Starting phenix.real_space_refine on Tue Feb 13 20:28:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oag_12776/02_2024/7oag_12776.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oag_12776/02_2024/7oag_12776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oag_12776/02_2024/7oag_12776.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oag_12776/02_2024/7oag_12776.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oag_12776/02_2024/7oag_12776.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oag_12776/02_2024/7oag_12776.pdb" } resolution = 3.4 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= 0.000 sd= 0.001 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 175 5.16 5 C 4750 2.51 5 N 1325 2.21 5 O 1350 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7600 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "B" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "C" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "D" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "E" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "F" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "G" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "H" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "I" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "K" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "M" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "N" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "O" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "P" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "Q" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "R" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "S" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "T" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "U" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "V" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "W" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "X" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "Y" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Time building chain proxies: 4.28, per 1000 atoms: 0.56 Number of scatterers: 7600 At special positions: 0 Unit cell: (76.911, 76.911, 124.877, 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 175 16.00 O 1350 8.00 N 1325 7.00 C 4750 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=75, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 30 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 37 " distance=2.03 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 39 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 30 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 37 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 39 " distance=2.02 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 30 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 37 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 39 " distance=2.03 Simple disulfide: pdb=" SG CYS D 4 " - pdb=" SG CYS D 30 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 37 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 39 " distance=2.03 Simple disulfide: pdb=" SG CYS E 4 " - pdb=" SG CYS E 30 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 37 " distance=2.03 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 39 " distance=2.02 Simple disulfide: pdb=" SG CYS F 4 " - pdb=" SG CYS F 30 " distance=2.03 Simple disulfide: pdb=" SG CYS F 15 " - pdb=" SG CYS F 37 " distance=2.03 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 39 " distance=2.03 Simple disulfide: pdb=" SG CYS G 4 " - pdb=" SG CYS G 30 " distance=2.03 Simple disulfide: pdb=" SG CYS G 15 " - pdb=" SG CYS G 37 " distance=2.03 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS G 39 " distance=2.03 Simple disulfide: pdb=" SG CYS H 4 " - pdb=" SG CYS H 30 " distance=2.03 Simple disulfide: pdb=" SG CYS H 15 " - pdb=" SG CYS H 37 " distance=2.03 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 39 " distance=2.03 Simple disulfide: pdb=" SG CYS I 4 " - pdb=" SG CYS I 30 " distance=2.03 Simple disulfide: pdb=" SG CYS I 15 " - pdb=" SG CYS I 37 " distance=2.03 Simple disulfide: pdb=" SG CYS I 19 " - pdb=" SG CYS I 39 " distance=2.03 Simple disulfide: pdb=" SG CYS J 4 " - pdb=" SG CYS J 30 " distance=2.03 Simple disulfide: pdb=" SG CYS J 15 " - pdb=" SG CYS J 37 " distance=2.03 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS J 39 " distance=2.03 Simple disulfide: pdb=" SG CYS K 4 " - pdb=" SG CYS K 30 " distance=2.03 Simple disulfide: pdb=" SG CYS K 15 " - pdb=" SG CYS K 37 " distance=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 39 " distance=2.03 Simple disulfide: pdb=" SG CYS L 4 " - pdb=" SG CYS L 30 " distance=2.03 Simple disulfide: pdb=" SG CYS L 15 " - pdb=" SG CYS L 37 " distance=2.03 Simple disulfide: pdb=" SG CYS L 19 " - pdb=" SG CYS L 39 " distance=2.03 Simple disulfide: pdb=" SG CYS M 4 " - pdb=" SG CYS M 30 " distance=2.03 Simple disulfide: pdb=" SG CYS M 15 " - pdb=" SG CYS M 37 " distance=2.03 Simple disulfide: pdb=" SG CYS M 19 " - pdb=" SG CYS M 39 " distance=2.02 Simple disulfide: pdb=" SG CYS N 4 " - pdb=" SG CYS N 30 " distance=2.03 Simple disulfide: pdb=" SG CYS N 15 " - pdb=" SG CYS N 37 " distance=2.03 Simple disulfide: pdb=" SG CYS N 19 " - pdb=" SG CYS N 39 " distance=2.03 Simple disulfide: pdb=" SG CYS O 4 " - pdb=" SG CYS O 30 " distance=2.03 Simple disulfide: pdb=" SG CYS O 15 " - pdb=" SG CYS O 37 " distance=2.03 Simple disulfide: pdb=" SG CYS O 19 " - pdb=" SG CYS O 39 " distance=2.03 Simple disulfide: pdb=" SG CYS P 4 " - pdb=" SG CYS P 30 " distance=2.03 Simple disulfide: pdb=" SG CYS P 15 " - pdb=" SG CYS P 37 " distance=2.03 Simple disulfide: pdb=" SG CYS P 19 " - pdb=" SG CYS P 39 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 4 " - pdb=" SG CYS Q 30 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 15 " - pdb=" SG CYS Q 37 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 19 " - pdb=" SG CYS Q 39 " distance=2.03 Simple disulfide: pdb=" SG CYS R 4 " - pdb=" SG CYS R 30 " distance=2.03 Simple disulfide: pdb=" SG CYS R 15 " - pdb=" SG CYS R 37 " distance=2.03 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 39 " distance=2.03 Simple disulfide: pdb=" SG CYS S 4 " - pdb=" SG CYS S 30 " distance=2.03 Simple disulfide: pdb=" SG CYS S 15 " - pdb=" SG CYS S 37 " distance=2.03 Simple disulfide: pdb=" SG CYS S 19 " - pdb=" SG CYS S 39 " distance=2.03 Simple disulfide: pdb=" SG CYS T 4 " - pdb=" SG CYS T 30 " distance=2.03 Simple disulfide: pdb=" SG CYS T 15 " - pdb=" SG CYS T 37 " distance=2.03 Simple disulfide: pdb=" SG CYS T 19 " - pdb=" SG CYS T 39 " distance=2.03 Simple disulfide: pdb=" SG CYS U 4 " - pdb=" SG CYS U 30 " distance=2.03 Simple disulfide: pdb=" SG CYS U 15 " - pdb=" SG CYS U 37 " distance=2.03 Simple disulfide: pdb=" SG CYS U 19 " - pdb=" SG CYS U 39 " distance=2.03 Simple disulfide: pdb=" SG CYS V 4 " - pdb=" SG CYS V 30 " distance=2.03 Simple disulfide: pdb=" SG CYS V 15 " - pdb=" SG CYS V 37 " distance=2.03 Simple disulfide: pdb=" SG CYS V 19 " - pdb=" SG CYS V 39 " distance=2.03 Simple disulfide: pdb=" SG CYS W 4 " - pdb=" SG CYS W 30 " distance=2.03 Simple disulfide: pdb=" SG CYS W 15 " - pdb=" SG CYS W 37 " distance=2.03 Simple disulfide: pdb=" SG CYS W 19 " - pdb=" SG CYS W 39 " distance=2.03 Simple disulfide: pdb=" SG CYS X 4 " - pdb=" SG CYS X 30 " distance=2.03 Simple disulfide: pdb=" SG CYS X 15 " - pdb=" SG CYS X 37 " distance=2.03 Simple disulfide: pdb=" SG CYS X 19 " - pdb=" SG CYS X 39 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 4 " - pdb=" SG CYS Y 30 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 15 " - pdb=" SG CYS Y 37 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 19 " - pdb=" SG CYS Y 39 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 1.5 seconds 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1600 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 25 sheets defined 47.5% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 13 through 21 Processing helix chain 'A' and resid 31 through 35 Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 13 through 21 Processing helix chain 'B' and resid 31 through 35 Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 13 through 21 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 13 through 21 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'E' and resid 5 through 9 Processing helix chain 'E' and resid 13 through 21 Processing helix chain 'E' and resid 31 through 35 Processing helix chain 'F' and resid 5 through 9 Processing helix chain 'F' and resid 13 through 21 Processing helix chain 'F' and resid 31 through 35 Processing helix chain 'G' and resid 5 through 9 Processing helix chain 'G' and resid 13 through 21 Processing helix chain 'G' and resid 31 through 35 Processing helix chain 'H' and resid 5 through 9 Processing helix chain 'H' and resid 13 through 21 Processing helix chain 'H' and resid 31 through 35 Processing helix chain 'I' and resid 5 through 9 Processing helix chain 'I' and resid 13 through 21 Processing helix chain 'I' and resid 31 through 35 Processing helix chain 'J' and resid 5 through 9 Processing helix chain 'J' and resid 13 through 21 Processing helix chain 'J' and resid 31 through 35 Processing helix chain 'K' and resid 5 through 9 Processing helix chain 'K' and resid 13 through 21 Processing helix chain 'K' and resid 31 through 35 Processing helix chain 'L' and resid 5 through 9 Processing helix chain 'L' and resid 13 through 21 Processing helix chain 'L' and resid 31 through 35 Processing helix chain 'M' and resid 5 through 9 Processing helix chain 'M' and resid 13 through 21 Processing helix chain 'M' and resid 31 through 35 Processing helix chain 'N' and resid 5 through 9 Processing helix chain 'N' and resid 13 through 21 Processing helix chain 'N' and resid 31 through 35 Processing helix chain 'O' and resid 5 through 9 Processing helix chain 'O' and resid 13 through 21 Processing helix chain 'O' and resid 31 through 35 Processing helix chain 'P' and resid 5 through 9 Processing helix chain 'P' and resid 13 through 21 Processing helix chain 'P' and resid 31 through 35 Processing helix chain 'Q' and resid 5 through 9 Processing helix chain 'Q' and resid 13 through 21 Processing helix chain 'Q' and resid 31 through 35 Processing helix chain 'R' and resid 5 through 9 Processing helix chain 'R' and resid 13 through 21 Processing helix chain 'R' and resid 31 through 35 Processing helix chain 'S' and resid 5 through 9 Processing helix chain 'S' and resid 13 through 21 Processing helix chain 'S' and resid 31 through 35 Processing helix chain 'T' and resid 5 through 9 Processing helix chain 'T' and resid 13 through 21 Processing helix chain 'T' and resid 31 through 35 Processing helix chain 'U' and resid 5 through 9 Processing helix chain 'U' and resid 13 through 21 Processing helix chain 'U' and resid 31 through 35 Processing helix chain 'V' and resid 5 through 9 Processing helix chain 'V' and resid 13 through 21 Processing helix chain 'V' and resid 31 through 35 Processing helix chain 'W' and resid 5 through 9 Processing helix chain 'W' and resid 13 through 21 Processing helix chain 'W' and resid 31 through 35 Processing helix chain 'X' and resid 5 through 9 Processing helix chain 'X' and resid 13 through 21 Processing helix chain 'X' and resid 31 through 35 Processing helix chain 'Y' and resid 5 through 9 Processing helix chain 'Y' and resid 13 through 21 Processing helix chain 'Y' and resid 31 through 35 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AA3, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AA4, first strand: chain 'D' and resid 28 through 30 Processing sheet with id=AA5, first strand: chain 'E' and resid 28 through 30 Processing sheet with id=AA6, first strand: chain 'F' and resid 28 through 30 Processing sheet with id=AA7, first strand: chain 'G' and resid 28 through 30 Processing sheet with id=AA8, first strand: chain 'H' and resid 28 through 30 Processing sheet with id=AA9, first strand: chain 'I' and resid 28 through 30 Processing sheet with id=AB1, first strand: chain 'J' and resid 28 through 30 Processing sheet with id=AB2, first strand: chain 'K' and resid 28 through 30 Processing sheet with id=AB3, first strand: chain 'L' and resid 28 through 30 Processing sheet with id=AB4, first strand: chain 'M' and resid 28 through 30 Processing sheet with id=AB5, first strand: chain 'N' and resid 28 through 30 Processing sheet with id=AB6, first strand: chain 'O' and resid 28 through 30 Processing sheet with id=AB7, first strand: chain 'P' and resid 28 through 30 Processing sheet with id=AB8, first strand: chain 'Q' and resid 28 through 30 Processing sheet with id=AB9, first strand: chain 'R' and resid 28 through 30 Processing sheet with id=AC1, first strand: chain 'S' and resid 28 through 30 Processing sheet with id=AC2, first strand: chain 'T' and resid 28 through 30 Processing sheet with id=AC3, first strand: chain 'U' and resid 28 through 30 Processing sheet with id=AC4, first strand: chain 'V' and resid 28 through 30 Processing sheet with id=AC5, first strand: chain 'W' and resid 28 through 30 Processing sheet with id=AC6, first strand: chain 'X' and resid 28 through 30 Processing sheet with id=AC7, first strand: chain 'Y' and resid 28 through 30 250 hydrogen bonds defined for protein. 600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.81 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2350 1.34 - 1.46: 2020 1.46 - 1.57: 3255 1.57 - 1.69: 0 1.69 - 1.80: 200 Bond restraints: 7825 Sorted by residual: bond pdb=" CB TRP V 8 " pdb=" CG TRP V 8 " ideal model delta sigma weight residual 1.498 1.460 0.038 3.10e-02 1.04e+03 1.50e+00 bond pdb=" CB TRP P 8 " pdb=" CG TRP P 8 " ideal model delta sigma weight residual 1.498 1.460 0.038 3.10e-02 1.04e+03 1.50e+00 bond pdb=" CB TRP M 8 " pdb=" CG TRP M 8 " ideal model delta sigma weight residual 1.498 1.460 0.038 3.10e-02 1.04e+03 1.49e+00 bond pdb=" CB TRP R 8 " pdb=" CG TRP R 8 " ideal model delta sigma weight residual 1.498 1.460 0.038 3.10e-02 1.04e+03 1.49e+00 bond pdb=" CB TRP J 8 " pdb=" CG TRP J 8 " ideal model delta sigma weight residual 1.498 1.460 0.038 3.10e-02 1.04e+03 1.49e+00 ... (remaining 7820 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.06: 200 107.06 - 113.77: 4025 113.77 - 120.47: 2831 120.47 - 127.18: 3194 127.18 - 133.89: 125 Bond angle restraints: 10375 Sorted by residual: angle pdb=" CA LYS U 26 " pdb=" CB LYS U 26 " pdb=" CG LYS U 26 " ideal model delta sigma weight residual 114.10 117.63 -3.53 2.00e+00 2.50e-01 3.11e+00 angle pdb=" C LEU Q 36 " pdb=" N CYS Q 37 " pdb=" CA CYS Q 37 " ideal model delta sigma weight residual 122.17 119.31 2.86 1.62e+00 3.81e-01 3.11e+00 angle pdb=" CA LYS B 26 " pdb=" CB LYS B 26 " pdb=" CG LYS B 26 " ideal model delta sigma weight residual 114.10 117.62 -3.52 2.00e+00 2.50e-01 3.10e+00 angle pdb=" CA LYS F 26 " pdb=" CB LYS F 26 " pdb=" CG LYS F 26 " ideal model delta sigma weight residual 114.10 117.62 -3.52 2.00e+00 2.50e-01 3.09e+00 angle pdb=" CA LYS G 26 " pdb=" CB LYS G 26 " pdb=" CG LYS G 26 " ideal model delta sigma weight residual 114.10 117.62 -3.52 2.00e+00 2.50e-01 3.09e+00 ... (remaining 10370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.37: 3548 8.37 - 16.74: 702 16.74 - 25.11: 175 25.11 - 33.48: 100 33.48 - 41.84: 100 Dihedral angle restraints: 4625 sinusoidal: 1975 harmonic: 2650 Sorted by residual: dihedral pdb=" CA ILE N 22 " pdb=" CB ILE N 22 " pdb=" CG1 ILE N 22 " pdb=" CD1 ILE N 22 " ideal model delta sinusoidal sigma weight residual 60.00 98.05 -38.05 3 1.50e+01 4.44e-03 6.68e+00 dihedral pdb=" CA ILE W 22 " pdb=" CB ILE W 22 " pdb=" CG1 ILE W 22 " pdb=" CD1 ILE W 22 " ideal model delta sinusoidal sigma weight residual 60.00 98.04 -38.04 3 1.50e+01 4.44e-03 6.68e+00 dihedral pdb=" CA ILE U 22 " pdb=" CB ILE U 22 " pdb=" CG1 ILE U 22 " pdb=" CD1 ILE U 22 " ideal model delta sinusoidal sigma weight residual 60.00 98.03 -38.03 3 1.50e+01 4.44e-03 6.68e+00 ... (remaining 4622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 463 0.025 - 0.049: 148 0.049 - 0.074: 89 0.074 - 0.098: 95 0.098 - 0.123: 55 Chirality restraints: 850 Sorted by residual: chirality pdb=" CA LYS K 26 " pdb=" N LYS K 26 " pdb=" C LYS K 26 " pdb=" CB LYS K 26 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA LYS N 26 " pdb=" N LYS N 26 " pdb=" C LYS N 26 " pdb=" CB LYS N 26 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.72e-01 chirality pdb=" CA LYS L 26 " pdb=" N LYS L 26 " pdb=" C LYS L 26 " pdb=" CB LYS L 26 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.67e-01 ... (remaining 847 not shown) Planarity restraints: 1350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 6 " 0.015 5.00e-02 4.00e+02 2.30e-02 8.49e-01 pdb=" N PRO C 7 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO C 7 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 7 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY Q 6 " 0.015 5.00e-02 4.00e+02 2.30e-02 8.49e-01 pdb=" N PRO Q 7 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO Q 7 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO Q 7 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 6 " 0.015 5.00e-02 4.00e+02 2.30e-02 8.48e-01 pdb=" N PRO H 7 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO H 7 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO H 7 " 0.013 5.00e-02 4.00e+02 ... (remaining 1347 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2997 2.84 - 3.35: 7691 3.35 - 3.87: 13985 3.87 - 4.38: 16356 4.38 - 4.90: 25243 Nonbonded interactions: 66272 Sorted by model distance: nonbonded pdb=" N PHE L 2 " pdb=" OD2 ASP P 11 " model vdw 2.321 2.520 nonbonded pdb=" OD2 ASP Q 11 " pdb=" N PHE U 2 " model vdw 2.358 2.520 nonbonded pdb=" O HIS K 18 " pdb=" OG SER K 21 " model vdw 2.401 2.440 nonbonded pdb=" O HIS E 18 " pdb=" OG SER E 21 " model vdw 2.402 2.440 nonbonded pdb=" O HIS M 18 " pdb=" OG SER M 21 " model vdw 2.402 2.440 ... (remaining 66267 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } 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: 1.320 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: 5.800 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 24.160 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 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 : 0.007 0.038 7825 Z= 0.447 Angle : 0.673 3.707 10375 Z= 0.381 Chirality : 0.049 0.123 850 Planarity : 0.004 0.023 1350 Dihedral : 10.390 38.045 2800 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.35 (0.28), residues: 950 helix: 1.41 (0.37), residues: 200 sheet: None (None), residues: 0 loop : -0.74 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP R 8 HIS 0.002 0.001 HIS U 16 PHE 0.008 0.001 PHE W 2 TYR 0.005 0.001 TYR F 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.967 Fit side-chains REVERT: L 23 LYS cc_start: 0.9235 (mppt) cc_final: 0.9034 (mmtm) REVERT: L 25 TYR cc_start: 0.9451 (m-80) cc_final: 0.9073 (m-80) REVERT: V 5 ASN cc_start: 0.9346 (t0) cc_final: 0.9021 (t0) REVERT: V 32 LYS cc_start: 0.9137 (mmtt) cc_final: 0.8150 (ttpt) REVERT: X 5 ASN cc_start: 0.9226 (t0) cc_final: 0.8941 (t0) REVERT: X 32 LYS cc_start: 0.9027 (mmtt) cc_final: 0.8137 (mtpt) REVERT: Y 5 ASN cc_start: 0.8722 (t0) cc_final: 0.8509 (t0) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.3865 time to fit residues: 55.0090 Evaluate side-chains 104 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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: 0.8792 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 7825 Z= 0.311 Angle : 0.549 4.129 10375 Z= 0.293 Chirality : 0.046 0.117 850 Planarity : 0.004 0.029 1350 Dihedral : 4.121 19.600 1075 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.13 % Allowed : 6.84 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.28), residues: 950 helix: 1.85 (0.36), residues: 225 sheet: None (None), residues: 0 loop : -0.43 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP W 8 HIS 0.002 0.000 HIS W 16 PHE 0.011 0.001 PHE Y 35 TYR 0.006 0.001 TYR J 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: C 26 LYS cc_start: 0.9485 (ptmm) cc_final: 0.9189 (ptmm) REVERT: I 13 MET cc_start: 0.8113 (mpp) cc_final: 0.7560 (mpp) REVERT: L 25 TYR cc_start: 0.9475 (m-80) cc_final: 0.9186 (m-80) REVERT: P 20 LYS cc_start: 0.9623 (mmmt) cc_final: 0.9310 (mmmm) REVERT: T 5 ASN cc_start: 0.9474 (t0) cc_final: 0.9042 (t0) REVERT: V 5 ASN cc_start: 0.9449 (t0) cc_final: 0.8966 (t0) REVERT: V 32 LYS cc_start: 0.9590 (mmtt) cc_final: 0.8860 (mtpt) REVERT: W 25 TYR cc_start: 0.9390 (m-80) cc_final: 0.9063 (m-80) REVERT: W 26 LYS cc_start: 0.9144 (ptmm) cc_final: 0.8887 (ptmm) REVERT: X 5 ASN cc_start: 0.9375 (t0) cc_final: 0.8984 (t0) REVERT: X 32 LYS cc_start: 0.9586 (mmtt) cc_final: 0.8944 (mtpt) outliers start: 1 outliers final: 0 residues processed: 113 average time/residue: 0.3947 time to fit residues: 52.5680 Evaluate side-chains 107 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 0.0270 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 overall best weight: 1.9844 ------------------------------------------------------------------------------- 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: 0.8781 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7825 Z= 0.177 Angle : 0.469 3.148 10375 Z= 0.247 Chirality : 0.042 0.109 850 Planarity : 0.003 0.026 1350 Dihedral : 3.630 18.340 1075 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.26 % Allowed : 9.94 % Favored : 89.81 % 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: 0.28 (0.28), residues: 950 helix: 2.18 (0.38), residues: 225 sheet: None (None), residues: 0 loop : -0.50 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP W 8 HIS 0.001 0.000 HIS B 16 PHE 0.004 0.001 PHE Y 35 TYR 0.014 0.001 TYR F 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 128 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: C 26 LYS cc_start: 0.9478 (ptmm) cc_final: 0.9183 (ptmm) REVERT: G 11 ASP cc_start: 0.8077 (t0) cc_final: 0.7703 (t0) REVERT: I 13 MET cc_start: 0.8199 (mpp) cc_final: 0.7710 (mpp) REVERT: K 5 ASN cc_start: 0.9282 (t0) cc_final: 0.8631 (t0) REVERT: M 26 LYS cc_start: 0.9398 (ptmt) cc_final: 0.9108 (ptmm) REVERT: O 5 ASN cc_start: 0.9292 (t0) cc_final: 0.8716 (t0) REVERT: P 20 LYS cc_start: 0.9633 (mmmt) cc_final: 0.9289 (mmmm) REVERT: T 5 ASN cc_start: 0.9399 (t0) cc_final: 0.8881 (t0) REVERT: T 20 LYS cc_start: 0.9653 (mmmt) cc_final: 0.9380 (mmmm) REVERT: V 5 ASN cc_start: 0.9410 (t0) cc_final: 0.8898 (t0) REVERT: V 32 LYS cc_start: 0.9515 (mmtt) cc_final: 0.8769 (mtpt) REVERT: W 25 TYR cc_start: 0.9426 (m-80) cc_final: 0.9086 (m-80) REVERT: W 26 LYS cc_start: 0.9101 (ptmm) cc_final: 0.8847 (ptmm) REVERT: X 5 ASN cc_start: 0.9239 (t0) cc_final: 0.8832 (t0) REVERT: X 11 ASP cc_start: 0.7998 (t0) cc_final: 0.7736 (t0) REVERT: X 32 LYS cc_start: 0.9527 (mmtt) cc_final: 0.8776 (ttpt) REVERT: Y 25 TYR cc_start: 0.9553 (m-80) cc_final: 0.9049 (m-80) outliers start: 2 outliers final: 0 residues processed: 128 average time/residue: 0.3957 time to fit residues: 59.5489 Evaluate side-chains 114 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 91 optimal weight: 0.4980 chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- 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: 0.8787 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 7825 Z= 0.191 Angle : 0.475 4.265 10375 Z= 0.249 Chirality : 0.041 0.107 850 Planarity : 0.003 0.026 1350 Dihedral : 3.544 18.128 1075 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.65 % Allowed : 10.84 % Favored : 88.52 % 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: 0.16 (0.28), residues: 950 helix: 2.18 (0.37), residues: 225 sheet: None (None), residues: 0 loop : -0.61 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP Q 8 HIS 0.001 0.000 HIS M 18 PHE 0.003 0.001 PHE Y 35 TYR 0.012 0.001 TYR D 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 127 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: C 26 LYS cc_start: 0.9452 (ptmm) cc_final: 0.9072 (ptmm) REVERT: D 20 LYS cc_start: 0.9623 (mmmt) cc_final: 0.9418 (mmmm) REVERT: D 25 TYR cc_start: 0.9503 (m-80) cc_final: 0.9290 (m-80) REVERT: G 11 ASP cc_start: 0.8071 (t0) cc_final: 0.7651 (t0) REVERT: I 5 ASN cc_start: 0.9311 (t0) cc_final: 0.8655 (t0) REVERT: I 13 MET cc_start: 0.8190 (mpp) cc_final: 0.7759 (mpp) REVERT: J 20 LYS cc_start: 0.9664 (mmmt) cc_final: 0.9428 (mmmm) REVERT: K 5 ASN cc_start: 0.9287 (t0) cc_final: 0.8655 (t0) REVERT: M 10 GLU cc_start: 0.8887 (pm20) cc_final: 0.8594 (pm20) REVERT: M 26 LYS cc_start: 0.9402 (ptmt) cc_final: 0.9091 (ptmm) REVERT: O 5 ASN cc_start: 0.9274 (t0) cc_final: 0.8676 (t0) REVERT: P 20 LYS cc_start: 0.9636 (mmmt) cc_final: 0.9289 (mmmm) REVERT: R 5 ASN cc_start: 0.9427 (t0) cc_final: 0.8858 (t0) REVERT: T 5 ASN cc_start: 0.9406 (t0) cc_final: 0.8883 (t0) REVERT: T 20 LYS cc_start: 0.9666 (mmmt) cc_final: 0.9386 (mmmm) REVERT: V 5 ASN cc_start: 0.9413 (t0) cc_final: 0.8907 (t0) REVERT: V 32 LYS cc_start: 0.9528 (mmtt) cc_final: 0.8788 (mtpt) REVERT: W 25 TYR cc_start: 0.9493 (m-80) cc_final: 0.9285 (m-80) REVERT: X 5 ASN cc_start: 0.9238 (t0) cc_final: 0.8849 (t0) REVERT: X 26 LYS cc_start: 0.9544 (OUTLIER) cc_final: 0.9210 (ptpp) REVERT: X 32 LYS cc_start: 0.9538 (mmtt) cc_final: 0.8881 (ttpt) outliers start: 5 outliers final: 3 residues processed: 127 average time/residue: 0.3812 time to fit residues: 57.1287 Evaluate side-chains 123 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 119 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain X residue 26 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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: 0.8785 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 7825 Z= 0.192 Angle : 0.473 5.643 10375 Z= 0.246 Chirality : 0.041 0.110 850 Planarity : 0.003 0.026 1350 Dihedral : 3.533 18.473 1075 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.90 % Allowed : 11.10 % Favored : 88.00 % 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: 0.13 (0.28), residues: 950 helix: 2.27 (0.37), residues: 225 sheet: None (None), residues: 0 loop : -0.68 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP Y 8 HIS 0.001 0.000 HIS C 16 PHE 0.003 0.001 PHE Y 35 TYR 0.009 0.001 TYR D 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: C 26 LYS cc_start: 0.9428 (ptmm) cc_final: 0.8977 (ptmm) REVERT: D 20 LYS cc_start: 0.9649 (mmmt) cc_final: 0.9433 (mmmm) REVERT: D 25 TYR cc_start: 0.9517 (m-80) cc_final: 0.9270 (m-80) REVERT: G 5 ASN cc_start: 0.9283 (t0) cc_final: 0.8617 (t0) REVERT: G 11 ASP cc_start: 0.8051 (t0) cc_final: 0.7618 (t0) REVERT: I 5 ASN cc_start: 0.9300 (t0) cc_final: 0.8596 (t0) REVERT: I 11 ASP cc_start: 0.7746 (t0) cc_final: 0.7501 (t0) REVERT: I 13 MET cc_start: 0.8179 (mpp) cc_final: 0.7712 (mpp) REVERT: J 20 LYS cc_start: 0.9676 (mmmt) cc_final: 0.9435 (mmmm) REVERT: J 23 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.9055 (mtmm) REVERT: K 5 ASN cc_start: 0.9291 (t0) cc_final: 0.8678 (t0) REVERT: M 5 ASN cc_start: 0.9300 (t0) cc_final: 0.8674 (t0) REVERT: M 10 GLU cc_start: 0.8899 (pm20) cc_final: 0.8621 (pm20) REVERT: M 26 LYS cc_start: 0.9357 (ptmt) cc_final: 0.8960 (ptmm) REVERT: O 5 ASN cc_start: 0.9251 (t0) cc_final: 0.8658 (t0) REVERT: P 20 LYS cc_start: 0.9660 (mmmt) cc_final: 0.9329 (mmmm) REVERT: R 5 ASN cc_start: 0.9413 (t0) cc_final: 0.8962 (t0) REVERT: T 5 ASN cc_start: 0.9410 (t0) cc_final: 0.8877 (t0) REVERT: T 20 LYS cc_start: 0.9674 (mmmt) cc_final: 0.9381 (mmmm) REVERT: V 5 ASN cc_start: 0.9359 (t0) cc_final: 0.8835 (t0) REVERT: V 32 LYS cc_start: 0.9522 (mmtt) cc_final: 0.8789 (mtpt) REVERT: X 5 ASN cc_start: 0.9237 (t0) cc_final: 0.8760 (t0) REVERT: X 26 LYS cc_start: 0.9501 (OUTLIER) cc_final: 0.9180 (ptpp) REVERT: X 32 LYS cc_start: 0.9547 (mmtt) cc_final: 0.8899 (ttpt) outliers start: 7 outliers final: 2 residues processed: 130 average time/residue: 0.3805 time to fit residues: 58.5760 Evaluate side-chains 127 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 123 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain T residue 13 MET Chi-restraints excluded: chain X residue 26 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 96 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- 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: 0.8782 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 7825 Z= 0.178 Angle : 0.482 6.741 10375 Z= 0.248 Chirality : 0.041 0.110 850 Planarity : 0.003 0.025 1350 Dihedral : 3.474 19.739 1075 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.65 % Allowed : 11.61 % Favored : 87.74 % 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: 0.10 (0.28), residues: 950 helix: 2.35 (0.37), residues: 225 sheet: None (None), residues: 0 loop : -0.73 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP Y 8 HIS 0.001 0.000 HIS M 18 PHE 0.003 0.001 PHE Y 35 TYR 0.015 0.001 TYR W 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9557 (ptpp) cc_final: 0.9351 (ptmt) REVERT: C 26 LYS cc_start: 0.9380 (ptmm) cc_final: 0.8931 (ptmm) REVERT: D 20 LYS cc_start: 0.9640 (mmmt) cc_final: 0.9417 (mmmm) REVERT: D 25 TYR cc_start: 0.9505 (m-80) cc_final: 0.9254 (m-80) REVERT: G 5 ASN cc_start: 0.9260 (t0) cc_final: 0.8571 (t0) REVERT: G 11 ASP cc_start: 0.8037 (t0) cc_final: 0.7586 (t0) REVERT: G 20 LYS cc_start: 0.9566 (mmmt) cc_final: 0.9314 (mmmm) REVERT: I 5 ASN cc_start: 0.9285 (t0) cc_final: 0.8555 (t0) REVERT: I 11 ASP cc_start: 0.7792 (t0) cc_final: 0.7529 (t0) REVERT: I 13 MET cc_start: 0.8166 (mpp) cc_final: 0.7674 (mpp) REVERT: J 20 LYS cc_start: 0.9690 (mmmt) cc_final: 0.9439 (mmmm) REVERT: J 23 LYS cc_start: 0.9344 (OUTLIER) cc_final: 0.9066 (mtmm) REVERT: K 5 ASN cc_start: 0.9263 (t0) cc_final: 0.8658 (t0) REVERT: K 10 GLU cc_start: 0.8814 (pm20) cc_final: 0.8563 (pm20) REVERT: M 5 ASN cc_start: 0.9296 (t0) cc_final: 0.8659 (t0) REVERT: M 10 GLU cc_start: 0.8893 (pm20) cc_final: 0.8617 (pm20) REVERT: M 26 LYS cc_start: 0.9340 (ptmt) cc_final: 0.8959 (ptmm) REVERT: O 5 ASN cc_start: 0.9232 (t0) cc_final: 0.8625 (t0) REVERT: P 5 ASN cc_start: 0.9399 (t0) cc_final: 0.8704 (t0) REVERT: P 20 LYS cc_start: 0.9642 (mmmt) cc_final: 0.9310 (mmmm) REVERT: R 5 ASN cc_start: 0.9393 (t0) cc_final: 0.8975 (t0) REVERT: T 5 ASN cc_start: 0.9395 (t0) cc_final: 0.9058 (t0) REVERT: T 20 LYS cc_start: 0.9670 (mmmt) cc_final: 0.9370 (mmmm) REVERT: T 25 TYR cc_start: 0.9477 (m-80) cc_final: 0.9139 (m-80) REVERT: V 5 ASN cc_start: 0.9344 (t0) cc_final: 0.8774 (t0) REVERT: V 32 LYS cc_start: 0.9504 (mmtt) cc_final: 0.8801 (mtpt) REVERT: W 25 TYR cc_start: 0.9442 (m-80) cc_final: 0.9206 (m-80) REVERT: X 5 ASN cc_start: 0.9241 (t0) cc_final: 0.8756 (t0) REVERT: X 26 LYS cc_start: 0.9490 (pttm) cc_final: 0.9155 (ptpp) REVERT: X 32 LYS cc_start: 0.9538 (mmtt) cc_final: 0.8906 (ttpt) outliers start: 5 outliers final: 3 residues processed: 131 average time/residue: 0.3661 time to fit residues: 56.8603 Evaluate side-chains 130 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 126 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain T residue 13 MET Chi-restraints excluded: chain U residue 13 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 96 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 38 optimal weight: 0.3980 chunk 57 optimal weight: 6.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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: 0.8778 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 7825 Z= 0.160 Angle : 0.475 6.288 10375 Z= 0.245 Chirality : 0.041 0.111 850 Planarity : 0.003 0.025 1350 Dihedral : 3.400 18.410 1075 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.65 % Allowed : 11.23 % Favored : 88.13 % 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: 0.08 (0.27), residues: 950 helix: 2.33 (0.37), residues: 225 sheet: None (None), residues: 0 loop : -0.75 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP Y 8 HIS 0.001 0.000 HIS M 18 PHE 0.003 0.000 PHE Y 35 TYR 0.013 0.001 TYR W 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 132 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9551 (ptpp) cc_final: 0.9342 (ptmt) REVERT: C 26 LYS cc_start: 0.9343 (ptmm) cc_final: 0.8879 (ptmm) REVERT: D 20 LYS cc_start: 0.9642 (mmmt) cc_final: 0.9412 (mmmm) REVERT: D 25 TYR cc_start: 0.9498 (m-80) cc_final: 0.9242 (m-80) REVERT: F 20 LYS cc_start: 0.9609 (mmmt) cc_final: 0.9357 (mmmm) REVERT: G 5 ASN cc_start: 0.9249 (t0) cc_final: 0.8547 (t0) REVERT: G 11 ASP cc_start: 0.8014 (t0) cc_final: 0.7548 (t0) REVERT: G 20 LYS cc_start: 0.9573 (mmmt) cc_final: 0.9314 (mmmm) REVERT: I 5 ASN cc_start: 0.9256 (t0) cc_final: 0.8514 (t0) REVERT: I 11 ASP cc_start: 0.7769 (t0) cc_final: 0.7515 (t0) REVERT: I 13 MET cc_start: 0.8182 (mpp) cc_final: 0.7693 (mpp) REVERT: J 20 LYS cc_start: 0.9701 (mmmt) cc_final: 0.9446 (mmmm) REVERT: J 23 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.9074 (mtmm) REVERT: K 5 ASN cc_start: 0.9243 (t0) cc_final: 0.8617 (t0) REVERT: K 10 GLU cc_start: 0.8798 (pm20) cc_final: 0.8542 (pm20) REVERT: M 5 ASN cc_start: 0.9287 (t0) cc_final: 0.8618 (t0) REVERT: M 10 GLU cc_start: 0.8877 (pm20) cc_final: 0.8623 (pm20) REVERT: M 26 LYS cc_start: 0.9328 (ptmt) cc_final: 0.8946 (ptmm) REVERT: O 5 ASN cc_start: 0.9210 (t0) cc_final: 0.8578 (t0) REVERT: P 5 ASN cc_start: 0.9378 (t0) cc_final: 0.9026 (t0) REVERT: P 20 LYS cc_start: 0.9648 (mmmt) cc_final: 0.9299 (mmmm) REVERT: R 5 ASN cc_start: 0.9357 (t0) cc_final: 0.8916 (t0) REVERT: T 5 ASN cc_start: 0.9366 (t0) cc_final: 0.9019 (t0) REVERT: T 20 LYS cc_start: 0.9675 (mmmt) cc_final: 0.9377 (mmmm) REVERT: T 25 TYR cc_start: 0.9475 (m-80) cc_final: 0.9101 (m-80) REVERT: V 5 ASN cc_start: 0.9331 (t0) cc_final: 0.8745 (t0) REVERT: V 32 LYS cc_start: 0.9494 (mmtt) cc_final: 0.8790 (mtpt) REVERT: W 5 ASN cc_start: 0.9283 (t0) cc_final: 0.8712 (t0) REVERT: W 25 TYR cc_start: 0.9455 (m-80) cc_final: 0.9236 (m-80) REVERT: X 5 ASN cc_start: 0.9224 (t0) cc_final: 0.8721 (t0) REVERT: X 26 LYS cc_start: 0.9468 (pttm) cc_final: 0.9152 (ptpp) REVERT: X 32 LYS cc_start: 0.9527 (mmtt) cc_final: 0.8780 (ttpt) outliers start: 5 outliers final: 3 residues processed: 132 average time/residue: 0.3661 time to fit residues: 57.3725 Evaluate side-chains 132 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain U residue 13 MET Chi-restraints excluded: chain X residue 13 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 47 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 89 optimal weight: 9.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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: 0.8784 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 7825 Z= 0.203 Angle : 0.496 6.720 10375 Z= 0.256 Chirality : 0.041 0.109 850 Planarity : 0.003 0.026 1350 Dihedral : 3.505 20.215 1075 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.65 % Allowed : 11.10 % Favored : 88.26 % 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: 0.10 (0.28), residues: 950 helix: 2.48 (0.37), residues: 225 sheet: None (None), residues: 0 loop : -0.79 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP Y 8 HIS 0.001 0.000 HIS Q 18 PHE 0.003 0.001 PHE U 2 TYR 0.012 0.001 TYR W 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 126 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9552 (ptpp) cc_final: 0.9196 (ptmm) REVERT: C 26 LYS cc_start: 0.9298 (ptmm) cc_final: 0.8825 (ptmm) REVERT: D 20 LYS cc_start: 0.9648 (mmmt) cc_final: 0.9411 (mmmm) REVERT: G 5 ASN cc_start: 0.9288 (t0) cc_final: 0.8626 (t0) REVERT: G 11 ASP cc_start: 0.8031 (t0) cc_final: 0.7550 (t0) REVERT: G 20 LYS cc_start: 0.9602 (mmmt) cc_final: 0.9339 (mmmm) REVERT: I 5 ASN cc_start: 0.9308 (t0) cc_final: 0.8583 (t0) REVERT: J 20 LYS cc_start: 0.9695 (mmmt) cc_final: 0.9441 (mmmm) REVERT: J 23 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.9022 (mtmm) REVERT: K 5 ASN cc_start: 0.9296 (t0) cc_final: 0.8673 (t0) REVERT: K 10 GLU cc_start: 0.8813 (pm20) cc_final: 0.8553 (pm20) REVERT: M 5 ASN cc_start: 0.9298 (t0) cc_final: 0.8672 (t0) REVERT: O 5 ASN cc_start: 0.9244 (t0) cc_final: 0.8634 (t0) REVERT: O 11 ASP cc_start: 0.8054 (t0) cc_final: 0.7559 (t0) REVERT: P 20 LYS cc_start: 0.9640 (mmmt) cc_final: 0.9294 (mmmm) REVERT: Q 10 GLU cc_start: 0.8959 (pm20) cc_final: 0.8695 (pm20) REVERT: R 5 ASN cc_start: 0.9414 (t0) cc_final: 0.8996 (t0) REVERT: T 5 ASN cc_start: 0.9415 (t0) cc_final: 0.8885 (t0) REVERT: T 20 LYS cc_start: 0.9682 (mmmt) cc_final: 0.9381 (mmmm) REVERT: T 25 TYR cc_start: 0.9464 (m-80) cc_final: 0.9110 (m-80) REVERT: V 5 ASN cc_start: 0.9413 (t0) cc_final: 0.8846 (t0) REVERT: V 32 LYS cc_start: 0.9512 (mmtt) cc_final: 0.8797 (mtpt) REVERT: W 25 TYR cc_start: 0.9494 (m-80) cc_final: 0.9259 (m-80) REVERT: X 5 ASN cc_start: 0.9247 (t0) cc_final: 0.8768 (t0) REVERT: X 26 LYS cc_start: 0.9457 (OUTLIER) cc_final: 0.9141 (ptpp) REVERT: X 32 LYS cc_start: 0.9554 (mmtt) cc_final: 0.8941 (ttpt) outliers start: 5 outliers final: 2 residues processed: 126 average time/residue: 0.3774 time to fit residues: 56.3284 Evaluate side-chains 130 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 126 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain U residue 13 MET Chi-restraints excluded: chain X residue 26 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7825 Z= 0.250 Angle : 0.522 7.370 10375 Z= 0.268 Chirality : 0.042 0.106 850 Planarity : 0.003 0.026 1350 Dihedral : 3.726 21.508 1075 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.77 % Allowed : 11.48 % Favored : 87.74 % 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: 0.11 (0.28), residues: 950 helix: 2.59 (0.37), residues: 225 sheet: None (None), residues: 0 loop : -0.81 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 8 HIS 0.002 0.000 HIS I 18 PHE 0.004 0.001 PHE U 2 TYR 0.014 0.001 TYR D 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9547 (ptpp) cc_final: 0.9174 (ptmm) REVERT: C 26 LYS cc_start: 0.9285 (ptmm) cc_final: 0.8836 (ptmm) REVERT: D 20 LYS cc_start: 0.9649 (mmmt) cc_final: 0.9409 (mmmm) REVERT: G 11 ASP cc_start: 0.8057 (t0) cc_final: 0.7628 (t0) REVERT: G 20 LYS cc_start: 0.9626 (mmmt) cc_final: 0.9356 (mmmm) REVERT: I 5 ASN cc_start: 0.9327 (t0) cc_final: 0.8634 (t0) REVERT: I 10 GLU cc_start: 0.8810 (pm20) cc_final: 0.8573 (pm20) REVERT: J 20 LYS cc_start: 0.9697 (mmmt) cc_final: 0.9439 (mmmm) REVERT: J 23 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.9030 (mtmm) REVERT: K 5 ASN cc_start: 0.9355 (t0) cc_final: 0.8714 (t0) REVERT: K 10 GLU cc_start: 0.8819 (pm20) cc_final: 0.8561 (pm20) REVERT: M 5 ASN cc_start: 0.9323 (t0) cc_final: 0.8706 (t0) REVERT: M 10 GLU cc_start: 0.8967 (pm20) cc_final: 0.8724 (pm20) REVERT: O 5 ASN cc_start: 0.9269 (t0) cc_final: 0.8668 (t0) REVERT: O 11 ASP cc_start: 0.8068 (t0) cc_final: 0.7688 (t0) REVERT: O 13 MET cc_start: 0.8140 (mmm) cc_final: 0.7901 (mmm) REVERT: P 20 LYS cc_start: 0.9644 (mmmt) cc_final: 0.9277 (mmmm) REVERT: Q 10 GLU cc_start: 0.8953 (pm20) cc_final: 0.8719 (pm20) REVERT: R 5 ASN cc_start: 0.9436 (t0) cc_final: 0.8863 (t0) REVERT: T 5 ASN cc_start: 0.9453 (t0) cc_final: 0.9000 (t0) REVERT: T 20 LYS cc_start: 0.9695 (mmmt) cc_final: 0.9394 (mmmm) REVERT: T 25 TYR cc_start: 0.9461 (m-80) cc_final: 0.9114 (m-80) REVERT: V 5 ASN cc_start: 0.9446 (t0) cc_final: 0.8907 (t0) REVERT: V 32 LYS cc_start: 0.9529 (mmtt) cc_final: 0.8797 (mtpt) REVERT: X 5 ASN cc_start: 0.9324 (t0) cc_final: 0.8929 (t0) REVERT: X 26 LYS cc_start: 0.9444 (OUTLIER) cc_final: 0.9132 (ptpp) REVERT: X 32 LYS cc_start: 0.9562 (mmtt) cc_final: 0.8835 (ttpt) outliers start: 6 outliers final: 2 residues processed: 126 average time/residue: 0.3715 time to fit residues: 55.5033 Evaluate side-chains 130 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 126 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain U residue 13 MET Chi-restraints excluded: chain X residue 26 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 84 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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: 0.8782 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7825 Z= 0.191 Angle : 0.498 7.861 10375 Z= 0.257 Chirality : 0.041 0.109 850 Planarity : 0.003 0.026 1350 Dihedral : 3.612 21.898 1075 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.65 % Allowed : 12.26 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.27), residues: 950 helix: 2.61 (0.37), residues: 225 sheet: None (None), residues: 0 loop : -0.83 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP Y 8 HIS 0.001 0.000 HIS L 18 PHE 0.004 0.001 PHE H 2 TYR 0.016 0.001 TYR W 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9536 (ptpp) cc_final: 0.9176 (ptmm) REVERT: B 10 GLU cc_start: 0.8869 (pm20) cc_final: 0.8608 (pm20) REVERT: C 26 LYS cc_start: 0.9270 (ptmm) cc_final: 0.8797 (ptmm) REVERT: D 20 LYS cc_start: 0.9664 (mmmt) cc_final: 0.9430 (mmmm) REVERT: F 20 LYS cc_start: 0.9647 (mmmt) cc_final: 0.9390 (mmmm) REVERT: G 5 ASN cc_start: 0.9272 (t0) cc_final: 0.8598 (t0) REVERT: G 11 ASP cc_start: 0.8004 (t0) cc_final: 0.7529 (t0) REVERT: G 20 LYS cc_start: 0.9616 (mmmt) cc_final: 0.9276 (mmmm) REVERT: I 5 ASN cc_start: 0.9291 (t0) cc_final: 0.8572 (t0) REVERT: I 10 GLU cc_start: 0.8800 (pm20) cc_final: 0.8569 (pm20) REVERT: J 20 LYS cc_start: 0.9696 (mmmt) cc_final: 0.9431 (mmmm) REVERT: J 23 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.9046 (mtmm) REVERT: K 5 ASN cc_start: 0.9284 (t0) cc_final: 0.8654 (t0) REVERT: K 10 GLU cc_start: 0.8806 (pm20) cc_final: 0.8564 (pm20) REVERT: M 5 ASN cc_start: 0.9302 (t0) cc_final: 0.8642 (t0) REVERT: M 10 GLU cc_start: 0.8950 (pm20) cc_final: 0.8706 (pm20) REVERT: O 5 ASN cc_start: 0.9230 (t0) cc_final: 0.8628 (t0) REVERT: O 11 ASP cc_start: 0.8042 (t0) cc_final: 0.7685 (t0) REVERT: O 13 MET cc_start: 0.8134 (mmm) cc_final: 0.7933 (mmm) REVERT: P 20 LYS cc_start: 0.9655 (mmmt) cc_final: 0.9291 (mmmm) REVERT: Q 10 GLU cc_start: 0.8934 (pm20) cc_final: 0.8728 (pm20) REVERT: R 5 ASN cc_start: 0.9400 (t0) cc_final: 0.8969 (t0) REVERT: T 5 ASN cc_start: 0.9417 (t0) cc_final: 0.8874 (t0) REVERT: T 20 LYS cc_start: 0.9697 (mmmt) cc_final: 0.9398 (mmmm) REVERT: T 25 TYR cc_start: 0.9451 (m-80) cc_final: 0.9118 (m-80) REVERT: V 5 ASN cc_start: 0.9361 (t0) cc_final: 0.8798 (t0) REVERT: V 10 GLU cc_start: 0.8638 (pm20) cc_final: 0.8337 (pm20) REVERT: V 32 LYS cc_start: 0.9493 (mmtt) cc_final: 0.8777 (mtpt) REVERT: X 5 ASN cc_start: 0.9243 (t0) cc_final: 0.8756 (t0) REVERT: X 26 LYS cc_start: 0.9430 (OUTLIER) cc_final: 0.9122 (ptpp) REVERT: X 32 LYS cc_start: 0.9534 (mmtt) cc_final: 0.8920 (ttpt) outliers start: 5 outliers final: 2 residues processed: 129 average time/residue: 0.3805 time to fit residues: 58.1771 Evaluate side-chains 132 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain U residue 13 MET Chi-restraints excluded: chain X residue 26 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 33 optimal weight: 0.0980 chunk 81 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- 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 = 0.2992 r_free = 0.2992 target = 0.038057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2375 r_free = 0.2375 target = 0.023555 restraints weight = 37552.474| |-----------------------------------------------------------------------------| r_work (start): 0.2304 rms_B_bonded: 5.06 r_work: 0.2146 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7825 Z= 0.264 Angle : 0.540 7.517 10375 Z= 0.276 Chirality : 0.042 0.108 850 Planarity : 0.003 0.027 1350 Dihedral : 3.777 23.886 1075 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.52 % Allowed : 12.77 % Favored : 86.71 % 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: 0.11 (0.28), residues: 950 helix: 2.71 (0.37), residues: 225 sheet: None (None), residues: 0 loop : -0.86 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP Y 8 HIS 0.001 0.000 HIS M 18 PHE 0.005 0.001 PHE Q 2 TYR 0.017 0.001 TYR W 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1949.74 seconds wall clock time: 36 minutes 11.23 seconds (2171.23 seconds total)