Starting phenix.real_space_refine (version: dev) on Sun Feb 19 12:51:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ob4_12794/02_2023/7ob4_12794.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ob4_12794/02_2023/7ob4_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_12794/02_2023/7ob4_12794.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ob4_12794/02_2023/7ob4_12794.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ob4_12794/02_2023/7ob4_12794.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ob4_12794/02_2023/7ob4_12794.pdb" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 5.50, per 1000 atoms: 0.55 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: 4.16 Conformation dependent library (CDL) restraints added in 1.5 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: 0.88 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: 1.03 Time building geometry restraints manager: 4.44 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 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. 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.060 Check model and map are aligned: 0.150 Process input model: 26.620 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.090 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 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 % 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 *********************** 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 : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 354 average time/residue: 0.2001 time to fit residues: 101.2462 Evaluate side-chains 306 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 305 time to evaluate : 1.179 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0926 time to fit residues: 1.7518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7873 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 10304 Z= 0.175 Angle : 0.649 11.934 14000 Z= 0.326 Chirality : 0.050 0.160 1638 Planarity : 0.003 0.037 1722 Dihedral : 5.630 18.056 1386 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 4.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.19), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.14), residues: 1232 *********************** 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: 44 poor density : 315 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 21 residues processed: 325 average time/residue: 0.1803 time to fit residues: 87.9550 Evaluate side-chains 318 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 297 time to evaluate : 1.056 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.0952 time to fit residues: 5.1808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.0170 chunk 35 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 114 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 overall best weight: 5.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.095 10304 Z= 0.273 Angle : 0.635 7.693 14000 Z= 0.337 Chirality : 0.050 0.191 1638 Planarity : 0.003 0.026 1722 Dihedral : 5.864 20.750 1386 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer Outliers : 2.20 % 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 *********************** 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 333 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 309 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 11 residues processed: 315 average time/residue: 0.1698 time to fit residues: 81.2950 Evaluate side-chains 310 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 299 time to evaluate : 1.020 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1195 time to fit residues: 3.6226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.2980 chunk 86 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 54 optimal weight: 30.0000 chunk 76 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 overall best weight: 3.8586 ------------------------------------------------------------------------------- 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: 0.7945 moved from start: 0.2685 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= 0.197 Angle : 0.595 6.279 14000 Z= 0.310 Chirality : 0.049 0.154 1638 Planarity : 0.003 0.024 1722 Dihedral : 5.727 20.431 1386 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 2.56 % 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: -3.72 (0.19), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.14), residues: 1232 *********************** 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 330 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 302 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 14 residues processed: 307 average time/residue: 0.1694 time to fit residues: 79.1377 Evaluate side-chains 307 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 293 time to evaluate : 1.198 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0953 time to fit residues: 4.1125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 1 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 62 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.060 10304 Z= 0.365 Angle : 0.707 8.252 14000 Z= 0.371 Chirality : 0.052 0.179 1638 Planarity : 0.003 0.021 1722 Dihedral : 6.281 23.214 1386 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer Outliers : 2.11 % 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: -3.93 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.14), residues: 1232 *********************** 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 339 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 316 time to evaluate : 1.167 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 325 average time/residue: 0.1773 time to fit residues: 87.9563 Evaluate side-chains 318 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 306 time to evaluate : 1.253 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1018 time to fit residues: 3.9070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 101 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 117 optimal weight: 30.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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: 0.7969 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 10304 Z= 0.209 Angle : 0.629 7.727 14000 Z= 0.321 Chirality : 0.051 0.199 1638 Planarity : 0.003 0.026 1722 Dihedral : 5.936 21.418 1386 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer Outliers : 1.92 % 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: -3.86 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.14), residues: 1232 *********************** 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 317 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 296 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 14 residues processed: 301 average time/residue: 0.1669 time to fit residues: 76.7965 Evaluate side-chains 300 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 286 time to evaluate : 1.213 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0956 time to fit residues: 4.0449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 89 optimal weight: 10.0000 chunk 68 optimal weight: 0.0770 chunk 102 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 chunk 74 optimal weight: 0.1980 chunk 56 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 overall best weight: 2.2542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 10304 Z= 0.144 Angle : 0.600 7.739 14000 Z= 0.305 Chirality : 0.050 0.165 1638 Planarity : 0.003 0.023 1722 Dihedral : 5.686 22.224 1386 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer Outliers : 0.82 % 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 *********************** 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 293 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 284 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 286 average time/residue: 0.1701 time to fit residues: 74.0922 Evaluate side-chains 279 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 274 time to evaluate : 1.172 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0969 time to fit residues: 2.5559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 77 optimal weight: 8.9990 chunk 82 optimal weight: 20.0000 chunk 60 optimal weight: 8.9990 chunk 11 optimal weight: 20.0000 chunk 95 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 116 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 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: 0.8013 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.055 10304 Z= 0.332 Angle : 0.697 7.792 14000 Z= 0.362 Chirality : 0.051 0.173 1638 Planarity : 0.004 0.023 1722 Dihedral : 6.108 21.703 1386 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.14), residues: 1232 *********************** 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 321 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 301 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 308 average time/residue: 0.1736 time to fit residues: 80.8337 Evaluate side-chains 304 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 291 time to evaluate : 1.103 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1398 time to fit residues: 4.6501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 4.9990 chunk 116 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 74 optimal weight: 0.0770 chunk 119 optimal weight: 8.9990 overall best weight: 2.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 10304 Z= 0.147 Angle : 0.620 8.604 14000 Z= 0.312 Chirality : 0.050 0.172 1638 Planarity : 0.003 0.026 1722 Dihedral : 5.726 21.553 1386 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer Outliers : 0.37 % 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 (0.19), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.14), residues: 1232 *********************** 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 287 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 283 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 284 average time/residue: 0.1646 time to fit residues: 71.9346 Evaluate side-chains 270 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 269 time to evaluate : 1.097 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1017 time to fit residues: 1.7552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 83 optimal weight: 0.2980 chunk 125 optimal weight: 0.0970 chunk 115 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 61 optimal weight: 20.0000 chunk 79 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 overall best weight: 2.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 10304 Z= 0.165 Angle : 0.643 10.920 14000 Z= 0.320 Chirality : 0.051 0.207 1638 Planarity : 0.003 0.028 1722 Dihedral : 5.720 20.030 1386 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer Outliers : 0.18 % 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 (0.19), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.14), residues: 1232 ********************** 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 277 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 275 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 275 average time/residue: 0.1721 time to fit residues: 72.1702 Evaluate side-chains 271 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 269 time to evaluate : 1.196 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1262 time to fit residues: 2.1021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 4.9990 chunk 92 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 5 optimal weight: 0.8980 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4786 r_free = 0.4786 target = 0.165648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.135505 restraints weight = 12013.085| |-----------------------------------------------------------------------------| r_work (start): 0.4540 rms_B_bonded: 2.83 r_work: 0.4409 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.045 10304 Z= 0.267 Angle : 0.676 8.366 14000 Z= 0.345 Chirality : 0.051 0.189 1638 Planarity : 0.003 0.025 1722 Dihedral : 5.926 19.991 1386 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer Outliers : 0.55 % 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: -3.95 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.14), residues: 1232 =============================================================================== Job complete usr+sys time: 2244.34 seconds wall clock time: 42 minutes 15.35 seconds (2535.35 seconds total)