cc_final: 0.7570 (mtt) REVERT: F 79 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8185 (m) REVERT: G 105 LEU cc_start: 0.8316 (mt) cc_final: 0.8037 (mp) REVERT: H 167 VAL cc_start: 0.8121 (t) cc_final: 0.7891 (m) REVERT: H 179 ARG cc_start: 0.7619 (ttm-80) cc_final: 0.7397 (ttm-80) REVERT: H 222 GLU cc_start: 0.7579 (mp0) cc_final: 0.7104 (mp0) REVERT: I 129 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6713 (tm-30) REVERT: L 133 ARG cc_start: 0.8151 (ptp-170) cc_final: 0.7805 (mtm180) outliers start: 49 outliers final: 26 residues processed: 215 average time/residue: 0.3764 time to fit residues: 91.9657 Evaluate side-chains 215 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 99 CYS Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 129 GLU Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 99 CYS Chi-restraints excluded: chain L residue 127 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 37 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 48 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 144 optimal weight: 0.3980 chunk 62 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 101 GLN B 137 GLN B 149 HIS B 201 GLN C 164 GLN D 177 ASN F 134 HIS F 177 ASN G 149 HIS H 149 HIS H 168 ASN I 149 HIS J 177 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.177828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.147299 restraints weight = 16439.518| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.38 r_work: 0.3873 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3714 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13726 Z= 0.150 Angle : 0.514 7.192 18636 Z= 0.275 Chirality : 0.042 0.136 2024 Planarity : 0.004 0.036 2430 Dihedral : 4.470 26.517 1860 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.35 % Allowed : 15.01 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.28 (0.20), residues: 1686 helix: None (None), residues: 0 sheet: 0.69 (0.25), residues: 468 loop : 0.04 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 128 TYR 0.009 0.001 TYR B 191 PHE 0.011 0.001 PHE A 228 TRP 0.010 0.001 TRP B 190 HIS 0.004 0.001 HIS L 134 Details of bonding type rmsd covalent geometry : bond 0.00345 (13660) covalent geometry : angle 0.50523 (18504) SS BOND : bond 0.00264 ( 66) SS BOND : angle 1.20271 ( 132) hydrogen bonds : bond 0.02829 ( 408) hydrogen bonds : angle 5.02649 ( 1044) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 200 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 TYR cc_start: 0.8516 (m-80) cc_final: 0.8223 (m-80) REVERT: B 192 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7438 (mm-30) REVERT: B 222 GLU cc_start: 0.7702 (mp0) cc_final: 0.7379 (mp0) REVERT: C 129 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6820 (tm-30) REVERT: D 177 ASN cc_start: 0.6030 (OUTLIER) cc_final: 0.5755 (t0) REVERT: G 105 LEU cc_start: 0.8299 (mt) cc_final: 0.8036 (mp) REVERT: H 129 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6845 (tm-30) REVERT: H 167 VAL cc_start: 0.8131 (t) cc_final: 0.7896 (m) REVERT: I 129 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6718 (tm-30) REVERT: I 137 GLN cc_start: 0.8363 (tt0) cc_final: 0.8163 (tt0) REVERT: J 177 ASN cc_start: 0.6963 (OUTLIER) cc_final: 0.6703 (t0) REVERT: L 133 ARG cc_start: 0.8129 (ptp-170) cc_final: 0.7800 (mtm180) outliers start: 50 outliers final: 28 residues processed: 225 average time/residue: 0.3671 time to fit residues: 94.1519 Evaluate side-chains 223 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 190 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 99 CYS Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 159 GLN Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 129 GLU Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain J residue 177 ASN Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 99 CYS Chi-restraints excluded: chain L residue 127 CYS Chi-restraints excluded: chain L residue 165 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 141 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 HIS B 201 GLN C 164 GLN D 177 ASN F 134 HIS ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 GLN H 149 HIS I 149 HIS J 177 ASN ** L 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.177253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.146499 restraints weight = 16328.523| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.38 r_work: 0.3859 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13726 Z= 0.200 Angle : 0.556 6.824 18636 Z= 0.297 Chirality : 0.043 0.136 2024 Planarity : 0.004 0.044 2430 Dihedral : 4.682 35.466 1860 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.35 % Allowed : 15.68 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % 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 aren not related in a simple way. whole: 0.15 (0.20), residues: 1686 helix: None (None), residues: 0 sheet: 0.62 (0.24), residues: 492 loop : -0.08 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 128 TYR 0.010 0.001 TYR I 191 PHE 0.013 0.002 PHE L 144 TRP 0.011 0.002 TRP B 190 HIS 0.006 0.001 HIS L 134 Details of bonding type rmsd covalent geometry : bond 0.00453 (13660) covalent geometry : angle 0.54505 (18504) SS BOND : bond 0.00304 ( 66) SS BOND : angle 1.42168 ( 132) hydrogen bonds : bond 0.03061 ( 408) hydrogen bonds : angle 5.11720 ( 1044) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 202 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7439 (mm-30) REVERT: B 222 GLU cc_start: 0.7655 (mp0) cc_final: 0.7336 (mp0) REVERT: G 105 LEU cc_start: 0.8311 (mt) cc_final: 0.8038 (mp) REVERT: H 129 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6859 (tm-30) REVERT: H 167 VAL cc_start: 0.8148 (t) cc_final: 0.7926 (m) REVERT: H 222 GLU cc_start: 0.7586 (mp0) cc_final: 0.7117 (mp0) REVERT: J 177 ASN cc_start: 0.6943 (OUTLIER) cc_final: 0.6707 (t0) REVERT: L 133 ARG cc_start: 0.8161 (ptp-170) cc_final: 0.7806 (mtm180) outliers start: 50 outliers final: 30 residues processed: 225 average time/residue: 0.3625 time to fit residues: 93.2027 Evaluate side-chains 221 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 99 CYS Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 159 GLN Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 129 GLU Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain J residue 177 ASN Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 99 CYS Chi-restraints excluded: chain L residue 127 CYS Chi-restraints excluded: chain L residue 165 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 144 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 102 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 99 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 HIS C 164 GLN F 134 HIS H 149 HIS H 168 ASN I 149 HIS ** L 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.174228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.144295 restraints weight = 16340.108| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 2.30 r_work: 0.3878 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3719 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13726 Z= 0.172 Angle : 0.546 6.865 18636 Z= 0.291 Chirality : 0.042 0.167 2024 Planarity : 0.004 0.035 2430 Dihedral : 4.697 32.079 1860 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.08 % Allowed : 15.82 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % 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 aren not related in a simple way. whole: 0.21 (0.21), residues: 1686 helix: None (None), residues: 0 sheet: 0.52 (0.24), residues: 498 loop : 0.03 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 128 TYR 0.009 0.001 TYR B 191 PHE 0.011 0.001 PHE L 141 TRP 0.011 0.001 TRP B 190 HIS 0.006 0.001 HIS F 134 Details of bonding type rmsd covalent geometry : bond 0.00392 (13660) covalent geometry : angle 0.53393 (18504) SS BOND : bond 0.00270 ( 66) SS BOND : angle 1.45730 ( 132) hydrogen bonds : bond 0.02883 ( 408) hydrogen bonds : angle 5.12179 ( 1044) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 200 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 TYR cc_start: 0.8559 (m-80) cc_final: 0.8122 (m-80) REVERT: B 129 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6834 (tm-30) REVERT: B 192 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7506 (mm-30) REVERT: B 222 GLU cc_start: 0.7715 (mp0) cc_final: 0.7384 (mp0) REVERT: G 105 LEU cc_start: 0.8331 (mt) cc_final: 0.8068 (mp) REVERT: H 129 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6842 (tm-30) REVERT: H 167 VAL cc_start: 0.8124 (t) cc_final: 0.7903 (m) REVERT: H 222 GLU cc_start: 0.7645 (mp0) cc_final: 0.7181 (mp0) REVERT: L 133 ARG cc_start: 0.8153 (ptp-170) cc_final: 0.7783 (mtm180) outliers start: 46 outliers final: 31 residues processed: 222 average time/residue: 0.4070 time to fit residues: 102.5466 Evaluate side-chains 230 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 99 CYS Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 129 GLU Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 99 CYS Chi-restraints excluded: chain L residue 127 CYS Chi-restraints excluded: chain L residue 148 LEU Chi-restraints excluded: chain L residue 165 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 149 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 69 optimal weight: 20.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 GLN B 149 HIS C 164 GLN F 134 HIS ** H 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 HIS I 149 HIS J 177 ASN ** L 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.173902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.144263 restraints weight = 16489.090| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 2.29 r_work: 0.3881 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13726 Z= 0.172 Angle : 0.545 6.429 18636 Z= 0.290 Chirality : 0.042 0.140 2024 Planarity : 0.004 0.036 2430 Dihedral : 4.673 29.426 1860 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.75 % Allowed : 16.15 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.19 (0.20), residues: 1686 helix: None (None), residues: 0 sheet: 0.48 (0.24), residues: 498 loop : 0.03 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 128 TYR 0.009 0.001 TYR I 191 PHE 0.012 0.002 PHE J 144 TRP 0.011 0.001 TRP B 190 HIS 0.007 0.001 HIS F 134 Details of bonding type rmsd covalent geometry : bond 0.00395 (13660) covalent geometry : angle 0.53398 (18504) SS BOND : bond 0.00284 ( 66) SS BOND : angle 1.37639 ( 132) hydrogen bonds : bond 0.02912 ( 408) hydrogen bonds : angle 5.15105 ( 1044) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 TYR cc_start: 0.8552 (m-80) cc_final: 0.8118 (m-80) REVERT: B 102 LEU cc_start: 0.8293 (tt) cc_final: 0.8078 (tp) REVERT: B 129 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6857 (tm-30) REVERT: B 143 GLN cc_start: 0.7965 (tp40) cc_final: 0.7649 (tp40) REVERT: B 192 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7493 (mm-30) REVERT: B 222 GLU cc_start: 0.7692 (mp0) cc_final: 0.7367 (mp0) REVERT: G 105 LEU cc_start: 0.8322 (mt) cc_final: 0.8048 (mp) REVERT: H 129 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6850 (tm-30) REVERT: H 167 VAL cc_start: 0.8138 (t) cc_final: 0.7921 (m) REVERT: H 222 GLU cc_start: 0.7615 (mp0) cc_final: 0.7160 (mp0) REVERT: J 177 ASN cc_start: 0.7025 (OUTLIER) cc_final: 0.6727 (t0) REVERT: L 133 ARG cc_start: 0.8150 (ptp-170) cc_final: 0.7805 (ptp-170) outliers start: 41 outliers final: 30 residues processed: 221 average time/residue: 0.3971 time to fit residues: 99.6396 Evaluate side-chains 228 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 99 CYS Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 129 GLU Chi-restraints excluded: chain J residue 177 ASN Chi-restraints excluded: chain L residue 72 CYS Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 99 CYS Chi-restraints excluded: chain L residue 127 CYS Chi-restraints excluded: chain L residue 165 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 144 optimal weight: 4.9990 chunk 6 optimal weight: 0.0770 chunk 138 optimal weight: 7.9990 chunk 89 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 151 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 GLN B 149 HIS C 164 GLN F 134 HIS H 149 HIS I 149 HIS J 177 ASN ** L 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.174566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.144689 restraints weight = 16434.797| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.30 r_work: 0.3882 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13726 Z= 0.154 Angle : 0.535 6.522 18636 Z= 0.285 Chirality : 0.042 0.138 2024 Planarity : 0.004 0.035 2430 Dihedral : 4.627 28.947 1860 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.82 % Allowed : 16.55 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.13 (0.20), residues: 1686 helix: None (None), residues: 0 sheet: 0.48 (0.24), residues: 492 loop : -0.03 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 128 TYR 0.008 0.001 TYR I 191 PHE 0.014 0.001 PHE A 228 TRP 0.011 0.001 TRP B 190 HIS 0.007 0.001 HIS F 134 Details of bonding type rmsd covalent geometry : bond 0.00356 (13660) covalent geometry : angle 0.52586 (18504) SS BOND : bond 0.00265 ( 66) SS BOND : angle 1.27055 ( 132) hydrogen bonds : bond 0.02837 ( 408) hydrogen bonds : angle 5.14499 ( 1044) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 198 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 TYR cc_start: 0.8549 (m-80) cc_final: 0.8113 (m-80) REVERT: B 102 LEU cc_start: 0.8271 (tt) cc_final: 0.8069 (tp) REVERT: B 129 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6799 (tm-30) REVERT: B 143 GLN cc_start: 0.7955 (tp40) cc_final: 0.7657 (tp40) REVERT: B 192 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7456 (mm-30) REVERT: B 222 GLU cc_start: 0.7712 (mp0) cc_final: 0.7381 (mp0) REVERT: E 141 PHE cc_start: 0.8717 (p90) cc_final: 0.8204 (p90) REVERT: G 105 LEU cc_start: 0.8317 (mt) cc_final: 0.8067 (mp) REVERT: H 129 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6824 (tm-30) REVERT: H 150 VAL cc_start: 0.8985 (OUTLIER) cc_final: 0.8718 (t) REVERT: H 167 VAL cc_start: 0.8130 (t) cc_final: 0.7914 (m) REVERT: H 222 GLU cc_start: 0.7646 (mp0) cc_final: 0.7184 (mp0) REVERT: J 177 ASN cc_start: 0.7048 (OUTLIER) cc_final: 0.6790 (t0) REVERT: L 133 ARG cc_start: 0.8146 (ptp-170) cc_final: 0.7799 (ptp-170) outliers start: 42 outliers final: 33 residues processed: 218 average time/residue: 0.3857 time to fit residues: 95.8096 Evaluate side-chains 234 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 197 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain F residue 99 CYS Chi-restraints excluded: chain F residue 127 CYS Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 129 GLU Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain J residue 177 ASN Chi-restraints excluded: chain L residue 72 CYS Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 99 CYS Chi-restraints excluded: chain L residue 127 CYS Chi-restraints excluded: chain L residue 148 LEU Chi-restraints excluded: chain L residue 159 GLN Chi-restraints excluded: chain L residue 165 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 1 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 141 optimal weight: 0.4980 chunk 101 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 144 optimal weight: 0.0040 chunk 131 optimal weight: 0.6980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 GLN B 149 HIS C 164 GLN F 134 HIS H 149 HIS I 149 HIS ** L 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.174329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.144686 restraints weight = 16482.916| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.28 r_work: 0.3886 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3728 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13726 Z= 0.155 Angle : 0.532 6.483 18636 Z= 0.284 Chirality : 0.042 0.138 2024 Planarity : 0.003 0.034 2430 Dihedral : 4.602 28.842 1860 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.88 % Allowed : 16.29 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.20), residues: 1686 helix: None (None), residues: 0 sheet: 0.47 (0.25), residues: 468 loop : 0.08 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 128 TYR 0.009 0.001 TYR G 191 PHE 0.013 0.001 PHE A 228 TRP 0.011 0.001 TRP H 190 HIS 0.007 0.001 HIS F 134 Details of bonding type rmsd covalent geometry : bond 0.00357 (13660) covalent geometry : angle 0.52328 (18504) SS BOND : bond 0.00245 ( 66) SS BOND : angle 1.26480 ( 132) hydrogen bonds : bond 0.02837 ( 408) hydrogen bonds : angle 5.08544 ( 1044) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5884.81 seconds wall clock time: 100 minutes 45.92 seconds (6045.92 seconds total)