Starting phenix.real_space_refine on Sun Dec 29 05:28:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ob4_12794/12_2024/7ob4_12794.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ob4_12794/12_2024/7ob4_12794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ob4_12794/12_2024/7ob4_12794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ob4_12794/12_2024/7ob4_12794.map" model { file = "/net/cci-nas-00/data/ceres_data/7ob4_12794/12_2024/7ob4_12794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ob4_12794/12_2024/7ob4_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 6.44, per 1000 atoms: 0.64 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: 2.47 Conformation dependent library (CDL) restraints added in 1.3 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: 1.78 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 13 through 16 current: chain 'C' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 13 through 16 current: chain 'E' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 13 through 16 current: chain 'G' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 13 through 16 current: chain 'I' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 13 through 16 current: chain 'K' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 13 through 16 current: chain 'M' and resid 13 through 16 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 19 through 21 current: chain 'C' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 19 through 21 current: chain 'E' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 19 through 21 current: chain 'G' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 19 through 21 current: chain 'I' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 19 through 21 current: chain 'K' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 19 through 21 current: chain 'M' and resid 19 through 21 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 25 through 34 current: chain 'C' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 25 through 34 current: chain 'E' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 25 through 34 current: chain 'G' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 25 through 34 current: chain 'I' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 25 through 34 current: chain 'K' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 25 through 34 current: chain 'M' and resid 25 through 34 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 59 through 65 current: chain 'C' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 59 through 65 current: chain 'E' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 59 through 65 current: chain 'G' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 59 through 65 current: chain 'I' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 59 through 65 current: chain 'K' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 59 through 65 current: chain 'M' and resid 59 through 65 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 71 through 73 current: chain 'C' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 71 through 73 current: chain 'E' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 71 through 73 current: chain 'G' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 71 through 73 current: chain 'I' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 71 through 73 current: chain 'K' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 71 through 73 current: chain 'M' and resid 71 through 73 No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 76 through 77 current: chain 'C' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 76 through 77 current: chain 'E' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 76 through 77 current: chain 'G' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 76 through 77 current: chain 'I' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 76 through 77 current: chain 'K' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 76 through 77 current: chain 'M' and resid 76 through 77 No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 79 through 82 current: chain 'C' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 79 through 82 current: chain 'E' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 79 through 82 current: chain 'G' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 79 through 82 current: chain 'I' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 79 through 82 current: chain 'K' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 79 through 82 current: chain 'M' and resid 79 through 82 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 92 through 99 current: chain 'C' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 92 through 99 current: chain 'E' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 92 through 99 current: chain 'G' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 92 through 99 current: chain 'I' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 92 through 99 current: chain 'K' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 92 through 99 current: chain 'M' and resid 92 through 99 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 103 through 108 current: chain 'C' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 103 through 108 current: chain 'E' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 103 through 108 current: chain 'G' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 103 through 108 current: chain 'I' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 103 through 108 current: chain 'K' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 103 through 108 current: chain 'M' and resid 103 through 108 No H-bonds generated for sheet with id=AA9 Processing sheet with id=A10, first strand: chain 'A' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 115 through 115 current: chain 'C' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 115 through 115 current: chain 'E' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 115 through 115 current: chain 'G' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 115 through 115 current: chain 'I' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 115 through 115 current: chain 'K' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 115 through 115 current: chain 'M' and resid 115 through 115 No H-bonds generated for sheet with id=A10 Processing sheet with id=A11, first strand: chain 'A' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 118 through 122 current: chain 'C' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 118 through 122 current: chain 'E' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 118 through 122 current: chain 'G' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 118 through 122 current: chain 'I' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 118 through 122 current: chain 'K' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 118 through 122 current: chain 'M' and resid 118 through 122 No H-bonds generated for sheet with id=A11 Processing sheet with id=BA1, first strand: chain 'B' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 13 through 16 current: chain 'D' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 13 through 16 current: chain 'F' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 13 through 16 current: chain 'H' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 13 through 16 current: chain 'J' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 13 through 16 current: chain 'L' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 13 through 16 current: chain 'N' and resid 13 through 16 No H-bonds generated for sheet with id=BA1 Processing sheet with id=BA2, first strand: chain 'B' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 19 through 21 current: chain 'D' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 19 through 21 current: chain 'F' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 19 through 21 current: chain 'H' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 19 through 21 current: chain 'J' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 19 through 21 current: chain 'L' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 19 through 21 current: chain 'N' and resid 19 through 21 No H-bonds generated for sheet with id=BA2 Processing sheet with id=BA3, first strand: chain 'B' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 25 through 34 current: chain 'D' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 25 through 34 current: chain 'F' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 25 through 34 current: chain 'H' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 25 through 34 current: chain 'J' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 25 through 34 current: chain 'L' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 25 through 34 current: chain 'N' and resid 25 through 34 No H-bonds generated for sheet with id=BA3 Processing sheet with id=BA4, first strand: chain 'B' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 59 through 65 current: chain 'D' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 59 through 65 current: chain 'F' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 59 through 65 current: chain 'H' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 59 through 65 current: chain 'J' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 59 through 65 current: chain 'L' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 59 through 65 current: chain 'N' and resid 59 through 65 No H-bonds generated for sheet with id=BA4 Processing sheet with id=BA5, first strand: chain 'B' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 71 through 73 current: chain 'D' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 71 through 73 current: chain 'F' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 71 through 73 current: chain 'H' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 71 through 73 current: chain 'J' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 71 through 73 current: chain 'L' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 71 through 73 current: chain 'N' and resid 71 through 73 No H-bonds generated for sheet with id=BA5 Processing sheet with id=BA6, first strand: chain 'B' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 76 through 77 current: chain 'D' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 76 through 77 current: chain 'F' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 76 through 77 current: chain 'H' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 76 through 77 current: chain 'J' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 76 through 77 current: chain 'L' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 76 through 77 current: chain 'N' and resid 76 through 77 No H-bonds generated for sheet with id=BA6 Processing sheet with id=BA7, first strand: chain 'B' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 79 through 82 current: chain 'D' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 79 through 82 current: chain 'F' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 79 through 82 current: chain 'H' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 79 through 82 current: chain 'J' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 79 through 82 current: chain 'L' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 79 through 82 current: chain 'N' and resid 79 through 82 No H-bonds generated for sheet with id=BA7 Processing sheet with id=BA8, first strand: chain 'B' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 92 through 99 current: chain 'D' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 92 through 99 current: chain 'F' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 92 through 99 current: chain 'H' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 92 through 99 current: chain 'J' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 92 through 99 current: chain 'L' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 92 through 99 current: chain 'N' and resid 92 through 99 No H-bonds generated for sheet with id=BA8 Processing sheet with id=BA9, first strand: chain 'B' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 103 through 108 current: chain 'D' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 103 through 108 current: chain 'F' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 103 through 108 current: chain 'H' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 103 through 108 current: chain 'J' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 103 through 108 current: chain 'L' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 103 through 108 current: chain 'N' and resid 103 through 108 No H-bonds generated for sheet with id=BA9 Processing sheet with id=B10, first strand: chain 'B' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 115 through 115 current: chain 'D' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 115 through 115 current: chain 'F' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 115 through 115 current: chain 'H' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 115 through 115 current: chain 'J' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 115 through 115 current: chain 'L' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 115 through 115 current: chain 'N' and resid 115 through 115 No H-bonds generated for sheet with id=B10 Processing sheet with id=B11, first strand: chain 'B' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 118 through 122 current: chain 'D' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 118 through 122 current: chain 'F' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 118 through 122 current: chain 'H' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 118 through 122 current: chain 'J' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 118 through 122 current: chain 'L' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 118 through 122 current: chain 'N' and resid 118 through 122 No H-bonds generated for sheet with id=B11 No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.89 Time building geometry restraints manager: 2.86 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: 0.00 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: 0.600 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.090 Find NCS groups from input model: 0.280 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.060 10304 Z= 0.534 Angle : 1.030 8.374 14000 Z= 0.651 Chirality : 0.073 0.397 1638 Planarity : 0.004 0.081 1722 Dihedral : 13.887 85.041 3654 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 23.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.09 % Allowed : 12.91 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP N 79 HIS 0.005 0.001 HIS M 31 PHE 0.012 0.002 PHE F 64 TYR 0.010 0.002 TYR H 114 ARG 0.002 0.000 ARG K 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 354 time to evaluate : 1.105 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: 0.2035 time to fit residues: 102.8027 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 : 1.162 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 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 *********************** 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 : 1.223 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: 0.5898 (mt-10) cc_final: 0.5254 (mt-10) REVERT: I 13 MET cc_start: 0.5877 (ttm) cc_final: 0.5524 (ttm) REVERT: J 15 LYS cc_start: 0.8110 (mttt) cc_final: 0.7904 (mttm) REVERT: M 30 MET cc_start: 0.7661 (ptm) cc_final: 0.6154 (mmt) REVERT: N 30 MET cc_start: 0.7281 (ptm) cc_final: 0.6541 (mmt) REVERT: A 31 HIS cc_start: 0.6591 (p90) cc_final: 0.5496 (m-70) REVERT: F 13 MET cc_start: 0.6002 (ttm) cc_final: 0.5578 (ttm) REVERT: F 15 LYS cc_start: 0.8244 (mttt) cc_final: 0.8037 (mttm) REVERT: F 74 ASP cc_start: 0.8255 (t0) cc_final: 0.7850 (t0) outliers start: 35 outliers final: 18 residues processed: 340 average time/residue: 0.1899 time to fit residues: 96.4345 Evaluate side-chains 330 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 312 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 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 63 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10304 Z= 0.177 Angle : 0.597 6.947 14000 Z= 0.311 Chirality : 0.051 0.195 1638 Planarity : 0.003 0.026 1722 Dihedral : 5.696 18.493 1386 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.66 % Allowed : 17.49 % Favored : 79.85 % 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: -3.79 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 79 HIS 0.018 0.002 HIS F 31 PHE 0.014 0.001 PHE M 33 TYR 0.021 0.001 TYR D 114 ARG 0.005 0.000 ARG K 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 319 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 13 MET cc_start: 0.5993 (ttm) cc_final: 0.5599 (ttm) REVERT: J 15 LYS cc_start: 0.8090 (mttt) cc_final: 0.7853 (mttm) REVERT: M 30 MET cc_start: 0.7463 (ptm) cc_final: 0.6081 (mmp) REVERT: N 30 MET cc_start: 0.7130 (ptm) cc_final: 0.6304 (mmt) REVERT: N 35 LYS cc_start: 0.7568 (mttt) cc_final: 0.7311 (mmtp) REVERT: A 13 MET cc_start: 0.6031 (ttm) cc_final: 0.5746 (ttm) REVERT: D 76 LYS cc_start: 0.8372 (mtpt) cc_final: 0.8161 (mtpt) outliers start: 29 outliers final: 19 residues processed: 322 average time/residue: 0.1775 time to fit residues: 85.3227 Evaluate side-chains 315 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 296 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 17 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 89 GLU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 6.9990 chunk 86 optimal weight: 0.1980 chunk 59 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 54 optimal weight: 30.0000 chunk 76 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 overall best weight: 5.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 HIS ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 10304 Z= 0.248 Angle : 0.633 8.691 14000 Z= 0.329 Chirality : 0.051 0.184 1638 Planarity : 0.003 0.027 1722 Dihedral : 5.904 19.783 1386 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.75 % Allowed : 19.41 % Favored : 77.84 % 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: -3.80 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 79 HIS 0.016 0.002 HIS F 31 PHE 0.014 0.002 PHE H 64 TYR 0.030 0.002 TYR C 114 ARG 0.008 0.000 ARG N 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 312 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 13 MET cc_start: 0.5944 (ttm) cc_final: 0.5537 (ttm) REVERT: J 15 LYS cc_start: 0.8195 (mttt) cc_final: 0.7777 (mttm) REVERT: J 66 GLU cc_start: 0.7001 (tp30) cc_final: 0.6709 (tp30) REVERT: N 30 MET cc_start: 0.7506 (ptm) cc_final: 0.6553 (mmt) REVERT: N 35 LYS cc_start: 0.7623 (mttt) cc_final: 0.7292 (mmtp) REVERT: E 85 SER cc_start: 0.8950 (t) cc_final: 0.8619 (p) REVERT: D 76 LYS cc_start: 0.8363 (mtpt) cc_final: 0.8075 (mtpt) outliers start: 30 outliers final: 23 residues processed: 316 average time/residue: 0.1788 time to fit residues: 84.6890 Evaluate side-chains 315 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 292 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 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 117 SER Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain F residue 117 SER 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 101 optimal weight: 20.0000 chunk 69 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 62 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 10304 Z= 0.336 Angle : 0.682 7.102 14000 Z= 0.357 Chirality : 0.053 0.217 1638 Planarity : 0.003 0.025 1722 Dihedral : 6.140 20.597 1386 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.21 % Allowed : 20.15 % Favored : 76.65 % 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 : -2.98 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 79 HIS 0.018 0.003 HIS I 31 PHE 0.018 0.002 PHE F 33 TYR 0.035 0.002 TYR D 114 ARG 0.009 0.000 ARG N 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 315 time to evaluate : 1.203 Fit side-chains REVERT: G 66 GLU cc_start: 0.7360 (tp30) cc_final: 0.6954 (tp30) REVERT: I 13 MET cc_start: 0.6035 (ttm) cc_final: 0.5609 (ttm) REVERT: I 66 GLU cc_start: 0.5622 (mt-10) cc_final: 0.5282 (mt-10) REVERT: J 15 LYS cc_start: 0.8182 (mttt) cc_final: 0.7837 (mttm) REVERT: N 30 MET cc_start: 0.7640 (ptm) cc_final: 0.6501 (mmt) REVERT: N 35 LYS cc_start: 0.7473 (mttt) cc_final: 0.7157 (mmtp) REVERT: E 85 SER cc_start: 0.8924 (t) cc_final: 0.8567 (p) REVERT: D 76 LYS cc_start: 0.8363 (mtpt) cc_final: 0.8069 (mtpt) outliers start: 35 outliers final: 28 residues processed: 322 average time/residue: 0.1783 time to fit residues: 86.1746 Evaluate side-chains 325 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 297 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain K residue 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 A residue 117 SER Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 31 HIS 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 40 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 101 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 64 optimal weight: 30.0000 chunk 117 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10304 Z= 0.171 Angle : 0.617 7.086 14000 Z= 0.315 Chirality : 0.051 0.251 1638 Planarity : 0.003 0.038 1722 Dihedral : 5.828 20.551 1386 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.84 % Allowed : 21.25 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 79 HIS 0.018 0.002 HIS F 31 PHE 0.015 0.001 PHE D 33 TYR 0.030 0.001 TYR C 114 ARG 0.009 0.000 ARG N 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 307 time to evaluate : 1.119 Fit side-chains revert: symmetry clash REVERT: I 13 MET cc_start: 0.5956 (ttm) cc_final: 0.5510 (ttm) REVERT: H 17 LEU cc_start: 0.7366 (mm) cc_final: 0.7136 (mp) REVERT: J 15 LYS cc_start: 0.8199 (mttt) cc_final: 0.7920 (mttm) REVERT: K 13 MET cc_start: 0.5769 (ttm) cc_final: 0.5550 (mtp) REVERT: L 70 LYS cc_start: 0.8355 (ttmt) cc_final: 0.8052 (ttmt) REVERT: N 30 MET cc_start: 0.7455 (ptm) cc_final: 0.6390 (mmt) REVERT: N 35 LYS cc_start: 0.7533 (mttt) cc_final: 0.7327 (mmtp) REVERT: N 70 LYS cc_start: 0.8200 (ttpt) cc_final: 0.7866 (ttmt) REVERT: E 66 GLU cc_start: 0.7311 (tp30) cc_final: 0.7006 (tp30) REVERT: E 85 SER cc_start: 0.8858 (t) cc_final: 0.8455 (p) outliers start: 31 outliers final: 26 residues processed: 315 average time/residue: 0.1952 time to fit residues: 91.6836 Evaluate side-chains 315 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 289 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 30 MET 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 75 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 10304 Z= 0.258 Angle : 0.657 7.262 14000 Z= 0.337 Chirality : 0.052 0.262 1638 Planarity : 0.003 0.032 1722 Dihedral : 5.981 20.865 1386 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.93 % Allowed : 21.98 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 79 HIS 0.019 0.002 HIS I 31 PHE 0.019 0.002 PHE D 33 TYR 0.032 0.002 TYR C 114 ARG 0.009 0.000 ARG N 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 305 time to evaluate : 1.139 Fit side-chains REVERT: G 74 ASP cc_start: 0.8107 (t70) cc_final: 0.7899 (t0) REVERT: I 13 MET cc_start: 0.6016 (ttm) cc_final: 0.5585 (ttm) REVERT: J 15 LYS cc_start: 0.8220 (mttt) cc_final: 0.7938 (mttm) REVERT: L 70 LYS cc_start: 0.8402 (ttmt) cc_final: 0.8101 (ttmt) REVERT: N 30 MET cc_start: 0.7680 (ptm) cc_final: 0.6484 (mmt) REVERT: E 85 SER cc_start: 0.8878 (t) cc_final: 0.8456 (p) outliers start: 32 outliers final: 28 residues processed: 314 average time/residue: 0.1943 time to fit residues: 92.3537 Evaluate side-chains 318 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 290 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 30 MET 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 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 82 LEU Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain N residue 31 HIS Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain A residue 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 23 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 82 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 95 optimal weight: 7.9990 chunk 110 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 10304 Z= 0.336 Angle : 0.716 8.530 14000 Z= 0.371 Chirality : 0.054 0.312 1638 Planarity : 0.003 0.026 1722 Dihedral : 6.262 21.719 1386 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 3.11 % Allowed : 21.52 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.17), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.13), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 79 HIS 0.018 0.003 HIS I 31 PHE 0.043 0.003 PHE M 33 TYR 0.015 0.002 TYR M 105 ARG 0.008 0.000 ARG N 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 303 time to evaluate : 0.990 Fit side-chains REVERT: I 13 MET cc_start: 0.6017 (ttm) cc_final: 0.5575 (ttm) REVERT: J 15 LYS cc_start: 0.8194 (mttt) cc_final: 0.7903 (mttm) REVERT: M 66 GLU cc_start: 0.7310 (tp30) cc_final: 0.7013 (tp30) REVERT: L 70 LYS cc_start: 0.8477 (ttmt) cc_final: 0.8113 (ttmt) REVERT: N 35 LYS cc_start: 0.7333 (mmtt) cc_final: 0.7053 (mmtp) REVERT: E 85 SER cc_start: 0.8878 (t) cc_final: 0.8464 (p) outliers start: 34 outliers final: 28 residues processed: 314 average time/residue: 0.1737 time to fit residues: 82.4722 Evaluate side-chains 317 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 289 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 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 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 82 LEU Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain N residue 31 HIS Chi-restraints excluded: chain N residue 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 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 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 113 optimal weight: 0.8980 chunk 116 optimal weight: 10.0000 chunk 68 optimal weight: 0.0770 chunk 49 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 34 optimal weight: 0.0030 chunk 102 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 119 optimal weight: 20.0000 overall best weight: 0.5750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10304 Z= 0.115 Angle : 0.640 8.438 14000 Z= 0.324 Chirality : 0.053 0.258 1638 Planarity : 0.003 0.032 1722 Dihedral : 5.785 20.439 1386 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.29 % Allowed : 22.53 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 79 HIS 0.018 0.002 HIS F 31 PHE 0.028 0.001 PHE A 33 TYR 0.016 0.001 TYR F 114 ARG 0.010 0.001 ARG H 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 307 time to evaluate : 1.051 Fit side-chains REVERT: I 13 MET cc_start: 0.5860 (ttm) cc_final: 0.5446 (ttm) REVERT: J 15 LYS cc_start: 0.8103 (mttt) cc_final: 0.7734 (mttm) REVERT: K 17 LEU cc_start: 0.7747 (mt) cc_final: 0.7409 (mt) REVERT: K 70 LYS cc_start: 0.8468 (ttmt) cc_final: 0.8171 (ttmt) REVERT: L 70 LYS cc_start: 0.8374 (ttmt) cc_final: 0.8058 (ttmt) REVERT: N 30 MET cc_start: 0.6171 (ptp) cc_final: 0.5637 (mmp) REVERT: N 35 LYS cc_start: 0.7395 (mmtt) cc_final: 0.7172 (mmtp) REVERT: E 66 GLU cc_start: 0.7331 (tp30) cc_final: 0.6870 (tp30) REVERT: E 85 SER cc_start: 0.8907 (t) cc_final: 0.8505 (p) REVERT: F 66 GLU cc_start: 0.7043 (tp30) cc_final: 0.6702 (mm-30) outliers start: 25 outliers final: 22 residues processed: 316 average time/residue: 0.1999 time to fit residues: 95.1086 Evaluate side-chains 302 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 280 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 106 THR 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 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 16 VAL Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain N residue 31 HIS Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain A residue 35 LYS 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 D residue 117 SER Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.8980 chunk 56 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 125 optimal weight: 8.9990 chunk 115 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10304 Z= 0.234 Angle : 0.676 8.606 14000 Z= 0.348 Chirality : 0.053 0.296 1638 Planarity : 0.003 0.030 1722 Dihedral : 5.928 20.386 1386 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.20 % Allowed : 22.80 % Favored : 75.00 % 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: -4.09 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 79 HIS 0.021 0.002 HIS N 31 PHE 0.024 0.002 PHE M 33 TYR 0.013 0.001 TYR D 114 ARG 0.007 0.000 ARG N 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 282 time to evaluate : 1.140 Fit side-chains REVERT: I 13 MET cc_start: 0.5957 (ttm) cc_final: 0.5526 (ttm) REVERT: J 15 LYS cc_start: 0.8125 (mttt) cc_final: 0.7712 (mttm) REVERT: K 70 LYS cc_start: 0.8384 (ttmt) cc_final: 0.8152 (ttmt) REVERT: M 30 MET cc_start: 0.7408 (ptm) cc_final: 0.6339 (mmp) REVERT: L 70 LYS cc_start: 0.8465 (ttmt) cc_final: 0.8062 (ttmt) REVERT: N 30 MET cc_start: 0.6378 (ptp) cc_final: 0.5913 (mmt) REVERT: N 35 LYS cc_start: 0.7417 (mmtt) cc_final: 0.7138 (mmtp) REVERT: E 85 SER cc_start: 0.8818 (t) cc_final: 0.8370 (p) REVERT: F 76 LYS cc_start: 0.8222 (mttt) cc_final: 0.8011 (mttt) outliers start: 24 outliers final: 21 residues processed: 293 average time/residue: 0.1799 time to fit residues: 78.4242 Evaluate side-chains 295 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 274 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 15 LYS 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 117 SER Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain N residue 31 HIS Chi-restraints excluded: chain N residue 106 THR 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 D residue 117 SER Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.166128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.135604 restraints weight = 12142.629| |-----------------------------------------------------------------------------| r_work (start): 0.4567 rms_B_bonded: 2.83 r_work: 0.4424 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 10304 Z= 0.280 Angle : 0.712 8.241 14000 Z= 0.364 Chirality : 0.054 0.336 1638 Planarity : 0.003 0.027 1722 Dihedral : 6.061 20.663 1386 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 2.38 % Allowed : 22.34 % Favored : 75.27 % 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: -4.14 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.13), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 79 HIS 0.020 0.003 HIS I 31 PHE 0.025 0.002 PHE M 33 TYR 0.016 0.002 TYR J 114 ARG 0.006 0.000 ARG N 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2393.26 seconds wall clock time: 45 minutes 6.11 seconds (2706.11 seconds total)