Starting phenix.real_space_refine on Mon Jul 28 01:52:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ob4_12794/07_2025/7ob4_12794.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ob4_12794/07_2025/7ob4_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/cci-nas-00/data/ceres_data/7ob4_12794/07_2025/7ob4_12794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ob4_12794/07_2025/7ob4_12794.map" model { file = "/net/cci-nas-00/data/ceres_data/7ob4_12794/07_2025/7ob4_12794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ob4_12794/07_2025/7ob4_12794.cif" } 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. Time to flip 45 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 5.62, per 1000 atoms: 0.56 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.1 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: 1.89 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: 1.20 Time building geometry restraints manager: 2.75 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: 0.00 - 1.67: 12799 1.67 - 3.35: 941 3.35 - 5.02: 209 5.02 - 6.70: 45 6.70 - 8.37: 6 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 3.040 nonbonded pdb=" NH2 ARG J 103 " pdb=" OD1 ASP L 74 " model vdw 2.254 3.120 nonbonded pdb=" O VAL D 28 " pdb=" OH TYR D 69 " model vdw 2.282 3.040 nonbonded pdb=" N SER B 85 " pdb=" O ILE D 84 " model vdw 2.306 3.120 nonbonded pdb=" NH2 ARG K 103 " pdb=" OD1 ASP M 74 " model vdw 2.309 3.120 ... (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 Time spend for trying shortcut: 0.01 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.190 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.440 ------------------------------------------------------------------------------- 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 Details of bonding type rmsd covalent geometry : bond 0.00932 (10304) covalent geometry : angle 1.02959 (14000) *********************** 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 to be fit. rotamer outliers: 1 poor density : 354 time to evaluate : 1.052 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: 0.1926 time to fit residues: 97.9771 Evaluate side-chains 306 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 305 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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: 7.9990 chunk 95 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 chunk 51 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 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 = 0.4758 r_free = 0.4758 target = 0.169731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.138936 restraints weight = 11829.567| |-----------------------------------------------------------------------------| r_work (start): 0.4506 rms_B_bonded: 2.85 r_work: 0.4379 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2156 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= 0.273 Angle : 0.697 12.028 14000 Z= 0.359 Chirality : 0.053 0.172 1638 Planarity : 0.004 0.038 1722 Dihedral : 6.004 23.751 1387 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.21 % Allowed : 15.02 % Favored : 81.78 % 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: -3.91 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 79 HIS 0.022 0.003 HIS F 31 PHE 0.020 0.003 PHE J 64 TYR 0.016 0.002 TYR M 114 ARG 0.006 0.001 ARG K 34 Details of bonding type rmsd covalent geometry : bond 0.00609 (10304) covalent geometry : angle 0.69724 (14000) *********************** 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 368 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 333 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 66 GLU cc_start: 0.7182 (mt-10) cc_final: 0.5482 (mt-10) REVERT: G 114 TYR cc_start: 0.8972 (p90) cc_final: 0.8368 (p90) REVERT: I 13 MET cc_start: 0.4229 (ttm) cc_final: 0.3837 (ttm) REVERT: I 17 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8053 (mp) REVERT: H 31 HIS cc_start: 0.7388 (OUTLIER) cc_final: 0.6872 (p-80) REVERT: J 15 LYS cc_start: 0.6862 (mttt) cc_final: 0.6558 (mttm) REVERT: K 114 TYR cc_start: 0.9005 (p90) cc_final: 0.8628 (p90) REVERT: M 30 MET cc_start: 0.8672 (ptm) cc_final: 0.5890 (mmt) REVERT: M 31 HIS cc_start: 0.8288 (p90) cc_final: 0.8073 (p90) REVERT: M 35 LYS cc_start: 0.7622 (tmtt) cc_final: 0.6994 (mtpt) REVERT: M 114 TYR cc_start: 0.8425 (p90) cc_final: 0.8135 (p90) REVERT: L 99 ASP cc_start: 0.8396 (t0) cc_final: 0.8175 (t0) REVERT: N 13 MET cc_start: 0.6491 (ttm) cc_final: 0.6204 (ttm) REVERT: N 17 LEU cc_start: 0.7897 (mm) cc_final: 0.7667 (mt) REVERT: N 30 MET cc_start: 0.8501 (ptm) cc_final: 0.6249 (mmt) REVERT: N 35 LYS cc_start: 0.7321 (mttt) cc_final: 0.7093 (mttt) REVERT: N 62 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7202 (tm-30) REVERT: A 15 LYS cc_start: 0.7057 (mttt) cc_final: 0.6746 (mttp) REVERT: A 31 HIS cc_start: 0.6911 (p90) cc_final: 0.5019 (m-70) REVERT: C 114 TYR cc_start: 0.9015 (p90) cc_final: 0.8738 (p90) REVERT: E 114 TYR cc_start: 0.8953 (p90) cc_final: 0.8399 (p90) REVERT: D 82 LEU cc_start: 0.8830 (tp) cc_final: 0.8574 (tp) REVERT: D 114 TYR cc_start: 0.9107 (p90) cc_final: 0.8633 (p90) REVERT: F 13 MET cc_start: 0.4304 (ttm) cc_final: 0.3883 (ttm) REVERT: F 15 LYS cc_start: 0.6994 (mttt) cc_final: 0.6728 (mttm) REVERT: F 74 ASP cc_start: 0.8841 (t0) cc_final: 0.8261 (t0) outliers start: 35 outliers final: 18 residues processed: 340 average time/residue: 0.2023 time to fit residues: 103.7746 Evaluate side-chains 333 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 313 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 17 LEU 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 31 HIS 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 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 117 SER 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 56 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 108 optimal weight: 30.0000 chunk 98 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 36 optimal weight: 30.0000 chunk 31 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 101 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.166469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.135821 restraints weight = 12111.169| |-----------------------------------------------------------------------------| r_work (start): 0.4473 rms_B_bonded: 2.79 r_work: 0.4344 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 10304 Z= 0.296 Angle : 0.649 7.297 14000 Z= 0.342 Chirality : 0.052 0.214 1638 Planarity : 0.003 0.027 1722 Dihedral : 5.969 19.594 1386 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.30 % Allowed : 16.30 % Favored : 80.40 % 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: -3.88 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (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 0.016 0.002 PHE J 64 TYR 0.018 0.002 TYR H 114 ARG 0.005 0.000 ARG K 34 Details of bonding type rmsd covalent geometry : bond 0.00661 (10304) covalent geometry : angle 0.64940 (14000) *********************** 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 366 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 330 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 82 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8338 (mm) REVERT: G 114 TYR cc_start: 0.8965 (p90) cc_final: 0.8475 (p90) REVERT: I 13 MET cc_start: 0.4070 (ttm) cc_final: 0.3684 (ttm) REVERT: I 66 GLU cc_start: 0.6766 (mt-10) cc_final: 0.6341 (mt-10) REVERT: I 82 LEU cc_start: 0.8798 (tp) cc_final: 0.8586 (tp) REVERT: H 114 TYR cc_start: 0.9023 (p90) cc_final: 0.8802 (p90) REVERT: J 15 LYS cc_start: 0.6818 (mttt) cc_final: 0.6300 (mttm) REVERT: K 15 LYS cc_start: 0.7197 (mttt) cc_final: 0.6908 (mttp) REVERT: K 114 TYR cc_start: 0.8999 (p90) cc_final: 0.8419 (p90) REVERT: M 35 LYS cc_start: 0.7746 (tmtt) cc_final: 0.6920 (mtmt) REVERT: M 74 ASP cc_start: 0.8935 (t0) cc_final: 0.8704 (t0) REVERT: M 114 TYR cc_start: 0.8325 (p90) cc_final: 0.7963 (p90) REVERT: L 17 LEU cc_start: 0.8336 (mm) cc_final: 0.8088 (mt) REVERT: N 13 MET cc_start: 0.6490 (ttm) cc_final: 0.6237 (ttm) REVERT: N 17 LEU cc_start: 0.7829 (mm) cc_final: 0.7557 (mt) REVERT: N 30 MET cc_start: 0.8699 (ptm) cc_final: 0.6220 (mmt) REVERT: N 34 ARG cc_start: 0.6659 (ttt-90) cc_final: 0.5504 (tmt170) REVERT: N 35 LYS cc_start: 0.7351 (mttt) cc_final: 0.6968 (mttt) REVERT: A 15 LYS cc_start: 0.7046 (mttt) cc_final: 0.6642 (mttp) REVERT: A 74 ASP cc_start: 0.7832 (t70) cc_final: 0.7595 (t0) REVERT: B 74 ASP cc_start: 0.8238 (t0) cc_final: 0.7675 (t0) REVERT: C 114 TYR cc_start: 0.9145 (p90) cc_final: 0.8674 (p90) REVERT: D 82 LEU cc_start: 0.8925 (tp) cc_final: 0.8719 (tp) REVERT: D 114 TYR cc_start: 0.9033 (p90) cc_final: 0.8504 (p90) REVERT: F 74 ASP cc_start: 0.8978 (t70) cc_final: 0.8473 (t0) outliers start: 36 outliers final: 25 residues processed: 335 average time/residue: 0.1712 time to fit residues: 86.2949 Evaluate side-chains 337 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 311 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 117 SER 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 82 LEU 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 17 LEU 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 117 SER Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 119 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 109 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 68 optimal weight: 0.0000 chunk 4 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 79 optimal weight: 0.0000 chunk 78 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 31 HIS N 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.174909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.143890 restraints weight = 11663.474| |-----------------------------------------------------------------------------| r_work (start): 0.4595 rms_B_bonded: 2.83 r_work: 0.4459 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10304 Z= 0.130 Angle : 0.601 10.583 14000 Z= 0.305 Chirality : 0.051 0.172 1638 Planarity : 0.003 0.022 1722 Dihedral : 5.614 19.801 1386 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.21 % Allowed : 18.13 % Favored : 78.66 % 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 0.008 0.001 TRP C 79 HIS 0.019 0.002 HIS F 31 PHE 0.025 0.001 PHE D 33 TYR 0.013 0.001 TYR J 105 ARG 0.006 0.000 ARG N 34 Details of bonding type rmsd covalent geometry : bond 0.00298 (10304) covalent geometry : angle 0.60081 (14000) *********************** 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 351 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 316 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 114 TYR cc_start: 0.8941 (p90) cc_final: 0.8193 (p90) REVERT: I 13 MET cc_start: 0.4246 (ttm) cc_final: 0.3839 (ttm) REVERT: I 74 ASP cc_start: 0.8714 (t0) cc_final: 0.8443 (t0) REVERT: I 114 TYR cc_start: 0.8912 (p90) cc_final: 0.8501 (p90) REVERT: J 15 LYS cc_start: 0.6774 (mttt) cc_final: 0.6325 (mttm) REVERT: J 82 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8432 (tp) REVERT: K 15 LYS cc_start: 0.7130 (mttt) cc_final: 0.6867 (mttp) REVERT: K 114 TYR cc_start: 0.8944 (p90) cc_final: 0.8434 (p90) REVERT: M 30 MET cc_start: 0.8560 (ptm) cc_final: 0.5764 (mmp) REVERT: M 35 LYS cc_start: 0.7615 (tmtt) cc_final: 0.6700 (mtmt) REVERT: M 66 GLU cc_start: 0.7977 (tp30) cc_final: 0.7587 (tp30) REVERT: M 114 TYR cc_start: 0.8319 (p90) cc_final: 0.8081 (p90) REVERT: N 13 MET cc_start: 0.6391 (ttm) cc_final: 0.6143 (ttm) REVERT: N 17 LEU cc_start: 0.7918 (mm) cc_final: 0.7662 (mt) REVERT: N 30 MET cc_start: 0.8537 (ptm) cc_final: 0.5964 (mmp) REVERT: N 35 LYS cc_start: 0.7386 (mttt) cc_final: 0.7049 (mttt) REVERT: N 114 TYR cc_start: 0.8450 (p90) cc_final: 0.8142 (p90) REVERT: A 15 LYS cc_start: 0.7012 (mttt) cc_final: 0.6727 (mttp) REVERT: A 74 ASP cc_start: 0.8048 (t70) cc_final: 0.7739 (t0) REVERT: B 74 ASP cc_start: 0.8135 (t0) cc_final: 0.7603 (t0) REVERT: B 99 ASP cc_start: 0.8683 (t0) cc_final: 0.8467 (t0) REVERT: C 70 LYS cc_start: 0.8289 (ttmt) cc_final: 0.8079 (ttmt) REVERT: E 114 TYR cc_start: 0.8974 (p90) cc_final: 0.8416 (p90) REVERT: D 114 TYR cc_start: 0.8944 (p90) cc_final: 0.8439 (p90) REVERT: F 74 ASP cc_start: 0.8885 (t70) cc_final: 0.8544 (t0) outliers start: 35 outliers final: 19 residues processed: 319 average time/residue: 0.1967 time to fit residues: 94.0317 Evaluate side-chains 317 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 297 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 117 SER 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 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 L residue 117 SER Chi-restraints excluded: chain N residue 31 HIS Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 69 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 63 optimal weight: 4.9990 chunk 117 optimal weight: 30.0000 chunk 38 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 31 HIS N 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.167917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.137714 restraints weight = 11882.789| |-----------------------------------------------------------------------------| r_work (start): 0.4538 rms_B_bonded: 2.79 r_work: 0.4394 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.3019 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= 0.241 Angle : 0.626 6.993 14000 Z= 0.323 Chirality : 0.051 0.200 1638 Planarity : 0.003 0.029 1722 Dihedral : 5.767 20.000 1386 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.02 % Allowed : 19.78 % Favored : 77.20 % 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: -3.84 (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 N 79 HIS 0.018 0.003 HIS F 31 PHE 0.014 0.002 PHE D 33 TYR 0.022 0.001 TYR C 114 ARG 0.008 0.000 ARG N 34 Details of bonding type rmsd covalent geometry : bond 0.00543 (10304) covalent geometry : angle 0.62622 (14000) *********************** 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 342 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 309 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: G 114 TYR cc_start: 0.8931 (p90) cc_final: 0.8394 (p90) REVERT: I 13 MET cc_start: 0.4275 (ttm) cc_final: 0.3867 (ttm) REVERT: I 82 LEU cc_start: 0.8812 (tp) cc_final: 0.8331 (mm) REVERT: H 82 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8212 (mm) REVERT: J 15 LYS cc_start: 0.6824 (mttt) cc_final: 0.6424 (mttm) REVERT: K 15 LYS cc_start: 0.7174 (mttt) cc_final: 0.6899 (mttp) REVERT: K 66 GLU cc_start: 0.8113 (tp30) cc_final: 0.7835 (tp30) REVERT: K 114 TYR cc_start: 0.8986 (p90) cc_final: 0.8562 (p90) REVERT: M 35 LYS cc_start: 0.7719 (tmtt) cc_final: 0.6912 (mtmt) REVERT: M 114 TYR cc_start: 0.8365 (p90) cc_final: 0.8040 (p90) REVERT: N 13 MET cc_start: 0.6347 (ttm) cc_final: 0.6096 (ttm) REVERT: N 30 MET cc_start: 0.8554 (ptm) cc_final: 0.6216 (mmt) REVERT: N 35 LYS cc_start: 0.7276 (mttt) cc_final: 0.7010 (mttt) REVERT: N 114 TYR cc_start: 0.8447 (p90) cc_final: 0.8050 (p90) REVERT: A 15 LYS cc_start: 0.7000 (mttt) cc_final: 0.6751 (mttp) REVERT: A 74 ASP cc_start: 0.8068 (t70) cc_final: 0.7743 (t0) REVERT: B 74 ASP cc_start: 0.8136 (t0) cc_final: 0.7602 (t0) REVERT: B 99 ASP cc_start: 0.8783 (t0) cc_final: 0.8523 (t0) REVERT: C 70 LYS cc_start: 0.8365 (ttmt) cc_final: 0.8122 (ttmt) REVERT: C 82 LEU cc_start: 0.8946 (tp) cc_final: 0.8279 (mm) REVERT: C 114 TYR cc_start: 0.8972 (p90) cc_final: 0.8473 (p90) REVERT: D 66 GLU cc_start: 0.7891 (tp30) cc_final: 0.7586 (tp30) REVERT: D 82 LEU cc_start: 0.8804 (tp) cc_final: 0.8349 (mm) REVERT: D 114 TYR cc_start: 0.9009 (p90) cc_final: 0.8547 (p90) REVERT: F 74 ASP cc_start: 0.8952 (t70) cc_final: 0.8582 (t0) outliers start: 33 outliers final: 25 residues processed: 315 average time/residue: 0.1776 time to fit residues: 84.5422 Evaluate side-chains 320 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 294 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 82 LEU 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 31 HIS 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 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 117 SER Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 107 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 chunk 125 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 54 optimal weight: 30.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.162388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.133105 restraints weight = 12433.382| |-----------------------------------------------------------------------------| r_work (start): 0.4490 rms_B_bonded: 2.80 r_work: 0.4355 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 10304 Z= 0.319 Angle : 0.680 7.269 14000 Z= 0.351 Chirality : 0.053 0.274 1638 Planarity : 0.003 0.038 1722 Dihedral : 6.062 22.445 1386 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.66 % Allowed : 20.51 % Favored : 75.82 % 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: -4.00 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.13), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 79 HIS 0.017 0.002 HIS F 31 PHE 0.020 0.002 PHE J 64 TYR 0.020 0.002 TYR C 114 ARG 0.009 0.000 ARG N 34 Details of bonding type rmsd covalent geometry : bond 0.00716 (10304) covalent geometry : angle 0.68014 (14000) *********************** 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 361 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 321 time to evaluate : 1.147 Fit side-chains revert: symmetry clash REVERT: G 74 ASP cc_start: 0.8865 (t70) cc_final: 0.8650 (t0) REVERT: G 82 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8077 (mm) REVERT: G 114 TYR cc_start: 0.8975 (p90) cc_final: 0.8549 (p90) REVERT: I 13 MET cc_start: 0.4420 (ttm) cc_final: 0.3986 (ttm) REVERT: H 17 LEU cc_start: 0.7669 (mm) cc_final: 0.7419 (mp) REVERT: J 15 LYS cc_start: 0.6926 (mttt) cc_final: 0.6467 (mttm) REVERT: K 15 LYS cc_start: 0.7197 (mttt) cc_final: 0.6895 (mttp) REVERT: K 66 GLU cc_start: 0.8213 (tp30) cc_final: 0.7751 (tp30) REVERT: M 35 LYS cc_start: 0.7590 (tmtt) cc_final: 0.6908 (mtmt) REVERT: M 66 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7636 (tp30) REVERT: M 114 TYR cc_start: 0.8295 (p90) cc_final: 0.7968 (p90) REVERT: L 66 GLU cc_start: 0.8132 (tp30) cc_final: 0.7897 (tp30) REVERT: N 13 MET cc_start: 0.6441 (ttm) cc_final: 0.6207 (ttm) REVERT: N 30 MET cc_start: 0.8729 (ptm) cc_final: 0.8158 (ptp) REVERT: N 35 LYS cc_start: 0.7210 (mttt) cc_final: 0.6927 (mttt) REVERT: A 15 LYS cc_start: 0.7122 (mttt) cc_final: 0.6874 (mttp) REVERT: A 74 ASP cc_start: 0.8126 (t70) cc_final: 0.7770 (t0) REVERT: B 74 ASP cc_start: 0.8275 (t0) cc_final: 0.8073 (t0) REVERT: B 99 ASP cc_start: 0.8830 (t0) cc_final: 0.8547 (t0) REVERT: C 114 TYR cc_start: 0.8960 (p90) cc_final: 0.8581 (p90) REVERT: E 66 GLU cc_start: 0.7538 (tp30) cc_final: 0.7286 (tp30) REVERT: D 82 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8338 (mm) REVERT: F 74 ASP cc_start: 0.8882 (t70) cc_final: 0.8547 (t0) outliers start: 40 outliers final: 29 residues processed: 329 average time/residue: 0.2169 time to fit residues: 106.2926 Evaluate side-chains 336 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 305 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 15 LYS 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 31 HIS 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 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 117 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 119 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 79 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 112 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 108 optimal weight: 30.0000 chunk 89 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.165232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.135838 restraints weight = 12307.044| |-----------------------------------------------------------------------------| r_work (start): 0.4531 rms_B_bonded: 2.82 r_work: 0.4383 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10304 Z= 0.230 Angle : 0.658 10.260 14000 Z= 0.333 Chirality : 0.053 0.277 1638 Planarity : 0.003 0.045 1722 Dihedral : 5.934 22.422 1386 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.57 % Allowed : 20.15 % Favored : 76.28 % 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: -4.02 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.13), 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 0.002 PHE F 33 TYR 0.016 0.001 TYR C 114 ARG 0.009 0.000 ARG N 34 Details of bonding type rmsd covalent geometry : bond 0.00518 (10304) covalent geometry : angle 0.65797 (14000) *********************** 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 342 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 303 time to evaluate : 3.169 Fit side-chains REVERT: G 74 ASP cc_start: 0.8901 (t70) cc_final: 0.8607 (t0) REVERT: G 82 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8106 (mm) REVERT: G 114 TYR cc_start: 0.8947 (p90) cc_final: 0.8450 (p90) REVERT: I 13 MET cc_start: 0.4481 (ttm) cc_final: 0.4044 (ttm) REVERT: I 82 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8546 (mm) REVERT: J 15 LYS cc_start: 0.6949 (mttt) cc_final: 0.6628 (mttm) REVERT: M 30 MET cc_start: 0.8729 (ptm) cc_final: 0.6151 (mmp) REVERT: M 35 LYS cc_start: 0.7604 (tmtt) cc_final: 0.6917 (mtmt) REVERT: M 114 TYR cc_start: 0.8360 (p90) cc_final: 0.8105 (p90) REVERT: L 114 TYR cc_start: 0.8863 (p90) cc_final: 0.8649 (p90) REVERT: N 13 MET cc_start: 0.6410 (ttm) cc_final: 0.6180 (ttm) REVERT: N 35 LYS cc_start: 0.7258 (mttt) cc_final: 0.6957 (mttt) REVERT: N 114 TYR cc_start: 0.8451 (p90) cc_final: 0.8134 (p90) REVERT: A 15 LYS cc_start: 0.7167 (mttt) cc_final: 0.6913 (mttp) REVERT: A 74 ASP cc_start: 0.8212 (t70) cc_final: 0.7871 (t0) REVERT: B 99 ASP cc_start: 0.8826 (t0) cc_final: 0.8570 (t0) REVERT: C 82 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8419 (mm) REVERT: C 114 TYR cc_start: 0.9002 (p90) cc_final: 0.8724 (p90) REVERT: E 66 GLU cc_start: 0.7526 (tp30) cc_final: 0.7291 (tp30) REVERT: D 82 LEU cc_start: 0.8920 (tp) cc_final: 0.8395 (mm) REVERT: F 74 ASP cc_start: 0.8863 (t70) cc_final: 0.8601 (t0) outliers start: 39 outliers final: 28 residues processed: 313 average time/residue: 0.2761 time to fit residues: 132.2899 Evaluate side-chains 321 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 290 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain H residue 31 HIS 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 117 SER Chi-restraints excluded: chain L residue 80 LYS Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 119 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 27 optimal weight: 6.9990 chunk 122 optimal weight: 0.5980 chunk 7 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 108 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 94 optimal weight: 0.0050 chunk 28 optimal weight: 7.9990 overall best weight: 2.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.171378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.140579 restraints weight = 11971.896| |-----------------------------------------------------------------------------| r_work (start): 0.4592 rms_B_bonded: 2.88 r_work: 0.4446 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10304 Z= 0.143 Angle : 0.639 14.164 14000 Z= 0.316 Chirality : 0.053 0.271 1638 Planarity : 0.003 0.041 1722 Dihedral : 5.707 21.042 1386 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.84 % Allowed : 21.34 % Favored : 75.82 % 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: -4.00 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 79 HIS 0.017 0.002 HIS F 31 PHE 0.013 0.001 PHE D 33 TYR 0.014 0.001 TYR C 114 ARG 0.009 0.000 ARG N 34 Details of bonding type rmsd covalent geometry : bond 0.00327 (10304) covalent geometry : angle 0.63939 (14000) *********************** 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 342 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 311 time to evaluate : 1.065 Fit side-chains REVERT: G 74 ASP cc_start: 0.8871 (t70) cc_final: 0.8603 (t0) REVERT: G 82 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7957 (mm) REVERT: G 114 TYR cc_start: 0.8881 (p90) cc_final: 0.8396 (p90) REVERT: I 13 MET cc_start: 0.4181 (ttm) cc_final: 0.3764 (ttm) REVERT: H 31 HIS cc_start: 0.7263 (OUTLIER) cc_final: 0.6870 (p-80) REVERT: J 15 LYS cc_start: 0.6724 (mttt) cc_final: 0.6367 (mttm) REVERT: J 82 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8434 (tp) REVERT: K 15 LYS cc_start: 0.6987 (mttt) cc_final: 0.6772 (mttp) REVERT: M 35 LYS cc_start: 0.7464 (tmtt) cc_final: 0.6742 (mtmt) REVERT: M 114 TYR cc_start: 0.8306 (p90) cc_final: 0.8091 (p90) REVERT: L 80 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7459 (tttm) REVERT: L 114 TYR cc_start: 0.8773 (p90) cc_final: 0.8557 (p90) REVERT: N 13 MET cc_start: 0.6332 (ttm) cc_final: 0.6117 (ttm) REVERT: N 30 MET cc_start: 0.8722 (ptp) cc_final: 0.6044 (mmt) REVERT: N 35 LYS cc_start: 0.7266 (mttt) cc_final: 0.7026 (mttt) REVERT: N 114 TYR cc_start: 0.8344 (p90) cc_final: 0.8049 (p90) REVERT: A 15 LYS cc_start: 0.6988 (mttt) cc_final: 0.6740 (mttp) REVERT: A 74 ASP cc_start: 0.8064 (t70) cc_final: 0.7460 (t0) REVERT: B 74 ASP cc_start: 0.8085 (t0) cc_final: 0.7747 (t0) REVERT: B 99 ASP cc_start: 0.8822 (t0) cc_final: 0.8529 (t0) REVERT: C 82 LEU cc_start: 0.9051 (tp) cc_final: 0.8406 (mm) REVERT: C 114 TYR cc_start: 0.8883 (p90) cc_final: 0.8595 (p90) REVERT: D 82 LEU cc_start: 0.8812 (tp) cc_final: 0.8294 (mm) REVERT: D 114 TYR cc_start: 0.8965 (p90) cc_final: 0.8513 (p90) REVERT: F 74 ASP cc_start: 0.8864 (t70) cc_final: 0.8580 (t0) outliers start: 31 outliers final: 23 residues processed: 321 average time/residue: 0.1857 time to fit residues: 88.1112 Evaluate side-chains 316 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 289 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain H residue 31 HIS 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 117 SER Chi-restraints excluded: chain L residue 80 LYS Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 36 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 101 optimal weight: 20.0000 chunk 56 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.162494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.132747 restraints weight = 12466.138| |-----------------------------------------------------------------------------| r_work (start): 0.4504 rms_B_bonded: 2.78 r_work: 0.4364 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 10304 Z= 0.331 Angle : 0.738 13.359 14000 Z= 0.375 Chirality : 0.055 0.315 1638 Planarity : 0.004 0.042 1722 Dihedral : 6.097 20.868 1386 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.84 % Allowed : 21.52 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.13 (0.17), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.13), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 79 HIS 0.016 0.002 HIS F 31 PHE 0.018 0.002 PHE J 64 TYR 0.020 0.002 TYR C 114 ARG 0.009 0.000 ARG N 34 Details of bonding type rmsd covalent geometry : bond 0.00748 (10304) covalent geometry : angle 0.73830 (14000) *********************** 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 331 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 300 time to evaluate : 1.078 Fit side-chains revert: symmetry clash REVERT: G 74 ASP cc_start: 0.8906 (t70) cc_final: 0.8649 (t0) REVERT: G 82 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8184 (mm) REVERT: I 13 MET cc_start: 0.4380 (ttm) cc_final: 0.3894 (ttm) REVERT: H 17 LEU cc_start: 0.7710 (mm) cc_final: 0.7444 (mp) REVERT: J 15 LYS cc_start: 0.6923 (mttt) cc_final: 0.6540 (mttm) REVERT: K 15 LYS cc_start: 0.7118 (mttt) cc_final: 0.6825 (mttp) REVERT: K 114 TYR cc_start: 0.8881 (p90) cc_final: 0.8658 (p90) REVERT: M 35 LYS cc_start: 0.7650 (tmtt) cc_final: 0.7397 (tmtt) REVERT: M 114 TYR cc_start: 0.8379 (p90) cc_final: 0.8071 (p90) REVERT: N 13 MET cc_start: 0.6448 (ttm) cc_final: 0.6179 (ttm) REVERT: N 30 MET cc_start: 0.8894 (ptp) cc_final: 0.6076 (mmp) REVERT: N 35 LYS cc_start: 0.7298 (mttt) cc_final: 0.6954 (mttt) REVERT: A 15 LYS cc_start: 0.7037 (mttt) cc_final: 0.6790 (mttp) REVERT: A 33 PHE cc_start: 0.6318 (t80) cc_final: 0.5941 (t80) REVERT: A 74 ASP cc_start: 0.8115 (t70) cc_final: 0.7482 (t0) REVERT: B 99 ASP cc_start: 0.8894 (t0) cc_final: 0.8607 (t0) REVERT: C 82 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8426 (mm) REVERT: C 114 TYR cc_start: 0.8954 (p90) cc_final: 0.8565 (p90) REVERT: E 66 GLU cc_start: 0.7324 (tp30) cc_final: 0.6513 (tp30) REVERT: D 82 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8420 (mm) REVERT: F 17 LEU cc_start: 0.8335 (mm) cc_final: 0.8111 (mt) REVERT: F 74 ASP cc_start: 0.8855 (t70) cc_final: 0.8610 (t0) outliers start: 31 outliers final: 26 residues processed: 312 average time/residue: 0.1755 time to fit residues: 81.8328 Evaluate side-chains 324 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 295 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain H residue 31 HIS 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 117 SER Chi-restraints excluded: chain L residue 80 LYS Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 54 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 17 optimal weight: 0.2980 chunk 55 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 113 optimal weight: 0.0030 chunk 119 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 overall best weight: 2.2594 ------------------------------------------------------------------------------- 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** ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.170891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.140045 restraints weight = 12055.823| |-----------------------------------------------------------------------------| r_work (start): 0.4607 rms_B_bonded: 2.89 r_work: 0.4461 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10304 Z= 0.152 Angle : 0.662 14.021 14000 Z= 0.328 Chirality : 0.053 0.197 1638 Planarity : 0.003 0.042 1722 Dihedral : 5.830 19.802 1386 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.75 % Allowed : 21.52 % Favored : 75.73 % 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: -4.12 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.13), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 79 HIS 0.020 0.002 HIS E 31 PHE 0.017 0.001 PHE F 33 TYR 0.015 0.001 TYR F 114 ARG 0.010 0.000 ARG N 34 Details of bonding type rmsd covalent geometry : bond 0.00349 (10304) covalent geometry : angle 0.66237 (14000) ********************** 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 326 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 296 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: G 74 ASP cc_start: 0.8831 (t70) cc_final: 0.8579 (t0) REVERT: G 82 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8052 (mm) REVERT: I 13 MET cc_start: 0.4323 (ttm) cc_final: 0.3876 (ttm) REVERT: H 17 LEU cc_start: 0.7727 (mm) cc_final: 0.7473 (mp) REVERT: H 31 HIS cc_start: 0.7241 (OUTLIER) cc_final: 0.6878 (p-80) REVERT: J 15 LYS cc_start: 0.6829 (mttt) cc_final: 0.6450 (mttm) REVERT: J 82 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8303 (tp) REVERT: J 114 TYR cc_start: 0.8909 (p90) cc_final: 0.8563 (p90) REVERT: K 15 LYS cc_start: 0.6886 (mttt) cc_final: 0.6663 (mttp) REVERT: M 35 LYS cc_start: 0.7519 (tmtt) cc_final: 0.6807 (mtmt) REVERT: L 80 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7510 (tttm) REVERT: L 114 TYR cc_start: 0.8787 (p90) cc_final: 0.8549 (p90) REVERT: N 13 MET cc_start: 0.6368 (ttm) cc_final: 0.6113 (ttm) REVERT: N 30 MET cc_start: 0.8805 (ptp) cc_final: 0.6123 (mmt) REVERT: N 35 LYS cc_start: 0.7289 (mttt) cc_final: 0.6975 (mttt) REVERT: N 114 TYR cc_start: 0.8366 (p90) cc_final: 0.8104 (p90) REVERT: A 15 LYS cc_start: 0.6991 (mttt) cc_final: 0.6741 (mttp) REVERT: A 74 ASP cc_start: 0.8057 (t70) cc_final: 0.7482 (t0) REVERT: B 74 ASP cc_start: 0.8202 (t0) cc_final: 0.7869 (t0) REVERT: B 99 ASP cc_start: 0.8838 (t0) cc_final: 0.8550 (t0) REVERT: C 82 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8430 (mm) REVERT: C 99 ASP cc_start: 0.8447 (t0) cc_final: 0.8101 (t0) REVERT: C 114 TYR cc_start: 0.8947 (p90) cc_final: 0.8700 (p90) REVERT: E 66 GLU cc_start: 0.7304 (tp30) cc_final: 0.6531 (tp30) REVERT: D 82 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8358 (mm) REVERT: D 114 TYR cc_start: 0.8971 (p90) cc_final: 0.8533 (p90) REVERT: F 17 LEU cc_start: 0.8280 (mm) cc_final: 0.8050 (mt) REVERT: F 74 ASP cc_start: 0.8833 (t70) cc_final: 0.8602 (t0) outliers start: 30 outliers final: 22 residues processed: 307 average time/residue: 0.1793 time to fit residues: 81.5850 Evaluate side-chains 314 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 286 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain H residue 31 HIS 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 106 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 117 SER Chi-restraints excluded: chain L residue 80 LYS Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 87 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 56 optimal weight: 30.0000 chunk 88 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 overall best weight: 6.5988 ------------------------------------------------------------------------------- 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** ** 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 = 0.4762 r_free = 0.4762 target = 0.164139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.133873 restraints weight = 12361.739| |-----------------------------------------------------------------------------| r_work (start): 0.4527 rms_B_bonded: 2.83 r_work: 0.4386 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 10304 Z= 0.300 Angle : 0.731 13.352 14000 Z= 0.368 Chirality : 0.054 0.186 1638 Planarity : 0.004 0.040 1722 Dihedral : 6.115 21.006 1386 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 3.11 % Allowed : 21.43 % 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: -4.19 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.13), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 79 HIS 0.018 0.002 HIS E 31 PHE 0.017 0.002 PHE J 64 TYR 0.019 0.002 TYR C 114 ARG 0.009 0.000 ARG N 34 Details of bonding type rmsd covalent geometry : bond 0.00678 (10304) covalent geometry : angle 0.73061 (14000) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4741.11 seconds wall clock time: 85 minutes 4.63 seconds (5104.63 seconds total)