Starting phenix.real_space_refine on Thu Feb 15 03:47:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6off_20044/02_2024/6off_20044_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6off_20044/02_2024/6off_20044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6off_20044/02_2024/6off_20044.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6off_20044/02_2024/6off_20044.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6off_20044/02_2024/6off_20044_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6off_20044/02_2024/6off_20044_neut.pdb" } resolution = 3.2 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= 0.004 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: 3 Type Number sf(0) Gaussians C 6966 2.51 5 N 1818 2.21 5 O 2232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11016 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "B" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "C" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "D" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "E" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "F" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "G" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "H" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "I" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "J" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "K" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "L" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "M" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "N" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "O" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "P" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "Q" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "R" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Time building chain proxies: 5.88, per 1000 atoms: 0.53 Number of scatterers: 11016 At special positions: 0 Unit cell: (90.915, 90.915, 145.255, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2232 8.00 N 1818 7.00 C 6966 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.36 Conformation dependent library (CDL) restraints added in 1.9 seconds 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2736 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 91.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 7 through 20 removed outlier: 3.883A pdb=" N PHE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 37 removed outlier: 3.820A pdb=" N THR A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 36 " --> pdb=" O ASP A 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 77 removed outlier: 3.700A pdb=" N LEU A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL A 65 " --> pdb=" O GLN A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'B' and resid 7 through 20 removed outlier: 3.883A pdb=" N PHE B 16 " --> pdb=" O VAL B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 37 removed outlier: 3.819A pdb=" N THR B 28 " --> pdb=" O GLN B 24 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 36 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 37 " --> pdb=" O LYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 77 removed outlier: 3.700A pdb=" N LEU B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 65 " --> pdb=" O GLN B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'C' and resid 7 through 20 removed outlier: 3.884A pdb=" N PHE C 16 " --> pdb=" O VAL C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 37 removed outlier: 3.821A pdb=" N THR C 28 " --> pdb=" O GLN C 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 36 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 77 removed outlier: 3.700A pdb=" N LEU C 56 " --> pdb=" O SER C 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL C 65 " --> pdb=" O GLN C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 80 No H-bonds generated for 'chain 'C' and resid 78 through 80' Processing helix chain 'D' and resid 7 through 20 removed outlier: 3.884A pdb=" N PHE D 16 " --> pdb=" O VAL D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 37 removed outlier: 3.820A pdb=" N THR D 28 " --> pdb=" O GLN D 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA D 36 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS D 37 " --> pdb=" O LYS D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 77 removed outlier: 3.700A pdb=" N LEU D 56 " --> pdb=" O SER D 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL D 65 " --> pdb=" O GLN D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 80 No H-bonds generated for 'chain 'D' and resid 78 through 80' Processing helix chain 'E' and resid 7 through 20 removed outlier: 3.883A pdb=" N PHE E 16 " --> pdb=" O VAL E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 37 removed outlier: 3.820A pdb=" N THR E 28 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS E 37 " --> pdb=" O LYS E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 77 removed outlier: 3.700A pdb=" N LEU E 56 " --> pdb=" O SER E 52 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL E 65 " --> pdb=" O GLN E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 80 No H-bonds generated for 'chain 'E' and resid 78 through 80' Processing helix chain 'F' and resid 7 through 20 removed outlier: 3.883A pdb=" N PHE F 16 " --> pdb=" O VAL F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 37 removed outlier: 3.820A pdb=" N THR F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 77 removed outlier: 3.700A pdb=" N LEU F 56 " --> pdb=" O SER F 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL F 65 " --> pdb=" O GLN F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 80 No H-bonds generated for 'chain 'F' and resid 78 through 80' Processing helix chain 'G' and resid 7 through 20 removed outlier: 3.883A pdb=" N PHE G 16 " --> pdb=" O VAL G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 37 removed outlier: 3.819A pdb=" N THR G 28 " --> pdb=" O GLN G 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA G 36 " --> pdb=" O ASP G 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS G 37 " --> pdb=" O LYS G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 77 removed outlier: 3.700A pdb=" N LEU G 56 " --> pdb=" O SER G 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL G 65 " --> pdb=" O GLN G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 80 No H-bonds generated for 'chain 'G' and resid 78 through 80' Processing helix chain 'H' and resid 7 through 20 removed outlier: 3.883A pdb=" N PHE H 16 " --> pdb=" O VAL H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 37 removed outlier: 3.819A pdb=" N THR H 28 " --> pdb=" O GLN H 24 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA H 36 " --> pdb=" O ASP H 32 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS H 37 " --> pdb=" O LYS H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 77 removed outlier: 3.699A pdb=" N LEU H 56 " --> pdb=" O SER H 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL H 65 " --> pdb=" O GLN H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 80 No H-bonds generated for 'chain 'H' and resid 78 through 80' Processing helix chain 'I' and resid 7 through 20 removed outlier: 3.884A pdb=" N PHE I 16 " --> pdb=" O VAL I 12 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 37 removed outlier: 3.820A pdb=" N THR I 28 " --> pdb=" O GLN I 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA I 36 " --> pdb=" O ASP I 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS I 37 " --> pdb=" O LYS I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 77 removed outlier: 3.700A pdb=" N LEU I 56 " --> pdb=" O SER I 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL I 65 " --> pdb=" O GLN I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 80 No H-bonds generated for 'chain 'I' and resid 78 through 80' Processing helix chain 'J' and resid 7 through 20 removed outlier: 3.884A pdb=" N PHE J 16 " --> pdb=" O VAL J 12 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 37 removed outlier: 3.819A pdb=" N THR J 28 " --> pdb=" O GLN J 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA J 36 " --> pdb=" O ASP J 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS J 37 " --> pdb=" O LYS J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 77 removed outlier: 3.701A pdb=" N LEU J 56 " --> pdb=" O SER J 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL J 65 " --> pdb=" O GLN J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'K' and resid 7 through 20 removed outlier: 3.884A pdb=" N PHE K 16 " --> pdb=" O VAL K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 37 removed outlier: 3.821A pdb=" N THR K 28 " --> pdb=" O GLN K 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA K 36 " --> pdb=" O ASP K 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS K 37 " --> pdb=" O LYS K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 77 removed outlier: 3.700A pdb=" N LEU K 56 " --> pdb=" O SER K 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL K 65 " --> pdb=" O GLN K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 80 No H-bonds generated for 'chain 'K' and resid 78 through 80' Processing helix chain 'L' and resid 7 through 20 removed outlier: 3.883A pdb=" N PHE L 16 " --> pdb=" O VAL L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 37 removed outlier: 3.820A pdb=" N THR L 28 " --> pdb=" O GLN L 24 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA L 36 " --> pdb=" O ASP L 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS L 37 " --> pdb=" O LYS L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 77 removed outlier: 3.700A pdb=" N LEU L 56 " --> pdb=" O SER L 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL L 65 " --> pdb=" O GLN L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 80 No H-bonds generated for 'chain 'L' and resid 78 through 80' Processing helix chain 'M' and resid 7 through 20 removed outlier: 3.883A pdb=" N PHE M 16 " --> pdb=" O VAL M 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 37 removed outlier: 3.821A pdb=" N THR M 28 " --> pdb=" O GLN M 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA M 36 " --> pdb=" O ASP M 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS M 37 " --> pdb=" O LYS M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 77 removed outlier: 3.700A pdb=" N LEU M 56 " --> pdb=" O SER M 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL M 65 " --> pdb=" O GLN M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 80 No H-bonds generated for 'chain 'M' and resid 78 through 80' Processing helix chain 'N' and resid 7 through 20 removed outlier: 3.883A pdb=" N PHE N 16 " --> pdb=" O VAL N 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 37 removed outlier: 3.820A pdb=" N THR N 28 " --> pdb=" O GLN N 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA N 36 " --> pdb=" O ASP N 32 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS N 37 " --> pdb=" O LYS N 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 77 removed outlier: 3.699A pdb=" N LEU N 56 " --> pdb=" O SER N 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL N 65 " --> pdb=" O GLN N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 80 No H-bonds generated for 'chain 'N' and resid 78 through 80' Processing helix chain 'O' and resid 7 through 20 removed outlier: 3.883A pdb=" N PHE O 16 " --> pdb=" O VAL O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 37 removed outlier: 3.820A pdb=" N THR O 28 " --> pdb=" O GLN O 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA O 36 " --> pdb=" O ASP O 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS O 37 " --> pdb=" O LYS O 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 77 removed outlier: 3.700A pdb=" N LEU O 56 " --> pdb=" O SER O 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL O 65 " --> pdb=" O GLN O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 78 through 80 No H-bonds generated for 'chain 'O' and resid 78 through 80' Processing helix chain 'P' and resid 7 through 20 removed outlier: 3.883A pdb=" N PHE P 16 " --> pdb=" O VAL P 12 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 37 removed outlier: 3.820A pdb=" N THR P 28 " --> pdb=" O GLN P 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA P 36 " --> pdb=" O ASP P 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS P 37 " --> pdb=" O LYS P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 77 removed outlier: 3.700A pdb=" N LEU P 56 " --> pdb=" O SER P 52 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL P 65 " --> pdb=" O GLN P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 80 No H-bonds generated for 'chain 'P' and resid 78 through 80' Processing helix chain 'Q' and resid 7 through 20 removed outlier: 3.883A pdb=" N PHE Q 16 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 37 removed outlier: 3.820A pdb=" N THR Q 28 " --> pdb=" O GLN Q 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA Q 36 " --> pdb=" O ASP Q 32 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS Q 37 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 77 removed outlier: 3.699A pdb=" N LEU Q 56 " --> pdb=" O SER Q 52 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL Q 65 " --> pdb=" O GLN Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 80 No H-bonds generated for 'chain 'Q' and resid 78 through 80' Processing helix chain 'R' and resid 7 through 20 removed outlier: 3.883A pdb=" N PHE R 16 " --> pdb=" O VAL R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 37 removed outlier: 3.821A pdb=" N THR R 28 " --> pdb=" O GLN R 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA R 36 " --> pdb=" O ASP R 32 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS R 37 " --> pdb=" O LYS R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 77 removed outlier: 3.700A pdb=" N LEU R 56 " --> pdb=" O SER R 52 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL R 65 " --> pdb=" O GLN R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 80 No H-bonds generated for 'chain 'R' and resid 78 through 80' 900 hydrogen bonds defined for protein. 2700 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: 2.49 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 1962 1.29 - 1.35: 1674 1.35 - 1.41: 1088 1.41 - 1.48: 1669 1.48 - 1.54: 4821 Bond restraints: 11214 Sorted by residual: bond pdb=" CG LEU Q 9 " pdb=" CD2 LEU Q 9 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.61e+00 bond pdb=" CG LEU L 9 " pdb=" CD2 LEU L 9 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.61e+00 bond pdb=" CG LEU R 9 " pdb=" CD2 LEU R 9 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.60e+00 bond pdb=" CG LEU B 9 " pdb=" CD2 LEU B 9 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 bond pdb=" CG LEU H 9 " pdb=" CD2 LEU H 9 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 ... (remaining 11209 not shown) Histogram of bond angle deviations from ideal: 102.76 - 108.99: 779 108.99 - 115.22: 6085 115.22 - 121.45: 6066 121.45 - 127.68: 2244 127.68 - 133.91: 90 Bond angle restraints: 15264 Sorted by residual: angle pdb=" CA GLN N 61 " pdb=" CB GLN N 61 " pdb=" CG GLN N 61 " ideal model delta sigma weight residual 114.10 119.38 -5.28 2.00e+00 2.50e-01 6.97e+00 angle pdb=" CA GLN M 61 " pdb=" CB GLN M 61 " pdb=" CG GLN M 61 " ideal model delta sigma weight residual 114.10 119.37 -5.27 2.00e+00 2.50e-01 6.95e+00 angle pdb=" CA GLN B 61 " pdb=" CB GLN B 61 " pdb=" CG GLN B 61 " ideal model delta sigma weight residual 114.10 119.37 -5.27 2.00e+00 2.50e-01 6.95e+00 angle pdb=" CA GLN G 61 " pdb=" CB GLN G 61 " pdb=" CG GLN G 61 " ideal model delta sigma weight residual 114.10 119.37 -5.27 2.00e+00 2.50e-01 6.94e+00 angle pdb=" CA GLN O 61 " pdb=" CB GLN O 61 " pdb=" CG GLN O 61 " ideal model delta sigma weight residual 114.10 119.36 -5.26 2.00e+00 2.50e-01 6.91e+00 ... (remaining 15259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.01: 6462 15.01 - 30.03: 252 30.03 - 45.04: 54 45.04 - 60.05: 18 60.05 - 75.06: 18 Dihedral angle restraints: 6804 sinusoidal: 2610 harmonic: 4194 Sorted by residual: dihedral pdb=" CA GLY A 19 " pdb=" C GLY A 19 " pdb=" N VAL A 20 " pdb=" CA VAL A 20 " ideal model delta harmonic sigma weight residual 180.00 164.34 15.66 0 5.00e+00 4.00e-02 9.81e+00 dihedral pdb=" CA GLY P 19 " pdb=" C GLY P 19 " pdb=" N VAL P 20 " pdb=" CA VAL P 20 " ideal model delta harmonic sigma weight residual 180.00 164.36 15.64 0 5.00e+00 4.00e-02 9.79e+00 dihedral pdb=" CA GLY B 19 " pdb=" C GLY B 19 " pdb=" N VAL B 20 " pdb=" CA VAL B 20 " ideal model delta harmonic sigma weight residual 180.00 164.36 15.64 0 5.00e+00 4.00e-02 9.78e+00 ... (remaining 6801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.020: 471 0.020 - 0.041: 597 0.041 - 0.061: 317 0.061 - 0.081: 305 0.081 - 0.101: 56 Chirality restraints: 1746 Sorted by residual: chirality pdb=" CA PRO N 41 " pdb=" N PRO N 41 " pdb=" C PRO N 41 " pdb=" CB PRO N 41 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.56e-01 chirality pdb=" CA PRO H 41 " pdb=" N PRO H 41 " pdb=" C PRO H 41 " pdb=" CB PRO H 41 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.42e-01 chirality pdb=" CA PRO J 41 " pdb=" N PRO J 41 " pdb=" C PRO J 41 " pdb=" CB PRO J 41 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.42e-01 ... (remaining 1743 not shown) Planarity restraints: 1998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL K 20 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.44e+00 pdb=" C VAL K 20 " -0.027 2.00e-02 2.50e+03 pdb=" O VAL K 20 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP K 21 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 20 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.43e+00 pdb=" C VAL A 20 " -0.027 2.00e-02 2.50e+03 pdb=" O VAL A 20 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP A 21 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL Q 20 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.43e+00 pdb=" C VAL Q 20 " -0.027 2.00e-02 2.50e+03 pdb=" O VAL Q 20 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP Q 21 " 0.009 2.00e-02 2.50e+03 ... (remaining 1995 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 248 2.70 - 3.25: 11456 3.25 - 3.80: 17333 3.80 - 4.35: 23717 4.35 - 4.90: 40635 Nonbonded interactions: 93389 Sorted by model distance: nonbonded pdb=" OD1 ASP I 10 " pdb=" OG SER O 49 " model vdw 2.147 2.440 nonbonded pdb=" OD1 ASP J 10 " pdb=" OG SER P 49 " model vdw 2.192 2.440 nonbonded pdb=" OD1 ASP D 10 " pdb=" OG SER J 49 " model vdw 2.217 2.440 nonbonded pdb=" N ASP A 10 " pdb=" OE2 GLU G 53 " model vdw 2.252 2.520 nonbonded pdb=" OD1 ASP E 17 " pdb=" OH TYR E 57 " model vdw 2.310 2.440 ... (remaining 93384 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' } 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.780 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 27.110 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 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 0.042 11214 Z= 0.565 Angle : 0.831 5.282 15264 Z= 0.500 Chirality : 0.045 0.101 1746 Planarity : 0.005 0.031 1998 Dihedral : 10.880 75.065 4068 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: -5.21 (0.13), residues: 1368 helix: -3.28 (0.09), residues: 1152 sheet: None (None), residues: 0 loop : -2.57 (0.28), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP H 5 PHE 0.012 0.003 PHE O 79 TYR 0.011 0.002 TYR O 57 ARG 0.004 0.001 ARG I 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 389 time to evaluate : 1.272 Fit side-chains REVERT: A 66 LYS cc_start: 0.8617 (tptp) cc_final: 0.7191 (mttm) REVERT: B 37 LYS cc_start: 0.7539 (ttmt) cc_final: 0.6639 (tptt) REVERT: C 4 PRO cc_start: 0.7523 (Cg_endo) cc_final: 0.7248 (Cg_exo) REVERT: C 10 ASP cc_start: 0.8562 (m-30) cc_final: 0.7963 (m-30) REVERT: C 37 LYS cc_start: 0.9078 (ttmt) cc_final: 0.7713 (tptt) REVERT: C 72 ASP cc_start: 0.9174 (m-30) cc_final: 0.8948 (m-30) REVERT: D 10 ASP cc_start: 0.7896 (m-30) cc_final: 0.7502 (m-30) REVERT: E 10 ASP cc_start: 0.8060 (m-30) cc_final: 0.7723 (m-30) REVERT: E 37 LYS cc_start: 0.9093 (ttmt) cc_final: 0.7985 (tptt) REVERT: E 52 SER cc_start: 0.8568 (m) cc_final: 0.8250 (p) REVERT: E 70 ASP cc_start: 0.8333 (m-30) cc_final: 0.7939 (m-30) REVERT: F 10 ASP cc_start: 0.8421 (m-30) cc_final: 0.8061 (m-30) REVERT: F 37 LYS cc_start: 0.9074 (ttmt) cc_final: 0.7655 (tptt) REVERT: G 33 LYS cc_start: 0.8397 (mttt) cc_final: 0.7936 (mtpp) REVERT: G 37 LYS cc_start: 0.8503 (ttmt) cc_final: 0.6720 (tptp) REVERT: H 37 LYS cc_start: 0.8965 (ttmt) cc_final: 0.7269 (tptt) REVERT: H 72 ASP cc_start: 0.9104 (m-30) cc_final: 0.8750 (m-30) REVERT: I 53 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7514 (mt-10) REVERT: K 10 ASP cc_start: 0.7953 (m-30) cc_final: 0.7545 (m-30) REVERT: L 53 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7571 (mt-10) REVERT: M 8 TYR cc_start: 0.8717 (t80) cc_final: 0.8480 (t80) REVERT: M 29 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7068 (mt-10) REVERT: M 69 LYS cc_start: 0.8962 (tmtt) cc_final: 0.7838 (ttmt) REVERT: N 25 THR cc_start: 0.8717 (m) cc_final: 0.8353 (p) REVERT: N 69 LYS cc_start: 0.8770 (tmtt) cc_final: 0.8159 (ttmt) REVERT: O 28 THR cc_start: 0.8751 (m) cc_final: 0.8371 (p) REVERT: O 33 LYS cc_start: 0.7967 (mttt) cc_final: 0.7095 (mttm) REVERT: R 33 LYS cc_start: 0.8610 (mttt) cc_final: 0.7864 (mttm) REVERT: R 69 LYS cc_start: 0.9078 (tmtt) cc_final: 0.7908 (ttmt) REVERT: R 72 ASP cc_start: 0.8863 (m-30) cc_final: 0.8630 (m-30) outliers start: 0 outliers final: 0 residues processed: 389 average time/residue: 0.2134 time to fit residues: 116.3825 Evaluate side-chains 275 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 GLN B 61 GLN C 61 GLN D 78 ASN E 61 GLN E 78 ASN F 61 GLN F 78 ASN G 61 GLN H 61 GLN I 78 ASN J 78 ASN ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 78 ASN M 61 GLN N 61 GLN O 61 GLN ** P 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 61 GLN Q 61 GLN R 61 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11214 Z= 0.177 Angle : 0.476 4.211 15264 Z= 0.261 Chirality : 0.034 0.123 1746 Planarity : 0.004 0.030 1998 Dihedral : 4.066 18.179 1512 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.19 % Allowed : 8.50 % Favored : 89.31 % 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: -0.48 (0.20), residues: 1368 helix: 0.00 (0.13), residues: 1206 sheet: None (None), residues: 0 loop : -1.73 (0.50), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 5 PHE 0.008 0.001 PHE O 68 TYR 0.016 0.001 TYR B 47 ARG 0.002 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 340 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8504 (m-30) cc_final: 0.8290 (m-30) REVERT: A 39 SER cc_start: 0.8626 (m) cc_final: 0.8365 (p) REVERT: A 69 LYS cc_start: 0.8685 (tmtt) cc_final: 0.8449 (tttm) REVERT: B 37 LYS cc_start: 0.8197 (ttmt) cc_final: 0.7029 (tptt) REVERT: B 66 LYS cc_start: 0.8142 (tptp) cc_final: 0.6865 (ttmt) REVERT: C 4 PRO cc_start: 0.7639 (Cg_endo) cc_final: 0.7370 (Cg_exo) REVERT: C 10 ASP cc_start: 0.8319 (m-30) cc_final: 0.7826 (m-30) REVERT: C 37 LYS cc_start: 0.9044 (ttmt) cc_final: 0.7636 (tptt) REVERT: C 69 LYS cc_start: 0.8843 (tmtt) cc_final: 0.8456 (tttm) REVERT: D 10 ASP cc_start: 0.8247 (m-30) cc_final: 0.7612 (m-30) REVERT: D 69 LYS cc_start: 0.8642 (tmtt) cc_final: 0.8293 (tptp) REVERT: D 72 ASP cc_start: 0.8971 (m-30) cc_final: 0.8599 (m-30) REVERT: E 10 ASP cc_start: 0.8316 (m-30) cc_final: 0.7849 (m-30) REVERT: E 37 LYS cc_start: 0.9108 (ttmt) cc_final: 0.7929 (tptt) REVERT: F 10 ASP cc_start: 0.8453 (m-30) cc_final: 0.7948 (m-30) REVERT: F 18 THR cc_start: 0.9045 (p) cc_final: 0.8827 (p) REVERT: F 37 LYS cc_start: 0.9014 (ttmt) cc_final: 0.7587 (tptt) REVERT: G 33 LYS cc_start: 0.8619 (mttt) cc_final: 0.8298 (mtpp) REVERT: H 37 LYS cc_start: 0.8958 (ttmt) cc_final: 0.7525 (tptt) REVERT: H 72 ASP cc_start: 0.8968 (m-30) cc_final: 0.8534 (m-30) REVERT: I 8 TYR cc_start: 0.8737 (t80) cc_final: 0.8293 (t80) REVERT: I 53 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7411 (mt-10) REVERT: K 10 ASP cc_start: 0.8210 (m-30) cc_final: 0.7866 (m-30) REVERT: K 31 LEU cc_start: 0.9164 (tp) cc_final: 0.8949 (tp) REVERT: M 8 TYR cc_start: 0.8805 (t80) cc_final: 0.8462 (t80) REVERT: M 49 SER cc_start: 0.8796 (t) cc_final: 0.8565 (t) REVERT: M 69 LYS cc_start: 0.9065 (tmtt) cc_final: 0.7829 (ttmt) REVERT: N 25 THR cc_start: 0.8717 (m) cc_final: 0.8431 (p) REVERT: N 29 GLU cc_start: 0.7106 (tp30) cc_final: 0.6800 (tp30) REVERT: N 69 LYS cc_start: 0.8973 (tmtt) cc_final: 0.7911 (ttmt) REVERT: N 70 ASP cc_start: 0.8239 (m-30) cc_final: 0.7782 (m-30) REVERT: O 29 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7254 (tp30) REVERT: O 69 LYS cc_start: 0.8677 (tmtt) cc_final: 0.8060 (ttmt) REVERT: Q 15 LYS cc_start: 0.8781 (mttp) cc_final: 0.7708 (ttpt) REVERT: Q 32 ASP cc_start: 0.7801 (m-30) cc_final: 0.7480 (m-30) REVERT: Q 69 LYS cc_start: 0.8826 (tmtt) cc_final: 0.7736 (tttt) REVERT: Q 72 ASP cc_start: 0.8526 (m-30) cc_final: 0.8309 (m-30) REVERT: R 15 LYS cc_start: 0.8459 (mttp) cc_final: 0.7427 (ttpt) REVERT: R 69 LYS cc_start: 0.8981 (tmtt) cc_final: 0.7801 (ttmt) outliers start: 26 outliers final: 7 residues processed: 350 average time/residue: 0.2145 time to fit residues: 106.5064 Evaluate side-chains 290 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 283 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain N residue 10 ASP Chi-restraints excluded: chain Q residue 6 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 31 optimal weight: 0.2980 chunk 114 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN A 78 ASN B 61 GLN C 61 GLN C 78 ASN D 55 ASN E 61 GLN G 61 GLN ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 ASN J 63 ASN K 63 ASN M 61 GLN ** N 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 63 ASN O 63 ASN ** P 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 11214 Z= 0.201 Angle : 0.452 4.419 15264 Z= 0.243 Chirality : 0.034 0.110 1746 Planarity : 0.003 0.025 1998 Dihedral : 3.773 16.865 1512 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.94 % Allowed : 11.95 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.21), residues: 1368 helix: 1.51 (0.14), residues: 1206 sheet: None (None), residues: 0 loop : -1.71 (0.51), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 5 PHE 0.007 0.001 PHE O 68 TYR 0.014 0.001 TYR B 47 ARG 0.002 0.000 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 331 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8771 (tmtt) cc_final: 0.8569 (tttm) REVERT: B 37 LYS cc_start: 0.8620 (ttmt) cc_final: 0.7337 (tptt) REVERT: B 40 ASP cc_start: 0.7932 (t0) cc_final: 0.7653 (t0) REVERT: B 56 LEU cc_start: 0.9250 (mt) cc_final: 0.8909 (mt) REVERT: B 66 LYS cc_start: 0.8628 (tptp) cc_final: 0.7458 (ttmt) REVERT: B 69 LYS cc_start: 0.8621 (tptp) cc_final: 0.8419 (tttm) REVERT: C 10 ASP cc_start: 0.8417 (m-30) cc_final: 0.7813 (m-30) REVERT: C 37 LYS cc_start: 0.8958 (ttmt) cc_final: 0.7555 (tptt) REVERT: C 69 LYS cc_start: 0.8837 (tmtt) cc_final: 0.8485 (tttm) REVERT: C 72 ASP cc_start: 0.9079 (m-30) cc_final: 0.8672 (m-30) REVERT: D 10 ASP cc_start: 0.8378 (m-30) cc_final: 0.7695 (m-30) REVERT: D 66 LYS cc_start: 0.8444 (tptp) cc_final: 0.7798 (ttmt) REVERT: D 69 LYS cc_start: 0.8760 (tmtt) cc_final: 0.8413 (tptp) REVERT: E 10 ASP cc_start: 0.8422 (m-30) cc_final: 0.7874 (m-30) REVERT: E 37 LYS cc_start: 0.9114 (ttmt) cc_final: 0.7947 (tptt) REVERT: F 10 ASP cc_start: 0.8310 (m-30) cc_final: 0.7959 (m-30) REVERT: F 37 LYS cc_start: 0.9010 (ttmt) cc_final: 0.7595 (tptt) REVERT: G 10 ASP cc_start: 0.8587 (m-30) cc_final: 0.8232 (m-30) REVERT: G 33 LYS cc_start: 0.8723 (mttt) cc_final: 0.8498 (mtpp) REVERT: G 52 SER cc_start: 0.8889 (m) cc_final: 0.8337 (p) REVERT: H 37 LYS cc_start: 0.9038 (ttmt) cc_final: 0.7504 (tptt) REVERT: H 72 ASP cc_start: 0.9113 (m-30) cc_final: 0.8740 (m-30) REVERT: I 53 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7371 (mt-10) REVERT: J 10 ASP cc_start: 0.8181 (m-30) cc_final: 0.7899 (m-30) REVERT: J 53 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7571 (mt-10) REVERT: J 72 ASP cc_start: 0.8404 (m-30) cc_final: 0.7898 (m-30) REVERT: K 10 ASP cc_start: 0.8312 (m-30) cc_final: 0.7853 (m-30) REVERT: K 31 LEU cc_start: 0.9202 (tp) cc_final: 0.9001 (tp) REVERT: L 39 SER cc_start: 0.8758 (m) cc_final: 0.7584 (m) REVERT: M 69 LYS cc_start: 0.9061 (tmtt) cc_final: 0.7824 (ttmt) REVERT: N 15 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.7515 (ttpt) REVERT: N 33 LYS cc_start: 0.8810 (mttm) cc_final: 0.8574 (mttm) REVERT: N 69 LYS cc_start: 0.8990 (tmtt) cc_final: 0.7928 (ttmt) REVERT: N 70 ASP cc_start: 0.8313 (m-30) cc_final: 0.7874 (m-30) REVERT: O 29 GLU cc_start: 0.7504 (tm-30) cc_final: 0.7290 (tp30) REVERT: O 69 LYS cc_start: 0.8974 (tmtt) cc_final: 0.8098 (ttmt) REVERT: O 72 ASP cc_start: 0.8405 (m-30) cc_final: 0.8190 (m-30) REVERT: P 32 ASP cc_start: 0.7864 (m-30) cc_final: 0.7621 (m-30) REVERT: P 69 LYS cc_start: 0.8805 (tmtt) cc_final: 0.7849 (ttmt) REVERT: Q 15 LYS cc_start: 0.8809 (mttp) cc_final: 0.7923 (ttpt) REVERT: Q 25 THR cc_start: 0.9053 (m) cc_final: 0.8690 (p) REVERT: Q 69 LYS cc_start: 0.8881 (tmtt) cc_final: 0.7522 (tttt) REVERT: R 15 LYS cc_start: 0.8534 (mttp) cc_final: 0.7589 (ttpt) REVERT: R 69 LYS cc_start: 0.9010 (tmtt) cc_final: 0.7845 (ttmt) REVERT: R 72 ASP cc_start: 0.8649 (m-30) cc_final: 0.8377 (m-30) REVERT: R 77 GLN cc_start: 0.8269 (tm-30) cc_final: 0.7775 (tm-30) outliers start: 23 outliers final: 12 residues processed: 343 average time/residue: 0.2261 time to fit residues: 108.3603 Evaluate side-chains 303 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 290 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain N residue 10 ASP Chi-restraints excluded: chain N residue 15 LYS Chi-restraints excluded: chain R residue 10 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 GLN D 55 ASN G 61 GLN ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 63 ASN ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 11214 Z= 0.150 Angle : 0.406 4.196 15264 Z= 0.217 Chirality : 0.034 0.103 1746 Planarity : 0.003 0.025 1998 Dihedral : 3.640 16.376 1512 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.60 % Allowed : 13.97 % Favored : 84.43 % 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: 2.65 (0.22), residues: 1368 helix: 2.18 (0.14), residues: 1206 sheet: None (None), residues: 0 loop : -1.65 (0.51), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP L 5 PHE 0.006 0.001 PHE N 68 TYR 0.009 0.001 TYR B 47 ARG 0.001 0.000 ARG K 58 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 301 time to evaluate : 1.348 Fit side-chains revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8777 (tmtt) cc_final: 0.8558 (tttm) REVERT: B 37 LYS cc_start: 0.8720 (ttmt) cc_final: 0.7477 (tptt) REVERT: B 56 LEU cc_start: 0.9202 (mt) cc_final: 0.8865 (mt) REVERT: B 66 LYS cc_start: 0.8623 (tptp) cc_final: 0.7437 (ttmt) REVERT: C 10 ASP cc_start: 0.8300 (m-30) cc_final: 0.7692 (m-30) REVERT: C 37 LYS cc_start: 0.8939 (ttmt) cc_final: 0.7540 (tptt) REVERT: C 69 LYS cc_start: 0.8852 (tmtt) cc_final: 0.8514 (tttm) REVERT: C 72 ASP cc_start: 0.8987 (m-30) cc_final: 0.8587 (m-30) REVERT: D 10 ASP cc_start: 0.8317 (m-30) cc_final: 0.7593 (m-30) REVERT: D 66 LYS cc_start: 0.8574 (tptp) cc_final: 0.7781 (ttmt) REVERT: D 69 LYS cc_start: 0.8731 (tmtt) cc_final: 0.8444 (tttm) REVERT: E 10 ASP cc_start: 0.8427 (m-30) cc_final: 0.7955 (m-30) REVERT: E 37 LYS cc_start: 0.9099 (ttmt) cc_final: 0.7960 (tptt) REVERT: F 10 ASP cc_start: 0.8332 (m-30) cc_final: 0.7950 (m-30) REVERT: F 37 LYS cc_start: 0.8975 (ttmt) cc_final: 0.7532 (tptt) REVERT: G 10 ASP cc_start: 0.8501 (m-30) cc_final: 0.8231 (m-30) REVERT: G 52 SER cc_start: 0.8932 (m) cc_final: 0.8371 (p) REVERT: H 37 LYS cc_start: 0.9042 (ttmt) cc_final: 0.7537 (tptt) REVERT: H 72 ASP cc_start: 0.9083 (m-30) cc_final: 0.8724 (m-30) REVERT: I 53 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7365 (mt-10) REVERT: J 53 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7499 (mt-10) REVERT: J 72 ASP cc_start: 0.8346 (m-30) cc_final: 0.7830 (m-30) REVERT: K 10 ASP cc_start: 0.8266 (m-30) cc_final: 0.7824 (m-30) REVERT: K 31 LEU cc_start: 0.9193 (tp) cc_final: 0.8988 (tp) REVERT: L 39 SER cc_start: 0.8608 (m) cc_final: 0.7956 (m) REVERT: M 69 LYS cc_start: 0.9056 (tmtt) cc_final: 0.7812 (ttmt) REVERT: N 15 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.7517 (ttpt) REVERT: N 69 LYS cc_start: 0.8959 (tmtt) cc_final: 0.7913 (ttmt) REVERT: O 69 LYS cc_start: 0.9020 (tmtt) cc_final: 0.8075 (ttmt) REVERT: O 72 ASP cc_start: 0.8444 (m-30) cc_final: 0.8200 (m-30) REVERT: P 69 LYS cc_start: 0.8830 (tmtt) cc_final: 0.7846 (ttmt) REVERT: Q 15 LYS cc_start: 0.8749 (mttp) cc_final: 0.7690 (tttt) REVERT: Q 25 THR cc_start: 0.9047 (m) cc_final: 0.8703 (p) REVERT: Q 32 ASP cc_start: 0.7861 (m-30) cc_final: 0.7494 (m-30) REVERT: Q 69 LYS cc_start: 0.8920 (tmtt) cc_final: 0.7505 (tttt) REVERT: R 15 LYS cc_start: 0.8540 (mttp) cc_final: 0.7575 (ttpt) REVERT: R 69 LYS cc_start: 0.9034 (tmtt) cc_final: 0.7846 (ttmt) REVERT: R 77 GLN cc_start: 0.8317 (tm-30) cc_final: 0.7791 (tm-30) outliers start: 19 outliers final: 14 residues processed: 311 average time/residue: 0.2162 time to fit residues: 94.4169 Evaluate side-chains 302 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 287 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain I residue 15 LYS Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain N residue 10 ASP Chi-restraints excluded: chain N residue 15 LYS Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain P residue 59 ASN Chi-restraints excluded: chain Q residue 6 SER Chi-restraints excluded: chain R residue 10 ASP Chi-restraints excluded: chain R residue 49 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 0.0030 chunk 50 optimal weight: 0.0970 chunk 103 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN C 59 ASN D 55 ASN E 59 ASN H 61 GLN ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 11214 Z= 0.110 Angle : 0.381 5.337 15264 Z= 0.201 Chirality : 0.033 0.099 1746 Planarity : 0.003 0.026 1998 Dihedral : 3.460 15.364 1512 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.26 % Allowed : 15.91 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.40 (0.21), residues: 1368 helix: 2.71 (0.13), residues: 1206 sheet: None (None), residues: 0 loop : -1.64 (0.51), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP P 5 PHE 0.005 0.001 PHE E 16 TYR 0.008 0.001 TYR B 47 ARG 0.002 0.000 ARG O 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 307 time to evaluate : 1.085 Fit side-chains revert: symmetry clash REVERT: A 61 GLN cc_start: 0.9092 (tt0) cc_final: 0.8890 (tt0) REVERT: A 69 LYS cc_start: 0.8802 (tmtt) cc_final: 0.8599 (tttm) REVERT: B 37 LYS cc_start: 0.8752 (ttmt) cc_final: 0.7494 (tptt) REVERT: B 56 LEU cc_start: 0.9172 (mt) cc_final: 0.8807 (mt) REVERT: B 66 LYS cc_start: 0.8596 (tptp) cc_final: 0.7441 (ttmt) REVERT: B 69 LYS cc_start: 0.8646 (tttm) cc_final: 0.8366 (tttm) REVERT: C 10 ASP cc_start: 0.8112 (m-30) cc_final: 0.7477 (m-30) REVERT: C 37 LYS cc_start: 0.8927 (ttmt) cc_final: 0.7587 (tptt) REVERT: C 69 LYS cc_start: 0.8829 (tmtt) cc_final: 0.8497 (tttm) REVERT: C 72 ASP cc_start: 0.8956 (m-30) cc_final: 0.8511 (m-30) REVERT: D 10 ASP cc_start: 0.8223 (m-30) cc_final: 0.7513 (m-30) REVERT: D 66 LYS cc_start: 0.8539 (tptp) cc_final: 0.7681 (ttmt) REVERT: D 69 LYS cc_start: 0.8694 (tmtt) cc_final: 0.8427 (tttm) REVERT: E 10 ASP cc_start: 0.8392 (m-30) cc_final: 0.7883 (m-30) REVERT: E 37 LYS cc_start: 0.9074 (ttmt) cc_final: 0.7938 (tptt) REVERT: E 66 LYS cc_start: 0.8403 (tptp) cc_final: 0.7623 (tppt) REVERT: F 10 ASP cc_start: 0.8325 (m-30) cc_final: 0.7966 (m-30) REVERT: F 37 LYS cc_start: 0.8958 (ttmt) cc_final: 0.7530 (tptt) REVERT: G 10 ASP cc_start: 0.8471 (m-30) cc_final: 0.8181 (m-30) REVERT: G 52 SER cc_start: 0.8982 (m) cc_final: 0.8441 (p) REVERT: H 37 LYS cc_start: 0.9024 (ttmt) cc_final: 0.7508 (tptt) REVERT: H 72 ASP cc_start: 0.9061 (m-30) cc_final: 0.8642 (m-30) REVERT: I 53 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7312 (mt-10) REVERT: I 77 GLN cc_start: 0.8640 (tp40) cc_final: 0.8427 (tp40) REVERT: J 53 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7425 (mt-10) REVERT: K 10 ASP cc_start: 0.8311 (m-30) cc_final: 0.7983 (m-30) REVERT: K 31 LEU cc_start: 0.9182 (tp) cc_final: 0.8975 (tp) REVERT: L 39 SER cc_start: 0.8605 (m) cc_final: 0.8015 (m) REVERT: M 69 LYS cc_start: 0.9062 (tmtt) cc_final: 0.7801 (ttmt) REVERT: N 15 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.7497 (ttpt) REVERT: N 69 LYS cc_start: 0.8906 (tmtt) cc_final: 0.7912 (ttmt) REVERT: O 69 LYS cc_start: 0.9011 (tmtt) cc_final: 0.7926 (ttmt) REVERT: P 69 LYS cc_start: 0.8886 (tmtt) cc_final: 0.7845 (ttmt) REVERT: P 77 GLN cc_start: 0.8094 (tm-30) cc_final: 0.7187 (tm-30) REVERT: Q 15 LYS cc_start: 0.8718 (mttp) cc_final: 0.7616 (tttt) REVERT: Q 25 THR cc_start: 0.9010 (m) cc_final: 0.8742 (p) REVERT: Q 32 ASP cc_start: 0.7775 (m-30) cc_final: 0.7434 (m-30) REVERT: Q 69 LYS cc_start: 0.8914 (tmtt) cc_final: 0.7444 (tttt) REVERT: R 15 LYS cc_start: 0.8513 (mttp) cc_final: 0.7549 (ttpt) REVERT: R 69 LYS cc_start: 0.9057 (tmtt) cc_final: 0.7712 (ttmt) REVERT: R 77 GLN cc_start: 0.8312 (tm-30) cc_final: 0.7792 (tm-30) outliers start: 15 outliers final: 8 residues processed: 315 average time/residue: 0.2261 time to fit residues: 100.0383 Evaluate side-chains 298 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 289 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain I residue 15 LYS Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain N residue 15 LYS Chi-restraints excluded: chain P residue 59 ASN Chi-restraints excluded: chain Q residue 6 SER Chi-restraints excluded: chain R residue 49 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 10 optimal weight: 0.0270 chunk 64 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN C 63 ASN D 55 ASN E 59 ASN ** N 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 11214 Z= 0.187 Angle : 0.423 5.548 15264 Z= 0.223 Chirality : 0.035 0.105 1746 Planarity : 0.003 0.024 1998 Dihedral : 3.567 16.400 1512 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.52 % Allowed : 16.16 % Favored : 82.32 % 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: 3.48 (0.21), residues: 1368 helix: 2.79 (0.13), residues: 1206 sheet: None (None), residues: 0 loop : -1.86 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 5 PHE 0.007 0.001 PHE O 68 TYR 0.010 0.001 TYR J 57 ARG 0.001 0.000 ARG N 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 304 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8792 (tmtt) cc_final: 0.8583 (tttm) REVERT: B 37 LYS cc_start: 0.8929 (ttmt) cc_final: 0.7613 (tptt) REVERT: B 56 LEU cc_start: 0.9170 (mt) cc_final: 0.8785 (mt) REVERT: B 66 LYS cc_start: 0.8592 (tptp) cc_final: 0.7485 (ttmt) REVERT: B 69 LYS cc_start: 0.8691 (tttm) cc_final: 0.8437 (tttm) REVERT: C 10 ASP cc_start: 0.8379 (m-30) cc_final: 0.7710 (m-30) REVERT: C 37 LYS cc_start: 0.8947 (ttmt) cc_final: 0.7577 (tptt) REVERT: C 69 LYS cc_start: 0.8868 (tmtt) cc_final: 0.8549 (tttm) REVERT: C 72 ASP cc_start: 0.9030 (m-30) cc_final: 0.8603 (m-30) REVERT: D 10 ASP cc_start: 0.8364 (m-30) cc_final: 0.7594 (m-30) REVERT: D 53 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7316 (mm-30) REVERT: D 66 LYS cc_start: 0.8565 (tptp) cc_final: 0.7143 (mttm) REVERT: D 69 LYS cc_start: 0.8761 (tmtt) cc_final: 0.8474 (tttm) REVERT: E 10 ASP cc_start: 0.8367 (m-30) cc_final: 0.7948 (m-30) REVERT: E 37 LYS cc_start: 0.9093 (ttmt) cc_final: 0.7931 (tptt) REVERT: E 66 LYS cc_start: 0.8405 (tptp) cc_final: 0.7617 (tppt) REVERT: F 10 ASP cc_start: 0.8377 (m-30) cc_final: 0.8015 (m-30) REVERT: F 37 LYS cc_start: 0.8981 (ttmt) cc_final: 0.7575 (tptt) REVERT: G 10 ASP cc_start: 0.8510 (m-30) cc_final: 0.8253 (m-30) REVERT: H 72 ASP cc_start: 0.9113 (m-30) cc_final: 0.8697 (m-30) REVERT: I 53 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7309 (mt-10) REVERT: I 69 LYS cc_start: 0.8709 (tmtt) cc_final: 0.8270 (tttp) REVERT: I 77 GLN cc_start: 0.8621 (tp40) cc_final: 0.8382 (tp40) REVERT: J 53 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7446 (mt-10) REVERT: K 10 ASP cc_start: 0.8305 (m-30) cc_final: 0.7834 (m-30) REVERT: M 69 LYS cc_start: 0.9043 (tmtt) cc_final: 0.7821 (ttmt) REVERT: N 15 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.7486 (ttpt) REVERT: N 69 LYS cc_start: 0.8927 (tmtt) cc_final: 0.7920 (ttmt) REVERT: O 69 LYS cc_start: 0.9051 (tmtt) cc_final: 0.7945 (ttmt) REVERT: P 69 LYS cc_start: 0.8924 (tmtt) cc_final: 0.7838 (ttmt) REVERT: P 77 GLN cc_start: 0.8079 (tm-30) cc_final: 0.7173 (tm-30) REVERT: Q 15 LYS cc_start: 0.8736 (mttp) cc_final: 0.7579 (ttpt) REVERT: Q 25 THR cc_start: 0.9009 (m) cc_final: 0.8702 (p) REVERT: Q 32 ASP cc_start: 0.7894 (m-30) cc_final: 0.7524 (m-30) REVERT: Q 69 LYS cc_start: 0.8923 (tmtt) cc_final: 0.7659 (tttt) REVERT: R 15 LYS cc_start: 0.8439 (mttp) cc_final: 0.7412 (ttpt) REVERT: R 69 LYS cc_start: 0.9052 (tmtt) cc_final: 0.7876 (ttmt) REVERT: R 77 GLN cc_start: 0.8309 (tm-30) cc_final: 0.7787 (tm-30) outliers start: 18 outliers final: 16 residues processed: 312 average time/residue: 0.2399 time to fit residues: 105.1756 Evaluate side-chains 305 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 288 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain I residue 15 LYS Chi-restraints excluded: chain I residue 21 ASP Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain M residue 53 GLU Chi-restraints excluded: chain N residue 15 LYS Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain P residue 59 ASN Chi-restraints excluded: chain Q residue 6 SER Chi-restraints excluded: chain R residue 10 ASP Chi-restraints excluded: chain R residue 49 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN D 55 ASN L 78 ASN ** N 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 11214 Z= 0.259 Angle : 0.461 5.741 15264 Z= 0.242 Chirality : 0.036 0.108 1746 Planarity : 0.003 0.024 1998 Dihedral : 3.687 17.996 1512 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.02 % Allowed : 16.25 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.20 (0.21), residues: 1368 helix: 2.62 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.76 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 5 PHE 0.009 0.001 PHE O 68 TYR 0.012 0.001 TYR G 57 ARG 0.002 0.000 ARG N 58 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 298 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8823 (tmtt) cc_final: 0.8584 (tttm) REVERT: B 37 LYS cc_start: 0.8930 (ttmt) cc_final: 0.7518 (tptt) REVERT: B 56 LEU cc_start: 0.9166 (mt) cc_final: 0.8800 (mt) REVERT: B 66 LYS cc_start: 0.8521 (tptp) cc_final: 0.7360 (ttmt) REVERT: C 10 ASP cc_start: 0.8403 (m-30) cc_final: 0.7718 (m-30) REVERT: C 37 LYS cc_start: 0.8970 (ttmt) cc_final: 0.7614 (tptt) REVERT: C 69 LYS cc_start: 0.8874 (tmtt) cc_final: 0.8546 (tttm) REVERT: C 72 ASP cc_start: 0.9054 (m-30) cc_final: 0.8656 (m-30) REVERT: D 10 ASP cc_start: 0.8361 (m-30) cc_final: 0.7526 (m-30) REVERT: D 53 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7293 (mm-30) REVERT: D 66 LYS cc_start: 0.8583 (tptp) cc_final: 0.7749 (ttmt) REVERT: E 10 ASP cc_start: 0.8370 (m-30) cc_final: 0.7970 (m-30) REVERT: E 37 LYS cc_start: 0.9102 (ttmt) cc_final: 0.7913 (tptt) REVERT: E 66 LYS cc_start: 0.8333 (tptp) cc_final: 0.7585 (tppt) REVERT: F 10 ASP cc_start: 0.8369 (m-30) cc_final: 0.8005 (m-30) REVERT: F 37 LYS cc_start: 0.9007 (ttmt) cc_final: 0.7566 (tptt) REVERT: G 32 ASP cc_start: 0.7931 (m-30) cc_final: 0.7428 (m-30) REVERT: H 72 ASP cc_start: 0.9140 (m-30) cc_final: 0.8750 (m-30) REVERT: I 53 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7184 (mt-10) REVERT: I 69 LYS cc_start: 0.8778 (tmtt) cc_final: 0.8290 (tttp) REVERT: I 77 GLN cc_start: 0.8618 (tp40) cc_final: 0.8363 (tp40) REVERT: J 53 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7418 (mt-10) REVERT: K 10 ASP cc_start: 0.8296 (m-30) cc_final: 0.7813 (m-30) REVERT: M 69 LYS cc_start: 0.9051 (tmtt) cc_final: 0.7819 (ttmt) REVERT: N 15 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.7538 (ttpt) REVERT: N 69 LYS cc_start: 0.8947 (tmtt) cc_final: 0.7872 (ttmt) REVERT: N 70 ASP cc_start: 0.8225 (m-30) cc_final: 0.7878 (m-30) REVERT: O 69 LYS cc_start: 0.8999 (tmtt) cc_final: 0.7923 (ttmt) REVERT: O 72 ASP cc_start: 0.8483 (m-30) cc_final: 0.8145 (m-30) REVERT: P 53 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7637 (mt-10) REVERT: P 54 TYR cc_start: 0.9054 (t80) cc_final: 0.8763 (t80) REVERT: P 69 LYS cc_start: 0.8939 (tmtt) cc_final: 0.7803 (ttmt) REVERT: P 77 GLN cc_start: 0.8079 (tm-30) cc_final: 0.7171 (tm-30) REVERT: Q 25 THR cc_start: 0.9032 (m) cc_final: 0.8683 (p) REVERT: Q 69 LYS cc_start: 0.8940 (tmtt) cc_final: 0.7669 (tttt) REVERT: R 69 LYS cc_start: 0.9059 (tmtt) cc_final: 0.7919 (ttmt) outliers start: 24 outliers final: 19 residues processed: 313 average time/residue: 0.2249 time to fit residues: 98.7601 Evaluate side-chains 307 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 287 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain N residue 10 ASP Chi-restraints excluded: chain N residue 15 LYS Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 59 ASN Chi-restraints excluded: chain Q residue 6 SER Chi-restraints excluded: chain R residue 10 ASP Chi-restraints excluded: chain R residue 49 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 ASN ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 11214 Z= 0.137 Angle : 0.402 5.596 15264 Z= 0.211 Chirality : 0.033 0.112 1746 Planarity : 0.003 0.022 1998 Dihedral : 3.544 15.805 1512 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.43 % Allowed : 17.17 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.64 (0.21), residues: 1368 helix: 2.92 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.70 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 5 PHE 0.005 0.001 PHE N 68 TYR 0.011 0.001 TYR K 47 ARG 0.001 0.000 ARG H 58 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 301 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8791 (tmtt) cc_final: 0.8586 (tttm) REVERT: B 37 LYS cc_start: 0.8903 (ttmt) cc_final: 0.7562 (tptt) REVERT: B 56 LEU cc_start: 0.9153 (mt) cc_final: 0.8777 (mt) REVERT: B 66 LYS cc_start: 0.8486 (tptp) cc_final: 0.7332 (ttmt) REVERT: C 10 ASP cc_start: 0.8174 (m-30) cc_final: 0.7501 (m-30) REVERT: C 69 LYS cc_start: 0.8838 (tmtt) cc_final: 0.8518 (tttm) REVERT: C 72 ASP cc_start: 0.8959 (m-30) cc_final: 0.8517 (m-30) REVERT: D 10 ASP cc_start: 0.8267 (m-30) cc_final: 0.7496 (m-30) REVERT: D 53 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7291 (mm-30) REVERT: D 66 LYS cc_start: 0.8577 (tptp) cc_final: 0.7110 (mttm) REVERT: E 10 ASP cc_start: 0.8348 (m-30) cc_final: 0.7964 (m-30) REVERT: E 37 LYS cc_start: 0.9068 (ttmt) cc_final: 0.7891 (tptt) REVERT: E 66 LYS cc_start: 0.8394 (tptp) cc_final: 0.7628 (tppt) REVERT: F 10 ASP cc_start: 0.8338 (m-30) cc_final: 0.7973 (m-30) REVERT: F 37 LYS cc_start: 0.8972 (ttmt) cc_final: 0.7511 (tptt) REVERT: G 53 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7377 (mm-30) REVERT: H 72 ASP cc_start: 0.9100 (m-30) cc_final: 0.8702 (m-30) REVERT: I 53 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7237 (mt-10) REVERT: I 69 LYS cc_start: 0.8715 (tmtt) cc_final: 0.8255 (tttp) REVERT: I 77 GLN cc_start: 0.8632 (tp40) cc_final: 0.8405 (tp40) REVERT: J 53 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7405 (mt-10) REVERT: K 10 ASP cc_start: 0.8316 (m-30) cc_final: 0.7836 (m-30) REVERT: M 53 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7364 (mt-10) REVERT: M 69 LYS cc_start: 0.9035 (tmtt) cc_final: 0.7816 (ttmt) REVERT: N 15 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.7514 (ttpt) REVERT: N 33 LYS cc_start: 0.8846 (mtmm) cc_final: 0.8438 (mtmm) REVERT: N 69 LYS cc_start: 0.8939 (tmtt) cc_final: 0.7903 (ttmt) REVERT: O 69 LYS cc_start: 0.9067 (tmtt) cc_final: 0.7924 (ttmt) REVERT: P 54 TYR cc_start: 0.9019 (t80) cc_final: 0.8725 (t80) REVERT: P 69 LYS cc_start: 0.8934 (tmtt) cc_final: 0.7783 (ttmt) REVERT: P 77 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7273 (tm-30) REVERT: Q 25 THR cc_start: 0.9025 (m) cc_final: 0.8714 (p) REVERT: Q 69 LYS cc_start: 0.8937 (tmtt) cc_final: 0.7633 (tttt) REVERT: R 69 LYS cc_start: 0.9037 (tmtt) cc_final: 0.7845 (ttmt) outliers start: 17 outliers final: 14 residues processed: 311 average time/residue: 0.2191 time to fit residues: 96.0456 Evaluate side-chains 310 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 295 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain I residue 15 LYS Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain N residue 10 ASP Chi-restraints excluded: chain N residue 15 LYS Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 59 ASN Chi-restraints excluded: chain R residue 10 ASP Chi-restraints excluded: chain R residue 49 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN D 55 ASN ** N 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11214 Z= 0.184 Angle : 0.427 6.463 15264 Z= 0.224 Chirality : 0.035 0.124 1746 Planarity : 0.003 0.023 1998 Dihedral : 3.578 15.845 1512 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.85 % Allowed : 16.58 % Favored : 81.57 % 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: 3.67 (0.21), residues: 1368 helix: 2.94 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.71 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP G 5 PHE 0.007 0.001 PHE N 68 TYR 0.016 0.001 TYR K 47 ARG 0.001 0.000 ARG N 58 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 293 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8806 (tmtt) cc_final: 0.8591 (tttm) REVERT: B 37 LYS cc_start: 0.8909 (ttmt) cc_final: 0.7559 (tptt) REVERT: B 56 LEU cc_start: 0.9160 (mt) cc_final: 0.8791 (mt) REVERT: B 66 LYS cc_start: 0.8503 (tptp) cc_final: 0.7349 (ttmt) REVERT: C 10 ASP cc_start: 0.8268 (m-30) cc_final: 0.7595 (m-30) REVERT: C 69 LYS cc_start: 0.8870 (tmtt) cc_final: 0.8559 (tttm) REVERT: C 72 ASP cc_start: 0.9016 (m-30) cc_final: 0.8595 (m-30) REVERT: D 10 ASP cc_start: 0.8313 (m-30) cc_final: 0.7502 (m-30) REVERT: D 53 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7369 (mm-30) REVERT: D 66 LYS cc_start: 0.8585 (tptp) cc_final: 0.7133 (mttm) REVERT: E 10 ASP cc_start: 0.8360 (m-30) cc_final: 0.7989 (m-30) REVERT: E 37 LYS cc_start: 0.9083 (ttmt) cc_final: 0.7893 (tptt) REVERT: E 66 LYS cc_start: 0.8378 (tptp) cc_final: 0.7628 (tppt) REVERT: F 10 ASP cc_start: 0.8358 (m-30) cc_final: 0.7991 (m-30) REVERT: F 37 LYS cc_start: 0.8989 (ttmt) cc_final: 0.7562 (tptt) REVERT: G 10 ASP cc_start: 0.8312 (m-30) cc_final: 0.7790 (m-30) REVERT: G 53 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7627 (mm-30) REVERT: H 72 ASP cc_start: 0.9121 (m-30) cc_final: 0.8707 (m-30) REVERT: I 53 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7187 (mt-10) REVERT: I 69 LYS cc_start: 0.8752 (tmtt) cc_final: 0.8263 (tttp) REVERT: J 53 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7389 (mt-10) REVERT: K 10 ASP cc_start: 0.8323 (m-30) cc_final: 0.7832 (m-30) REVERT: M 53 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7382 (mt-10) REVERT: M 69 LYS cc_start: 0.9042 (tmtt) cc_final: 0.7818 (ttmt) REVERT: N 15 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.7505 (ttpt) REVERT: N 33 LYS cc_start: 0.8875 (mtmm) cc_final: 0.8473 (mtmm) REVERT: N 69 LYS cc_start: 0.8940 (tmtt) cc_final: 0.7907 (ttmt) REVERT: O 69 LYS cc_start: 0.9044 (tmtt) cc_final: 0.7923 (ttmt) REVERT: P 54 TYR cc_start: 0.9052 (t80) cc_final: 0.8745 (t80) REVERT: P 69 LYS cc_start: 0.8942 (tmtt) cc_final: 0.7787 (ttmt) REVERT: P 77 GLN cc_start: 0.8157 (tm-30) cc_final: 0.7283 (tm-30) REVERT: Q 25 THR cc_start: 0.8998 (m) cc_final: 0.8693 (p) REVERT: Q 69 LYS cc_start: 0.8941 (tmtt) cc_final: 0.7633 (tttt) REVERT: R 69 LYS cc_start: 0.9045 (tmtt) cc_final: 0.7886 (ttmt) outliers start: 22 outliers final: 19 residues processed: 308 average time/residue: 0.2227 time to fit residues: 97.0660 Evaluate side-chains 310 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 290 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain N residue 10 ASP Chi-restraints excluded: chain N residue 15 LYS Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 59 ASN Chi-restraints excluded: chain Q residue 6 SER Chi-restraints excluded: chain R residue 10 ASP Chi-restraints excluded: chain R residue 49 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 10 optimal weight: 0.0060 chunk 77 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 ASN ** N 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11214 Z= 0.217 Angle : 0.445 6.762 15264 Z= 0.234 Chirality : 0.035 0.125 1746 Planarity : 0.003 0.023 1998 Dihedral : 3.641 16.668 1512 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.60 % Allowed : 17.17 % Favored : 81.23 % 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: 3.58 (0.21), residues: 1368 helix: 2.87 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.67 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 5 PHE 0.008 0.001 PHE O 68 TYR 0.018 0.001 TYR K 47 ARG 0.001 0.000 ARG N 58 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 295 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8815 (tmtt) cc_final: 0.8605 (tttm) REVERT: B 37 LYS cc_start: 0.8918 (ttmt) cc_final: 0.7491 (tptt) REVERT: B 56 LEU cc_start: 0.9160 (mt) cc_final: 0.8800 (mt) REVERT: B 66 LYS cc_start: 0.8510 (tptp) cc_final: 0.6874 (mttm) REVERT: C 10 ASP cc_start: 0.8362 (m-30) cc_final: 0.7696 (m-30) REVERT: C 69 LYS cc_start: 0.8856 (tmtt) cc_final: 0.8534 (tttm) REVERT: C 72 ASP cc_start: 0.9029 (m-30) cc_final: 0.8619 (m-30) REVERT: D 10 ASP cc_start: 0.8327 (m-30) cc_final: 0.7506 (m-30) REVERT: D 53 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7385 (mm-30) REVERT: D 66 LYS cc_start: 0.8608 (tptp) cc_final: 0.7756 (ttmt) REVERT: E 10 ASP cc_start: 0.8452 (m-30) cc_final: 0.7977 (m-30) REVERT: E 37 LYS cc_start: 0.9086 (ttmt) cc_final: 0.7902 (tptt) REVERT: E 66 LYS cc_start: 0.8450 (tptp) cc_final: 0.7632 (tppt) REVERT: F 10 ASP cc_start: 0.8365 (m-30) cc_final: 0.8001 (m-30) REVERT: F 37 LYS cc_start: 0.8999 (ttmt) cc_final: 0.7564 (tptt) REVERT: G 10 ASP cc_start: 0.8296 (m-30) cc_final: 0.7786 (m-30) REVERT: G 32 ASP cc_start: 0.7904 (m-30) cc_final: 0.7428 (m-30) REVERT: G 53 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7561 (mm-30) REVERT: H 72 ASP cc_start: 0.9137 (m-30) cc_final: 0.8739 (m-30) REVERT: I 53 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7206 (mt-10) REVERT: I 69 LYS cc_start: 0.8760 (tmtt) cc_final: 0.8275 (tttp) REVERT: J 53 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7412 (mt-10) REVERT: K 10 ASP cc_start: 0.8296 (m-30) cc_final: 0.7803 (m-30) REVERT: M 53 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7408 (mt-10) REVERT: M 69 LYS cc_start: 0.9045 (tmtt) cc_final: 0.7822 (ttmt) REVERT: N 15 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.7533 (ttpt) REVERT: N 29 GLU cc_start: 0.7186 (tp30) cc_final: 0.6972 (tp30) REVERT: N 33 LYS cc_start: 0.8888 (mtmm) cc_final: 0.8505 (mtmm) REVERT: N 69 LYS cc_start: 0.8970 (tmtt) cc_final: 0.7932 (ttmt) REVERT: O 32 ASP cc_start: 0.7853 (m-30) cc_final: 0.7524 (m-30) REVERT: O 69 LYS cc_start: 0.9044 (tmtt) cc_final: 0.7923 (ttmt) REVERT: P 21 ASP cc_start: 0.7815 (t0) cc_final: 0.7570 (t0) REVERT: P 53 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7830 (mt-10) REVERT: P 54 TYR cc_start: 0.9043 (t80) cc_final: 0.8753 (t80) REVERT: P 69 LYS cc_start: 0.8950 (tmtt) cc_final: 0.7791 (ttmt) REVERT: P 77 GLN cc_start: 0.8158 (tm-30) cc_final: 0.7304 (tm-30) REVERT: Q 25 THR cc_start: 0.9056 (m) cc_final: 0.8699 (p) REVERT: Q 69 LYS cc_start: 0.8943 (tmtt) cc_final: 0.7638 (tttt) REVERT: R 69 LYS cc_start: 0.9046 (tmtt) cc_final: 0.7890 (ttmt) outliers start: 19 outliers final: 18 residues processed: 307 average time/residue: 0.2300 time to fit residues: 99.7177 Evaluate side-chains 311 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 292 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain N residue 10 ASP Chi-restraints excluded: chain N residue 15 LYS Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 59 ASN Chi-restraints excluded: chain Q residue 6 SER Chi-restraints excluded: chain R residue 10 ASP Chi-restraints excluded: chain R residue 49 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN D 55 ASN E 59 ASN ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.093557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.084015 restraints weight = 18486.653| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.67 r_work: 0.2902 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11214 Z= 0.135 Angle : 0.407 6.373 15264 Z= 0.214 Chirality : 0.033 0.123 1746 Planarity : 0.003 0.022 1998 Dihedral : 3.544 15.177 1512 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.77 % Allowed : 17.26 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.88 (0.21), residues: 1368 helix: 3.07 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.62 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 5 PHE 0.006 0.001 PHE M 16 TYR 0.020 0.001 TYR K 47 ARG 0.001 0.000 ARG N 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2592.08 seconds wall clock time: 48 minutes 47.66 seconds (2927.66 seconds total)