Starting phenix.real_space_refine on Thu Mar 14 23:39:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ob4_12794/03_2024/7ob4_12794.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ob4_12794/03_2024/7ob4_12794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ob4_12794/03_2024/7ob4_12794.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ob4_12794/03_2024/7ob4_12794.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ob4_12794/03_2024/7ob4_12794.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ob4_12794/03_2024/7ob4_12794.pdb" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 28 5.16 5 C 6510 2.51 5 N 1652 2.21 5 O 1876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 72": "OE1" <-> "OE2" Residue "I PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 72": "OE1" <-> "OE2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 72": "OE1" <-> "OE2" Residue "J PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 72": "OE1" <-> "OE2" Residue "K PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 72": "OE1" <-> "OE2" Residue "M PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 72": "OE1" <-> "OE2" Residue "L PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 72": "OE1" <-> "OE2" Residue "N PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 72": "OE1" <-> "OE2" Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "B PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "C PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "E PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 72": "OE1" <-> "OE2" Residue "D PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "F PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 72": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10066 Number of models: 1 Model: "" Number of chains: 14 Chain: "G" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "I" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "J" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "K" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "M" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "L" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "N" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "A" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "B" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "C" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "E" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "F" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Time building chain proxies: 5.43, per 1000 atoms: 0.54 Number of scatterers: 10066 At special positions: 0 Unit cell: (161.355, 92.649, 52.05, 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 28 16.00 O 1876 8.00 N 1652 7.00 C 6510 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.95 Conformation dependent library (CDL) restraints added in 1.8 seconds 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2436 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 22 sheets defined 0.0% alpha, 45.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 13 through 16 current: chain 'C' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 13 through 16 current: chain 'E' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 13 through 16 current: chain 'G' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 13 through 16 current: chain 'I' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 13 through 16 current: chain 'K' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 13 through 16 current: chain 'M' and resid 13 through 16 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 19 through 21 current: chain 'C' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 19 through 21 current: chain 'E' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 19 through 21 current: chain 'G' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 19 through 21 current: chain 'I' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 19 through 21 current: chain 'K' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 19 through 21 current: chain 'M' and resid 19 through 21 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 25 through 34 current: chain 'C' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 25 through 34 current: chain 'E' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 25 through 34 current: chain 'G' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 25 through 34 current: chain 'I' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 25 through 34 current: chain 'K' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 25 through 34 current: chain 'M' and resid 25 through 34 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 59 through 65 current: chain 'C' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 59 through 65 current: chain 'E' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 59 through 65 current: chain 'G' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 59 through 65 current: chain 'I' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 59 through 65 current: chain 'K' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 59 through 65 current: chain 'M' and resid 59 through 65 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 71 through 73 current: chain 'C' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 71 through 73 current: chain 'E' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 71 through 73 current: chain 'G' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 71 through 73 current: chain 'I' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 71 through 73 current: chain 'K' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 71 through 73 current: chain 'M' and resid 71 through 73 No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 76 through 77 current: chain 'C' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 76 through 77 current: chain 'E' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 76 through 77 current: chain 'G' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 76 through 77 current: chain 'I' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 76 through 77 current: chain 'K' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 76 through 77 current: chain 'M' and resid 76 through 77 No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 79 through 82 current: chain 'C' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 79 through 82 current: chain 'E' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 79 through 82 current: chain 'G' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 79 through 82 current: chain 'I' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 79 through 82 current: chain 'K' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 79 through 82 current: chain 'M' and resid 79 through 82 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 92 through 99 current: chain 'C' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 92 through 99 current: chain 'E' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 92 through 99 current: chain 'G' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 92 through 99 current: chain 'I' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 92 through 99 current: chain 'K' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 92 through 99 current: chain 'M' and resid 92 through 99 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 103 through 108 current: chain 'C' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 103 through 108 current: chain 'E' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 103 through 108 current: chain 'G' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 103 through 108 current: chain 'I' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 103 through 108 current: chain 'K' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 103 through 108 current: chain 'M' and resid 103 through 108 No H-bonds generated for sheet with id=AA9 Processing sheet with id=A10, first strand: chain 'A' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 115 through 115 current: chain 'C' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 115 through 115 current: chain 'E' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 115 through 115 current: chain 'G' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 115 through 115 current: chain 'I' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 115 through 115 current: chain 'K' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 115 through 115 current: chain 'M' and resid 115 through 115 No H-bonds generated for sheet with id=A10 Processing sheet with id=A11, first strand: chain 'A' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 118 through 122 current: chain 'C' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 118 through 122 current: chain 'E' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 118 through 122 current: chain 'G' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 118 through 122 current: chain 'I' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 118 through 122 current: chain 'K' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 118 through 122 current: chain 'M' and resid 118 through 122 No H-bonds generated for sheet with id=A11 Processing sheet with id=BA1, first strand: chain 'B' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 13 through 16 current: chain 'D' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 13 through 16 current: chain 'F' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 13 through 16 current: chain 'H' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 13 through 16 current: chain 'J' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 13 through 16 current: chain 'L' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 13 through 16 current: chain 'N' and resid 13 through 16 No H-bonds generated for sheet with id=BA1 Processing sheet with id=BA2, first strand: chain 'B' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 19 through 21 current: chain 'D' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 19 through 21 current: chain 'F' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 19 through 21 current: chain 'H' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 19 through 21 current: chain 'J' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 19 through 21 current: chain 'L' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 19 through 21 current: chain 'N' and resid 19 through 21 No H-bonds generated for sheet with id=BA2 Processing sheet with id=BA3, first strand: chain 'B' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 25 through 34 current: chain 'D' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 25 through 34 current: chain 'F' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 25 through 34 current: chain 'H' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 25 through 34 current: chain 'J' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 25 through 34 current: chain 'L' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 25 through 34 current: chain 'N' and resid 25 through 34 No H-bonds generated for sheet with id=BA3 Processing sheet with id=BA4, first strand: chain 'B' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 59 through 65 current: chain 'D' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 59 through 65 current: chain 'F' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 59 through 65 current: chain 'H' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 59 through 65 current: chain 'J' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 59 through 65 current: chain 'L' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 59 through 65 current: chain 'N' and resid 59 through 65 No H-bonds generated for sheet with id=BA4 Processing sheet with id=BA5, first strand: chain 'B' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 71 through 73 current: chain 'D' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 71 through 73 current: chain 'F' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 71 through 73 current: chain 'H' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 71 through 73 current: chain 'J' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 71 through 73 current: chain 'L' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 71 through 73 current: chain 'N' and resid 71 through 73 No H-bonds generated for sheet with id=BA5 Processing sheet with id=BA6, first strand: chain 'B' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 76 through 77 current: chain 'D' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 76 through 77 current: chain 'F' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 76 through 77 current: chain 'H' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 76 through 77 current: chain 'J' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 76 through 77 current: chain 'L' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 76 through 77 current: chain 'N' and resid 76 through 77 No H-bonds generated for sheet with id=BA6 Processing sheet with id=BA7, first strand: chain 'B' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 79 through 82 current: chain 'D' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 79 through 82 current: chain 'F' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 79 through 82 current: chain 'H' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 79 through 82 current: chain 'J' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 79 through 82 current: chain 'L' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 79 through 82 current: chain 'N' and resid 79 through 82 No H-bonds generated for sheet with id=BA7 Processing sheet with id=BA8, first strand: chain 'B' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 92 through 99 current: chain 'D' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 92 through 99 current: chain 'F' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 92 through 99 current: chain 'H' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 92 through 99 current: chain 'J' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 92 through 99 current: chain 'L' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 92 through 99 current: chain 'N' and resid 92 through 99 No H-bonds generated for sheet with id=BA8 Processing sheet with id=BA9, first strand: chain 'B' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 103 through 108 current: chain 'D' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 103 through 108 current: chain 'F' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 103 through 108 current: chain 'H' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 103 through 108 current: chain 'J' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 103 through 108 current: chain 'L' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 103 through 108 current: chain 'N' and resid 103 through 108 No H-bonds generated for sheet with id=BA9 Processing sheet with id=B10, first strand: chain 'B' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 115 through 115 current: chain 'D' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 115 through 115 current: chain 'F' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 115 through 115 current: chain 'H' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 115 through 115 current: chain 'J' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 115 through 115 current: chain 'L' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 115 through 115 current: chain 'N' and resid 115 through 115 No H-bonds generated for sheet with id=B10 Processing sheet with id=B11, first strand: chain 'B' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 118 through 122 current: chain 'D' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 118 through 122 current: chain 'F' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 118 through 122 current: chain 'H' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 118 through 122 current: chain 'J' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 118 through 122 current: chain 'L' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 118 through 122 current: chain 'N' and resid 118 through 122 No H-bonds generated for sheet with id=B11 No hydrogen bonds 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: 0.91 Time building geometry restraints manager: 4.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1648 1.32 - 1.44: 2835 1.44 - 1.56: 5764 1.56 - 1.69: 1 1.69 - 1.81: 56 Bond restraints: 10304 Sorted by residual: bond pdb=" N GLY N 101 " pdb=" CA GLY N 101 " ideal model delta sigma weight residual 1.443 1.393 0.050 1.37e-02 5.33e+03 1.33e+01 bond pdb=" C LEU I 82 " pdb=" O LEU I 82 " ideal model delta sigma weight residual 1.236 1.277 -0.041 1.19e-02 7.06e+03 1.20e+01 bond pdb=" C MET M 30 " pdb=" O MET M 30 " ideal model delta sigma weight residual 1.233 1.274 -0.040 1.17e-02 7.31e+03 1.19e+01 bond pdb=" C ALA N 25 " pdb=" O ALA N 25 " ideal model delta sigma weight residual 1.234 1.193 0.040 1.19e-02 7.06e+03 1.16e+01 bond pdb=" CA SER N 100 " pdb=" C SER N 100 " ideal model delta sigma weight residual 1.525 1.564 -0.039 1.25e-02 6.40e+03 9.84e+00 ... (remaining 10299 not shown) Histogram of bond angle deviations from ideal: 99.12 - 106.08: 421 106.08 - 113.05: 5600 113.05 - 120.01: 3173 120.01 - 126.98: 4706 126.98 - 133.94: 100 Bond angle restraints: 14000 Sorted by residual: angle pdb=" N ALA B 81 " pdb=" CA ALA B 81 " pdb=" C ALA B 81 " ideal model delta sigma weight residual 108.02 100.98 7.04 1.78e+00 3.16e-01 1.57e+01 angle pdb=" N ALA I 81 " pdb=" CA ALA I 81 " pdb=" C ALA I 81 " ideal model delta sigma weight residual 107.49 99.12 8.37 2.16e+00 2.14e-01 1.50e+01 angle pdb=" CA TYR B 69 " pdb=" C TYR B 69 " pdb=" O TYR B 69 " ideal model delta sigma weight residual 120.70 116.53 4.17 1.08e+00 8.57e-01 1.49e+01 angle pdb=" N HIS A 31 " pdb=" CA HIS A 31 " pdb=" CB HIS A 31 " ideal model delta sigma weight residual 110.99 117.72 -6.73 1.77e+00 3.19e-01 1.45e+01 angle pdb=" N VAL B 32 " pdb=" CA VAL B 32 " pdb=" C VAL B 32 " ideal model delta sigma weight residual 108.12 102.66 5.46 1.44e+00 4.82e-01 1.44e+01 ... (remaining 13995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 5544 17.01 - 34.02: 432 34.02 - 51.02: 75 51.02 - 68.03: 25 68.03 - 85.04: 14 Dihedral angle restraints: 6090 sinusoidal: 2324 harmonic: 3766 Sorted by residual: dihedral pdb=" C SER N 100 " pdb=" N SER N 100 " pdb=" CA SER N 100 " pdb=" CB SER N 100 " ideal model delta harmonic sigma weight residual -122.60 -114.58 -8.02 0 2.50e+00 1.60e-01 1.03e+01 dihedral pdb=" C VAL B 32 " pdb=" N VAL B 32 " pdb=" CA VAL B 32 " pdb=" CB VAL B 32 " ideal model delta harmonic sigma weight residual -122.00 -114.04 -7.96 0 2.50e+00 1.60e-01 1.01e+01 dihedral pdb=" CB GLU C 89 " pdb=" CG GLU C 89 " pdb=" CD GLU C 89 " pdb=" OE1 GLU C 89 " ideal model delta sinusoidal sigma weight residual 0.00 -85.04 85.04 1 3.00e+01 1.11e-03 9.74e+00 ... (remaining 6087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1232 0.080 - 0.159: 324 0.159 - 0.239: 73 0.239 - 0.318: 8 0.318 - 0.397: 1 Chirality restraints: 1638 Sorted by residual: chirality pdb=" CA SER N 100 " pdb=" N SER N 100 " pdb=" C SER N 100 " pdb=" CB SER N 100 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" CA HIS B 31 " pdb=" N HIS B 31 " pdb=" C HIS B 31 " pdb=" CB HIS B 31 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA VAL B 32 " pdb=" N VAL B 32 " pdb=" C VAL B 32 " pdb=" CB VAL B 32 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 1635 not shown) Planarity restraints: 1722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET F 30 " 0.019 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C MET F 30 " -0.069 2.00e-02 2.50e+03 pdb=" O MET F 30 " 0.027 2.00e-02 2.50e+03 pdb=" N HIS F 31 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET H 30 " 0.018 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C MET H 30 " -0.065 2.00e-02 2.50e+03 pdb=" O MET H 30 " 0.025 2.00e-02 2.50e+03 pdb=" N HIS H 31 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET L 30 " 0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C MET L 30 " -0.057 2.00e-02 2.50e+03 pdb=" O MET L 30 " 0.022 2.00e-02 2.50e+03 pdb=" N HIS L 31 " 0.019 2.00e-02 2.50e+03 ... (remaining 1719 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1223 2.74 - 3.28: 10196 3.28 - 3.82: 17486 3.82 - 4.36: 21582 4.36 - 4.90: 40257 Nonbonded interactions: 90744 Sorted by model distance: nonbonded pdb=" OG1 THR A 119 " pdb=" OH TYR C 114 " model vdw 2.206 2.440 nonbonded pdb=" NH2 ARG J 103 " pdb=" OD1 ASP L 74 " model vdw 2.254 2.520 nonbonded pdb=" O VAL D 28 " pdb=" OH TYR D 69 " model vdw 2.282 2.440 nonbonded pdb=" N SER B 85 " pdb=" O ILE D 84 " model vdw 2.306 2.520 nonbonded pdb=" NH2 ARG K 103 " pdb=" OD1 ASP M 74 " model vdw 2.309 2.520 ... (remaining 90739 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 0.720 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: 0.000 Extract box with map and model: 2.670 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 27.800 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.060 10304 Z= 0.534 Angle : 1.030 8.374 14000 Z= 0.651 Chirality : 0.073 0.397 1638 Planarity : 0.004 0.081 1722 Dihedral : 13.887 85.041 3654 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 23.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.09 % Allowed : 12.91 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP N 79 HIS 0.005 0.001 HIS M 31 PHE 0.012 0.002 PHE F 64 TYR 0.010 0.002 TYR H 114 ARG 0.002 0.000 ARG K 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 354 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 13 MET cc_start: 0.5845 (ttm) cc_final: 0.5498 (ttm) REVERT: I 15 LYS cc_start: 0.7999 (mttt) cc_final: 0.7646 (mttt) REVERT: K 117 SER cc_start: 0.8679 (m) cc_final: 0.8457 (m) REVERT: M 13 MET cc_start: 0.6480 (ttm) cc_final: 0.5937 (ttm) REVERT: M 30 MET cc_start: 0.7164 (ptm) cc_final: 0.5558 (mmt) REVERT: N 13 MET cc_start: 0.6380 (ttm) cc_final: 0.6157 (ttm) REVERT: N 30 MET cc_start: 0.7094 (ptm) cc_final: 0.6149 (mmt) REVERT: N 34 ARG cc_start: 0.7353 (tmt170) cc_final: 0.6935 (tmt170) REVERT: N 117 SER cc_start: 0.8320 (m) cc_final: 0.8073 (m) REVERT: A 31 HIS cc_start: 0.6626 (p90) cc_final: 0.6285 (m-70) REVERT: B 31 HIS cc_start: 0.7129 (p90) cc_final: 0.6002 (m-70) REVERT: F 13 MET cc_start: 0.5381 (ttm) cc_final: 0.5089 (ttm) REVERT: F 74 ASP cc_start: 0.8274 (t0) cc_final: 0.8021 (t0) outliers start: 1 outliers final: 1 residues processed: 354 average time/residue: 0.1924 time to fit residues: 97.2963 Evaluate side-chains 306 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 305 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 119 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10304 Z= 0.175 Angle : 0.642 12.152 14000 Z= 0.323 Chirality : 0.050 0.169 1638 Planarity : 0.003 0.037 1722 Dihedral : 5.654 18.717 1387 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.12 % Allowed : 15.11 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.19), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 79 HIS 0.022 0.002 HIS F 31 PHE 0.014 0.002 PHE G 33 TYR 0.022 0.002 TYR N 69 ARG 0.007 0.000 ARG K 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 314 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 13 MET cc_start: 0.5999 (ttm) cc_final: 0.5614 (ttm) REVERT: H 114 TYR cc_start: 0.8750 (p90) cc_final: 0.8542 (p90) REVERT: J 15 LYS cc_start: 0.7999 (mttt) cc_final: 0.7533 (mttm) REVERT: K 66 GLU cc_start: 0.5796 (mt-10) cc_final: 0.4948 (mt-10) REVERT: M 30 MET cc_start: 0.7587 (ptm) cc_final: 0.6030 (mmt) REVERT: M 35 LYS cc_start: 0.7896 (tmtt) cc_final: 0.7695 (mtpt) REVERT: N 13 MET cc_start: 0.6325 (ttm) cc_final: 0.6104 (ttm) REVERT: N 30 MET cc_start: 0.7102 (ptm) cc_final: 0.6538 (mmp) REVERT: E 74 ASP cc_start: 0.7825 (t0) cc_final: 0.7539 (t0) REVERT: E 79 TRP cc_start: 0.8437 (OUTLIER) cc_final: 0.8032 (t60) REVERT: D 21 ARG cc_start: 0.7465 (tpt-90) cc_final: 0.7037 (ttt90) REVERT: F 13 MET cc_start: 0.5903 (ttm) cc_final: 0.5555 (ttm) REVERT: F 74 ASP cc_start: 0.8179 (t0) cc_final: 0.7806 (t0) outliers start: 45 outliers final: 21 residues processed: 324 average time/residue: 0.1742 time to fit residues: 83.7179 Evaluate side-chains 320 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 298 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 115 SER Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 79 TRP Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain D residue 117 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 114 optimal weight: 20.0000 chunk 123 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 10304 Z= 0.264 Angle : 0.625 6.699 14000 Z= 0.330 Chirality : 0.050 0.161 1638 Planarity : 0.003 0.028 1722 Dihedral : 5.803 19.487 1386 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.02 % Allowed : 17.31 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.19), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 79 HIS 0.019 0.003 HIS F 31 PHE 0.017 0.002 PHE F 64 TYR 0.027 0.002 TYR M 114 ARG 0.005 0.000 ARG K 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 309 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 13 MET cc_start: 0.6020 (ttm) cc_final: 0.5658 (ttm) REVERT: I 66 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6563 (tp30) REVERT: H 114 TYR cc_start: 0.8799 (p90) cc_final: 0.8536 (p90) REVERT: J 15 LYS cc_start: 0.8102 (mttt) cc_final: 0.7765 (mttm) REVERT: K 66 GLU cc_start: 0.5996 (mt-10) cc_final: 0.5523 (mt-10) REVERT: M 35 LYS cc_start: 0.8026 (tmtt) cc_final: 0.7548 (mtmt) REVERT: N 30 MET cc_start: 0.7371 (ptm) cc_final: 0.6644 (mmt) REVERT: N 35 LYS cc_start: 0.7585 (mttt) cc_final: 0.7357 (mmtp) REVERT: A 74 ASP cc_start: 0.8092 (t70) cc_final: 0.7754 (t0) REVERT: F 13 MET cc_start: 0.6049 (ttm) cc_final: 0.5791 (ttm) REVERT: F 74 ASP cc_start: 0.8154 (t0) cc_final: 0.7850 (t0) outliers start: 33 outliers final: 23 residues processed: 318 average time/residue: 0.1694 time to fit residues: 80.4435 Evaluate side-chains 325 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 301 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 66 GLU Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 54 optimal weight: 30.0000 chunk 76 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10304 Z= 0.175 Angle : 0.594 9.230 14000 Z= 0.304 Chirality : 0.049 0.148 1638 Planarity : 0.003 0.028 1722 Dihedral : 5.636 20.180 1386 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.30 % Allowed : 19.14 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.19), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 79 HIS 0.019 0.002 HIS I 31 PHE 0.017 0.001 PHE F 33 TYR 0.031 0.001 TYR D 114 ARG 0.008 0.000 ARG N 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 302 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 15 LYS cc_start: 0.8079 (mttt) cc_final: 0.7651 (mtmm) REVERT: I 66 GLU cc_start: 0.7165 (tp30) cc_final: 0.6602 (tp30) REVERT: H 114 TYR cc_start: 0.8746 (p90) cc_final: 0.8480 (p90) REVERT: J 15 LYS cc_start: 0.8089 (mttt) cc_final: 0.7802 (mttm) REVERT: K 66 GLU cc_start: 0.6028 (mt-10) cc_final: 0.5724 (mt-10) REVERT: K 82 LEU cc_start: 0.8532 (tp) cc_final: 0.8329 (tp) REVERT: M 30 MET cc_start: 0.7466 (ptm) cc_final: 0.6169 (mmp) REVERT: M 35 LYS cc_start: 0.8046 (tmtt) cc_final: 0.7545 (mtmt) REVERT: M 66 GLU cc_start: 0.6959 (mm-30) cc_final: 0.6750 (mm-30) REVERT: N 30 MET cc_start: 0.7268 (ptm) cc_final: 0.6518 (mmt) REVERT: N 35 LYS cc_start: 0.7617 (mttt) cc_final: 0.7313 (mmtp) REVERT: A 74 ASP cc_start: 0.8076 (t70) cc_final: 0.7771 (t0) REVERT: F 74 ASP cc_start: 0.8182 (t0) cc_final: 0.7807 (t0) outliers start: 36 outliers final: 26 residues processed: 311 average time/residue: 0.1755 time to fit residues: 82.1734 Evaluate side-chains 320 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 294 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 31 HIS Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 30.0000 chunk 69 optimal weight: 4.9990 chunk 1 optimal weight: 20.0000 chunk 90 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 62 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 10304 Z= 0.340 Angle : 0.678 6.498 14000 Z= 0.351 Chirality : 0.051 0.237 1638 Planarity : 0.003 0.023 1722 Dihedral : 6.048 21.116 1386 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 3.66 % Allowed : 20.24 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 79 HIS 0.020 0.003 HIS I 31 PHE 0.019 0.002 PHE L 64 TYR 0.034 0.002 TYR D 114 ARG 0.007 0.000 ARG N 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 307 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 15 LYS cc_start: 0.8162 (mttt) cc_final: 0.7820 (mttp) REVERT: H 114 TYR cc_start: 0.8757 (p90) cc_final: 0.8503 (p90) REVERT: J 15 LYS cc_start: 0.8182 (mttt) cc_final: 0.7842 (mttm) REVERT: M 35 LYS cc_start: 0.7997 (tmtt) cc_final: 0.7606 (mtmt) REVERT: N 30 MET cc_start: 0.7488 (ptm) cc_final: 0.6499 (mmt) REVERT: F 13 MET cc_start: 0.5666 (ttm) cc_final: 0.5458 (ttm) REVERT: F 74 ASP cc_start: 0.8151 (t0) cc_final: 0.7849 (t0) outliers start: 40 outliers final: 29 residues processed: 322 average time/residue: 0.1628 time to fit residues: 78.9040 Evaluate side-chains 328 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 299 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 115 SER Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 31 HIS Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 31 HIS Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 121 optimal weight: 0.5980 chunk 101 optimal weight: 20.0000 chunk 56 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 117 optimal weight: 30.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10304 Z= 0.170 Angle : 0.606 6.649 14000 Z= 0.306 Chirality : 0.050 0.187 1638 Planarity : 0.003 0.035 1722 Dihedral : 5.749 21.106 1386 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.30 % Allowed : 21.25 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.19), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 79 HIS 0.017 0.002 HIS F 31 PHE 0.017 0.001 PHE B 33 TYR 0.033 0.001 TYR D 114 ARG 0.008 0.000 ARG N 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 298 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 15 LYS cc_start: 0.8178 (mttt) cc_final: 0.7896 (mttp) REVERT: J 15 LYS cc_start: 0.8190 (mttt) cc_final: 0.7936 (mttm) REVERT: J 82 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8129 (tp) REVERT: M 35 LYS cc_start: 0.8048 (tmtt) cc_final: 0.7585 (mtmt) REVERT: N 30 MET cc_start: 0.7374 (ptm) cc_final: 0.6443 (mmt) REVERT: N 35 LYS cc_start: 0.7463 (mmtt) cc_final: 0.7167 (mmtp) REVERT: F 13 MET cc_start: 0.5790 (ttm) cc_final: 0.5544 (ttm) REVERT: F 74 ASP cc_start: 0.8141 (t0) cc_final: 0.7840 (t0) outliers start: 36 outliers final: 22 residues processed: 311 average time/residue: 0.1639 time to fit residues: 77.0118 Evaluate side-chains 313 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 290 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain K residue 98 ASN Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 89 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 74 optimal weight: 0.0060 chunk 56 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 overall best weight: 4.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10304 Z= 0.202 Angle : 0.623 7.954 14000 Z= 0.315 Chirality : 0.050 0.277 1638 Planarity : 0.003 0.032 1722 Dihedral : 5.724 20.759 1386 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.75 % Allowed : 22.53 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.19), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 79 HIS 0.018 0.002 HIS I 31 PHE 0.014 0.002 PHE B 33 TYR 0.036 0.001 TYR D 114 ARG 0.008 0.000 ARG N 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 289 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 15 LYS cc_start: 0.8155 (mttt) cc_final: 0.7672 (mtmm) REVERT: I 66 GLU cc_start: 0.7037 (tp30) cc_final: 0.6776 (tp30) REVERT: J 15 LYS cc_start: 0.8202 (mttt) cc_final: 0.7933 (mttm) REVERT: M 35 LYS cc_start: 0.7916 (tmtt) cc_final: 0.7548 (mtmt) REVERT: N 30 MET cc_start: 0.7480 (ptm) cc_final: 0.6442 (mmt) REVERT: F 74 ASP cc_start: 0.8140 (t0) cc_final: 0.7793 (t0) outliers start: 30 outliers final: 26 residues processed: 299 average time/residue: 0.1688 time to fit residues: 75.9848 Evaluate side-chains 311 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 285 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain M residue 31 HIS Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 23 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 11 optimal weight: 30.0000 chunk 95 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 116 optimal weight: 20.0000 chunk 106 optimal weight: 7.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 10304 Z= 0.339 Angle : 0.695 7.625 14000 Z= 0.358 Chirality : 0.052 0.235 1638 Planarity : 0.003 0.026 1722 Dihedral : 6.091 21.955 1386 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.02 % Allowed : 21.89 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N 79 HIS 0.019 0.003 HIS I 31 PHE 0.024 0.002 PHE N 33 TYR 0.042 0.002 TYR D 114 ARG 0.003 0.000 ARG N 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 306 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 15 LYS cc_start: 0.8164 (mttt) cc_final: 0.7860 (mttp) REVERT: H 114 TYR cc_start: 0.8742 (p90) cc_final: 0.8466 (p90) REVERT: J 15 LYS cc_start: 0.8270 (mttt) cc_final: 0.7856 (mttm) REVERT: M 35 LYS cc_start: 0.7952 (tmtt) cc_final: 0.7628 (mtmt) REVERT: N 35 LYS cc_start: 0.7577 (mmtp) cc_final: 0.7343 (mmtp) REVERT: F 74 ASP cc_start: 0.8118 (t0) cc_final: 0.7809 (t0) outliers start: 33 outliers final: 26 residues processed: 326 average time/residue: 0.1630 time to fit residues: 80.4796 Evaluate side-chains 323 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 297 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain M residue 31 HIS Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 68 optimal weight: 0.0770 chunk 49 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 74 optimal weight: 0.0010 chunk 119 optimal weight: 10.0000 overall best weight: 3.2150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10304 Z= 0.179 Angle : 0.645 10.484 14000 Z= 0.321 Chirality : 0.051 0.251 1638 Planarity : 0.003 0.031 1722 Dihedral : 5.807 20.796 1386 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.21 % Allowed : 22.34 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 79 HIS 0.019 0.002 HIS I 31 PHE 0.019 0.002 PHE E 33 TYR 0.037 0.001 TYR D 114 ARG 0.008 0.000 ARG N 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 295 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 15 LYS cc_start: 0.8151 (mttt) cc_final: 0.7635 (mtmm) REVERT: H 114 TYR cc_start: 0.8687 (p90) cc_final: 0.8442 (p90) REVERT: J 15 LYS cc_start: 0.8223 (mttt) cc_final: 0.7862 (mttm) REVERT: M 35 LYS cc_start: 0.7938 (tmtt) cc_final: 0.7599 (mtmt) REVERT: N 30 MET cc_start: 0.6996 (ptp) cc_final: 0.6017 (mmt) REVERT: N 35 LYS cc_start: 0.7480 (mmtp) cc_final: 0.7178 (mmtp) REVERT: F 74 ASP cc_start: 0.8111 (t0) cc_final: 0.7806 (t0) outliers start: 35 outliers final: 28 residues processed: 307 average time/residue: 0.1789 time to fit residues: 83.6419 Evaluate side-chains 316 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 288 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain K residue 13 MET Chi-restraints excluded: chain K residue 98 ASN Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain N residue 31 HIS Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 83 optimal weight: 7.9990 chunk 125 optimal weight: 0.4980 chunk 115 optimal weight: 4.9990 chunk 99 optimal weight: 30.0000 chunk 10 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 10304 Z= 0.265 Angle : 0.690 14.211 14000 Z= 0.344 Chirality : 0.051 0.248 1638 Planarity : 0.003 0.032 1722 Dihedral : 5.953 21.152 1386 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.93 % Allowed : 22.71 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 79 HIS 0.021 0.002 HIS I 31 PHE 0.016 0.002 PHE F 33 TYR 0.043 0.002 TYR D 114 ARG 0.008 0.000 ARG N 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 299 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 114 TYR cc_start: 0.8711 (p90) cc_final: 0.8433 (p90) REVERT: J 15 LYS cc_start: 0.8169 (mttt) cc_final: 0.7811 (mttm) REVERT: M 35 LYS cc_start: 0.7938 (tmtt) cc_final: 0.7500 (mtmt) REVERT: N 30 MET cc_start: 0.7440 (ptp) cc_final: 0.6006 (mmt) REVERT: F 74 ASP cc_start: 0.8144 (t0) cc_final: 0.7797 (t0) outliers start: 32 outliers final: 29 residues processed: 315 average time/residue: 0.1638 time to fit residues: 78.0805 Evaluate side-chains 324 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 295 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain N residue 31 HIS Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.165619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.136919 restraints weight = 12043.109| |-----------------------------------------------------------------------------| r_work (start): 0.4536 rms_B_bonded: 2.71 r_work: 0.4389 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10304 Z= 0.211 Angle : 0.673 14.276 14000 Z= 0.331 Chirality : 0.051 0.186 1638 Planarity : 0.003 0.042 1722 Dihedral : 5.860 20.878 1386 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.84 % Allowed : 23.26 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 79 HIS 0.019 0.002 HIS E 31 PHE 0.021 0.002 PHE N 33 TYR 0.039 0.002 TYR D 114 ARG 0.010 0.000 ARG N 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2276.81 seconds wall clock time: 42 minutes 6.22 seconds (2526.22 seconds total)