Starting phenix.real_space_refine on Fri Mar 15 12:21:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofh_20046/03_2024/6ofh_20046_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofh_20046/03_2024/6ofh_20046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofh_20046/03_2024/6ofh_20046.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofh_20046/03_2024/6ofh_20046.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofh_20046/03_2024/6ofh_20046_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofh_20046/03_2024/6ofh_20046_neut.pdb" } resolution = 3.7 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= 0.003 sd= 0.023 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 7353 2.51 5 N 1919 2.21 5 O 2356 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-5265/modules/chem_data/mon_lib" Total number of atoms: 11628 Number of models: 1 Model: "" Number of chains: 19 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: "U" 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: "V" 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} Chain: "S" 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: "T" 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: 6.33, per 1000 atoms: 0.54 Number of scatterers: 11628 At special positions: 0 Unit cell: (93.94, 92.232, 153.72, 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 2356 8.00 N 1919 7.00 C 7353 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.53 Conformation dependent library (CDL) restraints added in 2.2 seconds 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2888 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 0 sheets defined 88.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'D' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE D 16 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP D 17 " --> pdb=" O SER D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR D 28 " --> pdb=" O GLN D 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA D 36 " --> pdb=" O ASP D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 73 removed outlier: 3.681A pdb=" N ALA D 46 " --> pdb=" O ALA D 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 56 " --> pdb=" O SER D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN D 77 " --> pdb=" O ALA D 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE U 16 " --> pdb=" O VAL U 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP U 17 " --> pdb=" O SER U 13 " (cutoff:3.500A) Processing helix chain 'U' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR U 28 " --> pdb=" O GLN U 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA U 36 " --> pdb=" O ASP U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA U 46 " --> pdb=" O ALA U 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU U 56 " --> pdb=" O SER U 52 " (cutoff:3.500A) Processing helix chain 'U' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN U 77 " --> pdb=" O ALA U 74 " (cutoff:3.500A) Processing helix chain 'V' and resid 7 through 20 removed outlier: 3.744A pdb=" N PHE V 16 " --> pdb=" O VAL V 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP V 17 " --> pdb=" O SER V 13 " (cutoff:3.500A) Processing helix chain 'V' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR V 28 " --> pdb=" O GLN V 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA V 36 " --> pdb=" O ASP V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA V 46 " --> pdb=" O ALA V 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU V 56 " --> pdb=" O SER V 52 " (cutoff:3.500A) Processing helix chain 'V' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN V 77 " --> pdb=" O ALA V 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE E 16 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP E 17 " --> pdb=" O SER E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR E 28 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA E 46 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU E 56 " --> pdb=" O SER E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN E 77 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 20 removed outlier: 3.744A pdb=" N PHE F 16 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP F 17 " --> pdb=" O SER F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU F 56 " --> pdb=" O SER F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 79 removed outlier: 4.576A pdb=" N GLN F 77 " --> pdb=" O ALA F 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE G 16 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP G 17 " --> pdb=" O SER G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR G 28 " --> pdb=" O GLN G 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA G 36 " --> pdb=" O ASP G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 73 removed outlier: 3.681A pdb=" N ALA G 46 " --> pdb=" O ALA G 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU G 56 " --> pdb=" O SER G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN G 77 " --> pdb=" O ALA G 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE H 16 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP H 17 " --> pdb=" O SER H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR H 28 " --> pdb=" O GLN H 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA H 36 " --> pdb=" O ASP H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA H 46 " --> pdb=" O ALA H 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU H 56 " --> pdb=" O SER H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 79 removed outlier: 4.574A pdb=" N GLN H 77 " --> pdb=" O ALA H 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE I 16 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP I 17 " --> pdb=" O SER I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR I 28 " --> pdb=" O GLN I 24 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA I 36 " --> pdb=" O ASP I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA I 46 " --> pdb=" O ALA I 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU I 56 " --> pdb=" O SER I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN I 77 " --> pdb=" O ALA I 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE J 16 " --> pdb=" O VAL J 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP J 17 " --> pdb=" O SER J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR J 28 " --> pdb=" O GLN J 24 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA J 36 " --> pdb=" O ASP J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA J 46 " --> pdb=" O ALA J 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU J 56 " --> pdb=" O SER J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN J 77 " --> pdb=" O ALA J 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE K 16 " --> pdb=" O VAL K 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP K 17 " --> pdb=" O SER K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR K 28 " --> pdb=" O GLN K 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA K 36 " --> pdb=" O ASP K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA K 46 " --> pdb=" O ALA K 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU K 56 " --> pdb=" O SER K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN K 77 " --> pdb=" O ALA K 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 20 removed outlier: 3.744A pdb=" N PHE L 16 " --> pdb=" O VAL L 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP L 17 " --> pdb=" O SER L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR L 28 " --> pdb=" O GLN L 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA L 36 " --> pdb=" O ASP L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA L 46 " --> pdb=" O ALA L 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU L 56 " --> pdb=" O SER L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 79 removed outlier: 4.576A pdb=" N GLN L 77 " --> pdb=" O ALA L 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 20 removed outlier: 3.742A pdb=" N PHE M 16 " --> pdb=" O VAL M 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP M 17 " --> pdb=" O SER M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR M 28 " --> pdb=" O GLN M 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA M 36 " --> pdb=" O ASP M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 73 removed outlier: 3.681A pdb=" N ALA M 46 " --> pdb=" O ALA M 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU M 56 " --> pdb=" O SER M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN M 77 " --> pdb=" O ALA M 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 20 removed outlier: 3.744A pdb=" N PHE N 16 " --> pdb=" O VAL N 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP N 17 " --> pdb=" O SER N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR N 28 " --> pdb=" O GLN N 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA N 36 " --> pdb=" O ASP N 32 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 73 removed outlier: 3.681A pdb=" N ALA N 46 " --> pdb=" O ALA N 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU N 56 " --> pdb=" O SER N 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 74 through 79 removed outlier: 4.576A pdb=" N GLN N 77 " --> pdb=" O ALA N 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE O 16 " --> pdb=" O VAL O 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP O 17 " --> pdb=" O SER O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR O 28 " --> pdb=" O GLN O 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA O 36 " --> pdb=" O ASP O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 73 removed outlier: 3.681A pdb=" N ALA O 46 " --> pdb=" O ALA O 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU O 56 " --> pdb=" O SER O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN O 77 " --> pdb=" O ALA O 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 20 removed outlier: 3.742A pdb=" N PHE P 16 " --> pdb=" O VAL P 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP P 17 " --> pdb=" O SER P 13 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR P 28 " --> pdb=" O GLN P 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA P 36 " --> pdb=" O ASP P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 73 removed outlier: 3.681A pdb=" N ALA P 46 " --> pdb=" O ALA P 42 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU P 56 " --> pdb=" O SER P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN P 77 " --> pdb=" O ALA P 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE Q 16 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP Q 17 " --> pdb=" O SER Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR Q 28 " --> pdb=" O GLN Q 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA Q 36 " --> pdb=" O ASP Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU Q 56 " --> pdb=" O SER Q 52 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN Q 77 " --> pdb=" O ALA Q 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE R 16 " --> pdb=" O VAL R 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP R 17 " --> pdb=" O SER R 13 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR R 28 " --> pdb=" O GLN R 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA R 36 " --> pdb=" O ASP R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 73 removed outlier: 3.681A pdb=" N ALA R 46 " --> pdb=" O ALA R 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU R 56 " --> pdb=" O SER R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN R 77 " --> pdb=" O ALA R 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE S 16 " --> pdb=" O VAL S 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP S 17 " --> pdb=" O SER S 13 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR S 28 " --> pdb=" O GLN S 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA S 36 " --> pdb=" O ASP S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA S 46 " --> pdb=" O ALA S 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU S 56 " --> pdb=" O SER S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 74 through 79 removed outlier: 4.576A pdb=" N GLN S 77 " --> pdb=" O ALA S 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE T 16 " --> pdb=" O VAL T 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP T 17 " --> pdb=" O SER T 13 " (cutoff:3.500A) Processing helix chain 'T' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR T 28 " --> pdb=" O GLN T 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA T 36 " --> pdb=" O ASP T 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA T 46 " --> pdb=" O ALA T 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU T 56 " --> pdb=" O SER T 52 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN T 77 " --> pdb=" O ALA T 74 " (cutoff:3.500A) 893 hydrogen bonds defined for protein. 2565 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: 3.16 Time building geometry restraints manager: 4.87 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: 2071 1.29 - 1.35: 1767 1.35 - 1.41: 1130 1.41 - 1.48: 1777 1.48 - 1.54: 5092 Bond restraints: 11837 Sorted by residual: bond pdb=" CB GLU M 53 " pdb=" CG GLU M 53 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.21e+00 bond pdb=" CB GLU R 53 " pdb=" CG GLU R 53 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.20e+00 bond pdb=" CB GLU F 53 " pdb=" CG GLU F 53 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.20e+00 bond pdb=" CB GLU J 53 " pdb=" CG GLU J 53 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.19e+00 bond pdb=" CB GLU L 53 " pdb=" CG GLU L 53 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.19e+00 ... (remaining 11832 not shown) Histogram of bond angle deviations from ideal: 102.41 - 108.70: 553 108.70 - 115.00: 6786 115.00 - 121.29: 6406 121.29 - 127.58: 2272 127.58 - 133.88: 95 Bond angle restraints: 16112 Sorted by residual: angle pdb=" CA LEU N 56 " pdb=" CB LEU N 56 " pdb=" CG LEU N 56 " ideal model delta sigma weight residual 116.30 108.09 8.21 3.50e+00 8.16e-02 5.50e+00 angle pdb=" CA LEU L 56 " pdb=" CB LEU L 56 " pdb=" CG LEU L 56 " ideal model delta sigma weight residual 116.30 108.10 8.20 3.50e+00 8.16e-02 5.49e+00 angle pdb=" CA LEU K 56 " pdb=" CB LEU K 56 " pdb=" CG LEU K 56 " ideal model delta sigma weight residual 116.30 108.10 8.20 3.50e+00 8.16e-02 5.48e+00 angle pdb=" CA PRO H 38 " pdb=" C PRO H 38 " pdb=" O PRO H 38 " ideal model delta sigma weight residual 121.38 119.58 1.80 7.70e-01 1.69e+00 5.47e+00 angle pdb=" CA LEU J 56 " pdb=" CB LEU J 56 " pdb=" CG LEU J 56 " ideal model delta sigma weight residual 116.30 108.12 8.18 3.50e+00 8.16e-02 5.47e+00 ... (remaining 16107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.17: 5624 6.17 - 12.34: 1119 12.34 - 18.51: 324 18.51 - 24.68: 77 24.68 - 30.85: 38 Dihedral angle restraints: 7182 sinusoidal: 2755 harmonic: 4427 Sorted by residual: dihedral pdb=" CA ASP D 70 " pdb=" C ASP D 70 " pdb=" N ILE D 71 " pdb=" CA ILE D 71 " ideal model delta harmonic sigma weight residual 180.00 164.46 15.54 0 5.00e+00 4.00e-02 9.66e+00 dihedral pdb=" CA ASP Q 70 " pdb=" C ASP Q 70 " pdb=" N ILE Q 71 " pdb=" CA ILE Q 71 " ideal model delta harmonic sigma weight residual 180.00 164.47 15.53 0 5.00e+00 4.00e-02 9.65e+00 dihedral pdb=" CA ASP S 70 " pdb=" C ASP S 70 " pdb=" N ILE S 71 " pdb=" CA ILE S 71 " ideal model delta harmonic sigma weight residual 180.00 164.48 15.52 0 5.00e+00 4.00e-02 9.64e+00 ... (remaining 7179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.020: 423 0.020 - 0.041: 702 0.041 - 0.061: 378 0.061 - 0.082: 212 0.082 - 0.102: 128 Chirality restraints: 1843 Sorted by residual: chirality pdb=" CA SER N 39 " pdb=" N SER N 39 " pdb=" C SER N 39 " pdb=" CB SER N 39 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.60e-01 chirality pdb=" CA SER U 39 " pdb=" N SER U 39 " pdb=" C SER U 39 " pdb=" CB SER U 39 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.60e-01 chirality pdb=" CA PRO U 38 " pdb=" N PRO U 38 " pdb=" C PRO U 38 " pdb=" CB PRO U 38 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.56e-01 ... (remaining 1840 not shown) Planarity restraints: 2109 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE P 76 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C ILE P 76 " -0.027 2.00e-02 2.50e+03 pdb=" O ILE P 76 " 0.010 2.00e-02 2.50e+03 pdb=" N GLN P 77 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 76 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C ILE R 76 " 0.027 2.00e-02 2.50e+03 pdb=" O ILE R 76 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN R 77 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE O 76 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C ILE O 76 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE O 76 " 0.010 2.00e-02 2.50e+03 pdb=" N GLN O 77 " 0.009 2.00e-02 2.50e+03 ... (remaining 2106 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 106 2.66 - 3.22: 11323 3.22 - 3.78: 17158 3.78 - 4.34: 24963 4.34 - 4.90: 40716 Nonbonded interactions: 94266 Sorted by model distance: nonbonded pdb=" OD1 ASP D 10 " pdb=" OG SER H 49 " model vdw 2.097 2.440 nonbonded pdb=" NZ LYS G 66 " pdb=" OD2 ASP G 70 " model vdw 2.098 2.520 nonbonded pdb=" NZ LYS F 66 " pdb=" OD2 ASP F 70 " model vdw 2.098 2.520 nonbonded pdb=" NZ LYS P 66 " pdb=" OD2 ASP P 70 " model vdw 2.098 2.520 nonbonded pdb=" NZ LYS L 66 " pdb=" OD2 ASP L 70 " model vdw 2.098 2.520 ... (remaining 94261 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 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.950 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 32.290 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.090 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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 : 0.008 0.035 11837 Z= 0.495 Angle : 0.752 8.205 16112 Z= 0.416 Chirality : 0.045 0.102 1843 Planarity : 0.005 0.028 2109 Dihedral : 7.705 30.854 4294 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.76 (0.10), residues: 1444 helix: -4.06 (0.06), residues: 1254 sheet: None (None), residues: 0 loop : -4.86 (0.27), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP G 5 PHE 0.020 0.004 PHE U 68 TYR 0.010 0.002 TYR D 57 ARG 0.004 0.001 ARG U 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 643 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 10 ASP cc_start: 0.7305 (m-30) cc_final: 0.7001 (m-30) REVERT: D 12 VAL cc_start: 0.9496 (t) cc_final: 0.9264 (t) REVERT: D 26 GLN cc_start: 0.7390 (mt0) cc_final: 0.7068 (mt0) REVERT: D 33 LYS cc_start: 0.8263 (mttt) cc_final: 0.7696 (mmtt) REVERT: D 54 TYR cc_start: 0.8293 (t80) cc_final: 0.8030 (t80) REVERT: U 15 LYS cc_start: 0.8811 (mttt) cc_final: 0.8488 (mmmm) REVERT: U 25 THR cc_start: 0.8574 (m) cc_final: 0.8034 (p) REVERT: U 28 THR cc_start: 0.8521 (m) cc_final: 0.8288 (p) REVERT: U 37 LYS cc_start: 0.8180 (ttmt) cc_final: 0.7199 (tptt) REVERT: U 43 LEU cc_start: 0.9411 (mt) cc_final: 0.8678 (mt) REVERT: U 53 GLU cc_start: 0.8675 (tp30) cc_final: 0.8447 (tp30) REVERT: U 66 LYS cc_start: 0.8544 (tptp) cc_final: 0.7280 (mttt) REVERT: V 28 THR cc_start: 0.8981 (m) cc_final: 0.8129 (p) REVERT: V 33 LYS cc_start: 0.8265 (mttt) cc_final: 0.7499 (mtmt) REVERT: V 37 LYS cc_start: 0.9168 (ttmt) cc_final: 0.7889 (tptt) REVERT: V 47 TYR cc_start: 0.9134 (t80) cc_final: 0.8045 (t80) REVERT: V 53 GLU cc_start: 0.8174 (tp30) cc_final: 0.7797 (tp30) REVERT: E 28 THR cc_start: 0.7588 (m) cc_final: 0.7083 (p) REVERT: E 32 ASP cc_start: 0.7929 (m-30) cc_final: 0.7719 (m-30) REVERT: E 37 LYS cc_start: 0.7405 (ttmt) cc_final: 0.6675 (tptt) REVERT: F 28 THR cc_start: 0.9130 (m) cc_final: 0.8353 (p) REVERT: F 34 LEU cc_start: 0.9349 (tp) cc_final: 0.9102 (tt) REVERT: F 37 LYS cc_start: 0.8687 (ttmt) cc_final: 0.7915 (tptt) REVERT: F 39 SER cc_start: 0.9258 (m) cc_final: 0.8971 (t) REVERT: F 47 TYR cc_start: 0.9116 (t80) cc_final: 0.8106 (t80) REVERT: F 49 SER cc_start: 0.8330 (t) cc_final: 0.8086 (p) REVERT: F 63 ASN cc_start: 0.8789 (m-40) cc_final: 0.8179 (m-40) REVERT: F 66 LYS cc_start: 0.8562 (tptp) cc_final: 0.7287 (mttm) REVERT: G 8 TYR cc_start: 0.8726 (t80) cc_final: 0.8493 (t80) REVERT: G 11 ASP cc_start: 0.8244 (m-30) cc_final: 0.7717 (m-30) REVERT: G 23 LEU cc_start: 0.8811 (tp) cc_final: 0.8543 (tp) REVERT: G 37 LYS cc_start: 0.8371 (ttmt) cc_final: 0.7112 (tptt) REVERT: G 57 TYR cc_start: 0.8778 (t80) cc_final: 0.8165 (t80) REVERT: H 22 ASN cc_start: 0.8247 (p0) cc_final: 0.7969 (p0) REVERT: H 28 THR cc_start: 0.9268 (m) cc_final: 0.8613 (p) REVERT: H 32 ASP cc_start: 0.8001 (m-30) cc_final: 0.7663 (m-30) REVERT: H 37 LYS cc_start: 0.8567 (ttmt) cc_final: 0.7180 (tptt) REVERT: H 39 SER cc_start: 0.9287 (m) cc_final: 0.8695 (m) REVERT: I 28 THR cc_start: 0.9439 (m) cc_final: 0.9119 (m) REVERT: I 31 LEU cc_start: 0.9475 (tp) cc_final: 0.9100 (tp) REVERT: I 32 ASP cc_start: 0.8545 (m-30) cc_final: 0.8200 (m-30) REVERT: I 37 LYS cc_start: 0.8662 (ttmt) cc_final: 0.7393 (tptt) REVERT: I 47 TYR cc_start: 0.9254 (t80) cc_final: 0.8950 (t80) REVERT: I 49 SER cc_start: 0.9083 (t) cc_final: 0.8777 (t) REVERT: J 6 SER cc_start: 0.8989 (m) cc_final: 0.8766 (p) REVERT: J 24 GLN cc_start: 0.7828 (mp10) cc_final: 0.7618 (tp-100) REVERT: J 37 LYS cc_start: 0.8754 (ttmt) cc_final: 0.7266 (tptt) REVERT: J 47 TYR cc_start: 0.9064 (t80) cc_final: 0.8457 (t80) REVERT: J 49 SER cc_start: 0.9100 (t) cc_final: 0.8862 (t) REVERT: J 51 LEU cc_start: 0.8744 (tp) cc_final: 0.8259 (tt) REVERT: J 54 TYR cc_start: 0.8899 (t80) cc_final: 0.8495 (t80) REVERT: J 57 TYR cc_start: 0.8689 (t80) cc_final: 0.8452 (t80) REVERT: J 58 ARG cc_start: 0.8180 (mmt180) cc_final: 0.7880 (mmt180) REVERT: J 64 THR cc_start: 0.8630 (m) cc_final: 0.8232 (m) REVERT: K 9 LEU cc_start: 0.9230 (mt) cc_final: 0.8980 (mm) REVERT: K 37 LYS cc_start: 0.9113 (ttmt) cc_final: 0.7915 (tptp) REVERT: K 39 SER cc_start: 0.8861 (m) cc_final: 0.8641 (t) REVERT: K 47 TYR cc_start: 0.9029 (t80) cc_final: 0.8021 (t80) REVERT: K 54 TYR cc_start: 0.8955 (t80) cc_final: 0.8625 (t80) REVERT: K 61 GLN cc_start: 0.8940 (tt0) cc_final: 0.8709 (tt0) REVERT: L 23 LEU cc_start: 0.8841 (tp) cc_final: 0.8296 (tt) REVERT: L 26 GLN cc_start: 0.8671 (mt0) cc_final: 0.8421 (mt0) REVERT: L 37 LYS cc_start: 0.9006 (ttmt) cc_final: 0.7242 (tptt) REVERT: L 39 SER cc_start: 0.9050 (m) cc_final: 0.8790 (t) REVERT: L 53 GLU cc_start: 0.8349 (tp30) cc_final: 0.7778 (tp30) REVERT: M 28 THR cc_start: 0.9247 (m) cc_final: 0.8054 (p) REVERT: M 31 LEU cc_start: 0.9203 (tp) cc_final: 0.8779 (tt) REVERT: M 33 LYS cc_start: 0.9116 (mttt) cc_final: 0.8861 (mtmt) REVERT: M 39 SER cc_start: 0.9295 (m) cc_final: 0.8820 (p) REVERT: M 47 TYR cc_start: 0.9139 (t80) cc_final: 0.8715 (t80) REVERT: M 51 LEU cc_start: 0.9386 (tp) cc_final: 0.9087 (tp) REVERT: M 54 TYR cc_start: 0.9097 (t80) cc_final: 0.8803 (t80) REVERT: N 31 LEU cc_start: 0.9170 (tp) cc_final: 0.8881 (tt) REVERT: N 43 LEU cc_start: 0.9280 (mt) cc_final: 0.8975 (mt) REVERT: N 47 TYR cc_start: 0.9145 (t80) cc_final: 0.8732 (t80) REVERT: N 51 LEU cc_start: 0.9065 (tp) cc_final: 0.8697 (tt) REVERT: N 58 ARG cc_start: 0.8693 (mmt180) cc_final: 0.8489 (mmt180) REVERT: O 9 LEU cc_start: 0.9010 (mt) cc_final: 0.8703 (mt) REVERT: O 15 LYS cc_start: 0.8916 (mttt) cc_final: 0.8674 (tppt) REVERT: O 17 ASP cc_start: 0.7785 (m-30) cc_final: 0.7428 (t0) REVERT: O 22 ASN cc_start: 0.9063 (p0) cc_final: 0.7894 (p0) REVERT: O 25 THR cc_start: 0.8817 (m) cc_final: 0.8390 (m) REVERT: O 28 THR cc_start: 0.8657 (m) cc_final: 0.8345 (p) REVERT: O 33 LYS cc_start: 0.9062 (mttt) cc_final: 0.8847 (mmmm) REVERT: O 47 TYR cc_start: 0.8941 (t80) cc_final: 0.8642 (t80) REVERT: O 50 LYS cc_start: 0.9063 (mmtt) cc_final: 0.8834 (mmtm) REVERT: O 53 GLU cc_start: 0.8604 (tp30) cc_final: 0.8305 (tp30) REVERT: O 55 ASN cc_start: 0.9010 (t0) cc_final: 0.7921 (t0) REVERT: O 58 ARG cc_start: 0.8940 (mmt180) cc_final: 0.8618 (mmt-90) REVERT: O 59 ASN cc_start: 0.8739 (m-40) cc_final: 0.8134 (m110) REVERT: O 69 LYS cc_start: 0.8210 (tttm) cc_final: 0.7947 (tptt) REVERT: P 22 ASN cc_start: 0.9054 (p0) cc_final: 0.8649 (p0) REVERT: P 40 ASP cc_start: 0.7928 (t0) cc_final: 0.7707 (t0) REVERT: P 56 LEU cc_start: 0.9466 (mt) cc_final: 0.8965 (mp) REVERT: Q 33 LYS cc_start: 0.8819 (mttt) cc_final: 0.8523 (mttp) REVERT: Q 47 TYR cc_start: 0.9157 (t80) cc_final: 0.8888 (t80) REVERT: Q 51 LEU cc_start: 0.9225 (tp) cc_final: 0.8827 (tp) REVERT: Q 56 LEU cc_start: 0.9501 (mt) cc_final: 0.9244 (mm) REVERT: Q 57 TYR cc_start: 0.9030 (t80) cc_final: 0.8534 (t80) REVERT: Q 58 ARG cc_start: 0.8919 (mmt180) cc_final: 0.8668 (mmt-90) REVERT: Q 69 LYS cc_start: 0.8488 (tttm) cc_final: 0.7627 (tptt) REVERT: R 6 SER cc_start: 0.8532 (m) cc_final: 0.8202 (t) REVERT: R 22 ASN cc_start: 0.8994 (p0) cc_final: 0.7796 (p0) REVERT: R 25 THR cc_start: 0.8501 (m) cc_final: 0.7824 (p) REVERT: R 28 THR cc_start: 0.8689 (m) cc_final: 0.8055 (p) REVERT: R 39 SER cc_start: 0.9221 (m) cc_final: 0.8748 (t) REVERT: R 56 LEU cc_start: 0.9130 (mt) cc_final: 0.8747 (mt) REVERT: S 22 ASN cc_start: 0.8719 (p0) cc_final: 0.8454 (p0) REVERT: S 25 THR cc_start: 0.7755 (m) cc_final: 0.6977 (p) REVERT: S 31 LEU cc_start: 0.8716 (tp) cc_final: 0.8107 (tp) REVERT: S 33 LYS cc_start: 0.8394 (mttt) cc_final: 0.8104 (ttmm) REVERT: T 22 ASN cc_start: 0.8787 (p0) cc_final: 0.8096 (p0) REVERT: T 25 THR cc_start: 0.8429 (m) cc_final: 0.7695 (p) REVERT: T 26 GLN cc_start: 0.9243 (mt0) cc_final: 0.8906 (mt0) REVERT: T 28 THR cc_start: 0.8064 (m) cc_final: 0.7510 (p) REVERT: T 39 SER cc_start: 0.9144 (m) cc_final: 0.8937 (p) REVERT: T 43 LEU cc_start: 0.9287 (mt) cc_final: 0.8440 (mt) REVERT: T 47 TYR cc_start: 0.9026 (t80) cc_final: 0.8042 (t80) REVERT: T 50 LYS cc_start: 0.9094 (mmtt) cc_final: 0.8752 (mmtt) REVERT: T 57 TYR cc_start: 0.8561 (t80) cc_final: 0.7517 (t80) REVERT: T 58 ARG cc_start: 0.8754 (mmt180) cc_final: 0.6824 (mtt180) outliers start: 0 outliers final: 0 residues processed: 643 average time/residue: 0.2345 time to fit residues: 209.8661 Evaluate side-chains 527 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 527 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 GLN U 26 GLN ** U 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 GLN F 77 GLN F 78 ASN G 61 GLN G 78 ASN I 63 ASN I 78 ASN J 26 GLN L 63 ASN M 61 GLN M 78 ASN N 78 ASN ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 48 GLN R 61 GLN R 63 ASN S 48 GLN ** T 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11837 Z= 0.207 Angle : 0.541 5.601 16112 Z= 0.296 Chirality : 0.037 0.133 1843 Planarity : 0.004 0.021 2109 Dihedral : 4.196 22.236 1596 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.55 % Allowed : 12.52 % Favored : 84.93 % 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: -2.07 (0.18), residues: 1444 helix: -0.78 (0.12), residues: 1292 sheet: None (None), residues: 0 loop : -5.22 (0.25), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 5 PHE 0.009 0.001 PHE T 79 TYR 0.016 0.002 TYR O 54 ARG 0.005 0.000 ARG J 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 583 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 15 LYS cc_start: 0.8953 (mttt) cc_final: 0.8483 (mmmm) REVERT: U 37 LYS cc_start: 0.8164 (ttmt) cc_final: 0.7250 (tptp) REVERT: U 53 GLU cc_start: 0.8334 (tp30) cc_final: 0.8058 (tp30) REVERT: U 66 LYS cc_start: 0.8691 (tptp) cc_final: 0.6627 (mttt) REVERT: V 28 THR cc_start: 0.8728 (m) cc_final: 0.8282 (p) REVERT: V 37 LYS cc_start: 0.9267 (ttmt) cc_final: 0.7893 (tptt) REVERT: V 47 TYR cc_start: 0.9015 (t80) cc_final: 0.8253 (t80) REVERT: V 49 SER cc_start: 0.8646 (t) cc_final: 0.8286 (p) REVERT: V 53 GLU cc_start: 0.8190 (tp30) cc_final: 0.7793 (mm-30) REVERT: V 77 GLN cc_start: 0.8333 (tp40) cc_final: 0.7818 (tp-100) REVERT: E 32 ASP cc_start: 0.8106 (m-30) cc_final: 0.7879 (m-30) REVERT: E 37 LYS cc_start: 0.7826 (ttmt) cc_final: 0.7042 (tptt) REVERT: F 28 THR cc_start: 0.8718 (m) cc_final: 0.8208 (p) REVERT: F 32 ASP cc_start: 0.7665 (m-30) cc_final: 0.7395 (m-30) REVERT: F 34 LEU cc_start: 0.9250 (tp) cc_final: 0.8986 (tt) REVERT: F 37 LYS cc_start: 0.8634 (ttmt) cc_final: 0.7956 (tptt) REVERT: F 39 SER cc_start: 0.8717 (m) cc_final: 0.8302 (t) REVERT: F 47 TYR cc_start: 0.8935 (t80) cc_final: 0.8208 (t80) REVERT: F 49 SER cc_start: 0.9295 (t) cc_final: 0.8965 (p) REVERT: F 53 GLU cc_start: 0.8329 (tp30) cc_final: 0.7683 (mm-30) REVERT: F 66 LYS cc_start: 0.8709 (tptp) cc_final: 0.7167 (mttm) REVERT: G 8 TYR cc_start: 0.8633 (t80) cc_final: 0.8350 (t80) REVERT: G 11 ASP cc_start: 0.8299 (m-30) cc_final: 0.8015 (t0) REVERT: G 37 LYS cc_start: 0.8470 (ttmt) cc_final: 0.7213 (tptt) REVERT: G 49 SER cc_start: 0.8769 (t) cc_final: 0.8272 (m) REVERT: G 69 LYS cc_start: 0.8585 (tttm) cc_final: 0.8337 (tttt) REVERT: H 28 THR cc_start: 0.9010 (m) cc_final: 0.8463 (p) REVERT: H 31 LEU cc_start: 0.8883 (tp) cc_final: 0.8625 (tt) REVERT: H 32 ASP cc_start: 0.8025 (m-30) cc_final: 0.7582 (m-30) REVERT: H 37 LYS cc_start: 0.8218 (ttmt) cc_final: 0.7088 (tptt) REVERT: H 39 SER cc_start: 0.9085 (m) cc_final: 0.8766 (m) REVERT: H 47 TYR cc_start: 0.9175 (t80) cc_final: 0.7437 (t80) REVERT: H 51 LEU cc_start: 0.9241 (tp) cc_final: 0.8727 (tp) REVERT: I 28 THR cc_start: 0.9032 (m) cc_final: 0.8715 (p) REVERT: I 37 LYS cc_start: 0.8716 (ttmt) cc_final: 0.7337 (tptp) REVERT: I 47 TYR cc_start: 0.9272 (t80) cc_final: 0.8963 (t80) REVERT: I 49 SER cc_start: 0.8991 (t) cc_final: 0.8771 (t) REVERT: J 24 GLN cc_start: 0.8169 (mp10) cc_final: 0.7893 (tp-100) REVERT: J 37 LYS cc_start: 0.8738 (ttmt) cc_final: 0.7361 (tptt) REVERT: J 47 TYR cc_start: 0.9238 (t80) cc_final: 0.8698 (t80) REVERT: J 49 SER cc_start: 0.9262 (t) cc_final: 0.8879 (p) REVERT: K 37 LYS cc_start: 0.9111 (ttmt) cc_final: 0.7798 (tptt) REVERT: K 47 TYR cc_start: 0.9149 (t80) cc_final: 0.8179 (t80) REVERT: K 77 GLN cc_start: 0.8555 (tp40) cc_final: 0.8345 (tp-100) REVERT: L 15 LYS cc_start: 0.8982 (mtpp) cc_final: 0.8735 (mmmm) REVERT: L 26 GLN cc_start: 0.8589 (mt0) cc_final: 0.7949 (tt0) REVERT: L 31 LEU cc_start: 0.9144 (tp) cc_final: 0.8933 (tp) REVERT: L 37 LYS cc_start: 0.8767 (ttmt) cc_final: 0.7155 (tptt) REVERT: L 53 GLU cc_start: 0.8115 (tp30) cc_final: 0.7767 (tp30) REVERT: M 28 THR cc_start: 0.8823 (m) cc_final: 0.8391 (p) REVERT: M 31 LEU cc_start: 0.9163 (tp) cc_final: 0.8713 (tt) REVERT: M 32 ASP cc_start: 0.8384 (p0) cc_final: 0.8166 (p0) REVERT: M 39 SER cc_start: 0.9217 (m) cc_final: 0.8932 (p) REVERT: M 47 TYR cc_start: 0.9102 (t80) cc_final: 0.8636 (t80) REVERT: M 50 LYS cc_start: 0.9089 (mmtt) cc_final: 0.8772 (mmtt) REVERT: M 66 LYS cc_start: 0.8747 (tptt) cc_final: 0.8171 (tmtt) REVERT: N 10 ASP cc_start: 0.8891 (m-30) cc_final: 0.8323 (m-30) REVERT: N 47 TYR cc_start: 0.8961 (t80) cc_final: 0.8553 (t80) REVERT: N 49 SER cc_start: 0.9599 (m) cc_final: 0.9336 (t) REVERT: N 50 LYS cc_start: 0.9227 (mmtp) cc_final: 0.8809 (mmmt) REVERT: N 51 LEU cc_start: 0.9014 (tp) cc_final: 0.8771 (tt) REVERT: N 53 GLU cc_start: 0.8235 (tp30) cc_final: 0.7749 (tp30) REVERT: N 56 LEU cc_start: 0.9252 (mp) cc_final: 0.8941 (mt) REVERT: N 58 ARG cc_start: 0.8426 (mmt180) cc_final: 0.7920 (mmm160) REVERT: O 17 ASP cc_start: 0.7681 (m-30) cc_final: 0.7388 (t0) REVERT: O 22 ASN cc_start: 0.9279 (p0) cc_final: 0.8403 (p0) REVERT: O 23 LEU cc_start: 0.9279 (tp) cc_final: 0.8933 (tp) REVERT: O 25 THR cc_start: 0.9064 (m) cc_final: 0.8690 (m) REVERT: O 28 THR cc_start: 0.8558 (m) cc_final: 0.7216 (p) REVERT: O 33 LYS cc_start: 0.9149 (mttt) cc_final: 0.8464 (mtmm) REVERT: O 58 ARG cc_start: 0.8648 (mmt180) cc_final: 0.8324 (mmt-90) REVERT: O 59 ASN cc_start: 0.8549 (m-40) cc_final: 0.7952 (m110) REVERT: O 69 LYS cc_start: 0.8404 (tttm) cc_final: 0.7855 (tttt) REVERT: P 22 ASN cc_start: 0.9168 (p0) cc_final: 0.8715 (p0) REVERT: P 26 GLN cc_start: 0.9257 (mt0) cc_final: 0.9006 (tt0) REVERT: P 39 SER cc_start: 0.8431 (m) cc_final: 0.8160 (m) REVERT: P 43 LEU cc_start: 0.8984 (mp) cc_final: 0.8749 (mp) REVERT: P 58 ARG cc_start: 0.7943 (mmt180) cc_final: 0.6416 (mtt180) REVERT: Q 28 THR cc_start: 0.8241 (m) cc_final: 0.8028 (p) REVERT: Q 54 TYR cc_start: 0.8438 (t80) cc_final: 0.7881 (t80) REVERT: Q 69 LYS cc_start: 0.8596 (tttm) cc_final: 0.8142 (ttmt) REVERT: Q 76 ILE cc_start: 0.8280 (mm) cc_final: 0.7978 (tt) REVERT: R 22 ASN cc_start: 0.8886 (p0) cc_final: 0.8138 (p0) REVERT: R 24 GLN cc_start: 0.8383 (mp10) cc_final: 0.8141 (pm20) REVERT: R 25 THR cc_start: 0.8683 (m) cc_final: 0.8123 (p) REVERT: R 26 GLN cc_start: 0.8909 (mt0) cc_final: 0.8676 (tt0) REVERT: R 39 SER cc_start: 0.9177 (m) cc_final: 0.8953 (t) REVERT: S 25 THR cc_start: 0.8192 (m) cc_final: 0.7848 (p) REVERT: S 39 SER cc_start: 0.8954 (m) cc_final: 0.8081 (m) REVERT: T 22 ASN cc_start: 0.8702 (p0) cc_final: 0.8165 (p0) REVERT: T 31 LEU cc_start: 0.8851 (tp) cc_final: 0.8633 (tp) REVERT: T 39 SER cc_start: 0.9064 (m) cc_final: 0.8696 (p) REVERT: T 40 ASP cc_start: 0.8276 (t0) cc_final: 0.8065 (t0) REVERT: T 43 LEU cc_start: 0.9188 (mt) cc_final: 0.8927 (mt) REVERT: T 48 GLN cc_start: 0.9070 (tm-30) cc_final: 0.8839 (tm-30) REVERT: T 50 LYS cc_start: 0.8857 (mmtt) cc_final: 0.8622 (mmtt) REVERT: T 69 LYS cc_start: 0.7191 (tttm) cc_final: 0.6774 (ttmt) outliers start: 32 outliers final: 20 residues processed: 594 average time/residue: 0.2230 time to fit residues: 185.9845 Evaluate side-chains 553 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 533 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain V residue 23 LEU Chi-restraints excluded: chain V residue 39 SER Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain I residue 21 ASP Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain O residue 21 ASP Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 65 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 119 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 GLN D 77 GLN U 26 GLN ** U 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 59 ASN F 59 ASN F 78 ASN K 24 GLN K 63 ASN L 78 ASN M 26 GLN N 48 GLN N 55 ASN ** O 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN O 77 GLN ** O 78 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: 0.8209 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11837 Z= 0.231 Angle : 0.512 8.297 16112 Z= 0.271 Chirality : 0.038 0.132 1843 Planarity : 0.003 0.020 2109 Dihedral : 3.866 23.209 1596 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.59 % Allowed : 16.83 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.21), residues: 1444 helix: 0.77 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -5.00 (0.25), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 5 PHE 0.009 0.001 PHE N 68 TYR 0.018 0.002 TYR Q 57 ARG 0.004 0.001 ARG J 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 570 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 22 ASN cc_start: 0.7400 (p0) cc_final: 0.7131 (p0) REVERT: D 34 LEU cc_start: 0.8443 (tp) cc_final: 0.8224 (tp) REVERT: D 44 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8138 (mt) REVERT: D 76 ILE cc_start: 0.9223 (mt) cc_final: 0.9009 (mt) REVERT: U 15 LYS cc_start: 0.9029 (mttt) cc_final: 0.8546 (mmmm) REVERT: U 25 THR cc_start: 0.8357 (m) cc_final: 0.8058 (p) REVERT: U 37 LYS cc_start: 0.8264 (ttmt) cc_final: 0.7334 (tptp) REVERT: U 43 LEU cc_start: 0.9436 (mt) cc_final: 0.9187 (mt) REVERT: U 66 LYS cc_start: 0.8563 (tptp) cc_final: 0.6972 (mttt) REVERT: V 37 LYS cc_start: 0.9219 (ttmt) cc_final: 0.7743 (tptt) REVERT: V 47 TYR cc_start: 0.9110 (t80) cc_final: 0.8338 (t80) REVERT: V 49 SER cc_start: 0.8654 (t) cc_final: 0.8281 (p) REVERT: V 53 GLU cc_start: 0.8056 (tp30) cc_final: 0.7820 (mm-30) REVERT: V 77 GLN cc_start: 0.8606 (tp40) cc_final: 0.8036 (tp-100) REVERT: E 11 ASP cc_start: 0.8375 (m-30) cc_final: 0.7832 (m-30) REVERT: E 37 LYS cc_start: 0.8149 (ttmt) cc_final: 0.7298 (tptt) REVERT: E 47 TYR cc_start: 0.8747 (t80) cc_final: 0.8194 (t80) REVERT: E 54 TYR cc_start: 0.8679 (t80) cc_final: 0.8429 (t80) REVERT: E 66 LYS cc_start: 0.8145 (tptp) cc_final: 0.6476 (mttt) REVERT: E 69 LYS cc_start: 0.7957 (tttm) cc_final: 0.7618 (tptp) REVERT: E 72 ASP cc_start: 0.8695 (m-30) cc_final: 0.8448 (t0) REVERT: F 28 THR cc_start: 0.8725 (m) cc_final: 0.8125 (p) REVERT: F 32 ASP cc_start: 0.7795 (m-30) cc_final: 0.7486 (m-30) REVERT: F 34 LEU cc_start: 0.9219 (tp) cc_final: 0.8936 (tt) REVERT: F 37 LYS cc_start: 0.8473 (ttmt) cc_final: 0.7890 (tptt) REVERT: F 39 SER cc_start: 0.8812 (m) cc_final: 0.8230 (t) REVERT: F 47 TYR cc_start: 0.8927 (t80) cc_final: 0.8302 (t80) REVERT: F 49 SER cc_start: 0.9196 (t) cc_final: 0.8780 (p) REVERT: F 53 GLU cc_start: 0.8294 (tp30) cc_final: 0.7761 (mm-30) REVERT: F 66 LYS cc_start: 0.8795 (tptp) cc_final: 0.7318 (mttm) REVERT: G 11 ASP cc_start: 0.8325 (m-30) cc_final: 0.8068 (t0) REVERT: G 37 LYS cc_start: 0.8370 (ttmt) cc_final: 0.7137 (tptt) REVERT: G 69 LYS cc_start: 0.8725 (tttm) cc_final: 0.8404 (tttt) REVERT: G 77 GLN cc_start: 0.8403 (tp40) cc_final: 0.8202 (tp40) REVERT: H 10 ASP cc_start: 0.8553 (m-30) cc_final: 0.8348 (m-30) REVERT: H 28 THR cc_start: 0.8962 (m) cc_final: 0.8332 (p) REVERT: H 31 LEU cc_start: 0.8826 (tp) cc_final: 0.8558 (tt) REVERT: H 32 ASP cc_start: 0.7873 (m-30) cc_final: 0.7478 (m-30) REVERT: H 37 LYS cc_start: 0.8224 (ttmt) cc_final: 0.7010 (tptt) REVERT: H 47 TYR cc_start: 0.9095 (t80) cc_final: 0.7384 (t80) REVERT: H 51 LEU cc_start: 0.9282 (tp) cc_final: 0.8741 (tp) REVERT: I 37 LYS cc_start: 0.8727 (ttmt) cc_final: 0.7399 (tptp) REVERT: I 47 TYR cc_start: 0.9269 (t80) cc_final: 0.8961 (t80) REVERT: I 49 SER cc_start: 0.8887 (t) cc_final: 0.8664 (t) REVERT: J 22 ASN cc_start: 0.7958 (p0) cc_final: 0.7487 (p0) REVERT: J 37 LYS cc_start: 0.8816 (ttmt) cc_final: 0.7370 (tptt) REVERT: J 47 TYR cc_start: 0.9167 (t80) cc_final: 0.8628 (t80) REVERT: J 49 SER cc_start: 0.9311 (t) cc_final: 0.8930 (p) REVERT: K 33 LYS cc_start: 0.9184 (mttt) cc_final: 0.8820 (mtpp) REVERT: K 37 LYS cc_start: 0.9120 (ttmt) cc_final: 0.7772 (tptt) REVERT: K 47 TYR cc_start: 0.9142 (t80) cc_final: 0.7772 (t80) REVERT: L 8 TYR cc_start: 0.8554 (t80) cc_final: 0.8230 (t80) REVERT: L 13 SER cc_start: 0.8382 (t) cc_final: 0.7981 (t) REVERT: L 23 LEU cc_start: 0.8631 (tp) cc_final: 0.8006 (tt) REVERT: L 26 GLN cc_start: 0.8663 (mt0) cc_final: 0.8056 (tt0) REVERT: L 37 LYS cc_start: 0.8750 (ttmt) cc_final: 0.7040 (tptt) REVERT: L 53 GLU cc_start: 0.8207 (tp30) cc_final: 0.7745 (tp30) REVERT: M 28 THR cc_start: 0.8815 (m) cc_final: 0.8245 (p) REVERT: M 31 LEU cc_start: 0.9197 (tp) cc_final: 0.8713 (tt) REVERT: M 32 ASP cc_start: 0.8359 (p0) cc_final: 0.8079 (p0) REVERT: M 39 SER cc_start: 0.9155 (m) cc_final: 0.8645 (p) REVERT: M 47 TYR cc_start: 0.9242 (t80) cc_final: 0.8612 (t80) REVERT: M 66 LYS cc_start: 0.8520 (tptt) cc_final: 0.8021 (tmtt) REVERT: N 15 LYS cc_start: 0.8625 (ttmm) cc_final: 0.8197 (ttmm) REVERT: N 23 LEU cc_start: 0.8983 (tp) cc_final: 0.8522 (tp) REVERT: N 47 TYR cc_start: 0.8942 (t80) cc_final: 0.8579 (t80) REVERT: N 49 SER cc_start: 0.9519 (m) cc_final: 0.9247 (t) REVERT: N 53 GLU cc_start: 0.8240 (tp30) cc_final: 0.7733 (tp30) REVERT: N 58 ARG cc_start: 0.8189 (mmt180) cc_final: 0.7967 (mmt180) REVERT: O 17 ASP cc_start: 0.7603 (m-30) cc_final: 0.7330 (t0) REVERT: O 22 ASN cc_start: 0.9263 (p0) cc_final: 0.7859 (p0) REVERT: O 25 THR cc_start: 0.9044 (m) cc_final: 0.8376 (p) REVERT: O 28 THR cc_start: 0.8304 (m) cc_final: 0.8069 (p) REVERT: O 33 LYS cc_start: 0.9128 (mttt) cc_final: 0.8415 (mtmm) REVERT: O 49 SER cc_start: 0.9279 (m) cc_final: 0.9066 (t) REVERT: O 52 SER cc_start: 0.9059 (m) cc_final: 0.8718 (t) REVERT: O 59 ASN cc_start: 0.8547 (m-40) cc_final: 0.7978 (m110) REVERT: O 69 LYS cc_start: 0.8131 (tttm) cc_final: 0.7827 (ttmt) REVERT: P 22 ASN cc_start: 0.9279 (p0) cc_final: 0.8753 (p0) REVERT: P 26 GLN cc_start: 0.9286 (tt0) cc_final: 0.8903 (tt0) REVERT: P 39 SER cc_start: 0.8753 (m) cc_final: 0.8254 (m) REVERT: P 58 ARG cc_start: 0.8067 (mmt180) cc_final: 0.6359 (mtt180) REVERT: P 64 THR cc_start: 0.9231 (m) cc_final: 0.8789 (t) REVERT: Q 25 THR cc_start: 0.8783 (m) cc_final: 0.8303 (p) REVERT: Q 28 THR cc_start: 0.8248 (m) cc_final: 0.7971 (p) REVERT: Q 40 ASP cc_start: 0.8504 (t0) cc_final: 0.8178 (t0) REVERT: Q 54 TYR cc_start: 0.8309 (t80) cc_final: 0.7895 (t80) REVERT: Q 69 LYS cc_start: 0.8618 (tttm) cc_final: 0.8110 (ttmt) REVERT: R 22 ASN cc_start: 0.9108 (p0) cc_final: 0.8436 (p0) REVERT: R 26 GLN cc_start: 0.9019 (mt0) cc_final: 0.8747 (tt0) REVERT: R 33 LYS cc_start: 0.9108 (ttmt) cc_final: 0.8621 (mtmt) REVERT: R 39 SER cc_start: 0.9349 (m) cc_final: 0.9053 (t) REVERT: R 55 ASN cc_start: 0.8717 (t0) cc_final: 0.8406 (t0) REVERT: R 56 LEU cc_start: 0.8843 (mt) cc_final: 0.8639 (mt) REVERT: S 5 TRP cc_start: 0.8347 (t60) cc_final: 0.7555 (t60) REVERT: S 25 THR cc_start: 0.8182 (m) cc_final: 0.7896 (p) REVERT: S 39 SER cc_start: 0.9145 (m) cc_final: 0.8265 (m) REVERT: S 59 ASN cc_start: 0.8554 (m-40) cc_final: 0.7908 (m110) REVERT: S 69 LYS cc_start: 0.7756 (tttm) cc_final: 0.7506 (ttmt) REVERT: T 22 ASN cc_start: 0.8729 (p0) cc_final: 0.8220 (p0) REVERT: T 25 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8204 (t) REVERT: T 39 SER cc_start: 0.9112 (m) cc_final: 0.8669 (p) REVERT: T 40 ASP cc_start: 0.8195 (t0) cc_final: 0.7857 (t0) REVERT: T 48 GLN cc_start: 0.9042 (tm-30) cc_final: 0.8791 (tm-30) REVERT: T 50 LYS cc_start: 0.9033 (mmtt) cc_final: 0.8689 (mmmt) REVERT: T 69 LYS cc_start: 0.7158 (tttm) cc_final: 0.6487 (tttt) outliers start: 45 outliers final: 29 residues processed: 583 average time/residue: 0.2241 time to fit residues: 184.8783 Evaluate side-chains 582 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 551 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain V residue 23 LEU Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 80 ARG Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 21 ASP Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 25 THR Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 65 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 GLN ** U 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 59 ASN F 59 ASN K 24 GLN K 26 GLN K 78 ASN L 61 GLN L 78 ASN ** O 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 GLN R 61 GLN R 63 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11837 Z= 0.255 Angle : 0.526 6.438 16112 Z= 0.275 Chirality : 0.039 0.115 1843 Planarity : 0.003 0.020 2109 Dihedral : 3.861 26.527 1596 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.15 % Allowed : 19.06 % Favored : 76.79 % 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: 1.08 (0.22), residues: 1444 helix: 1.36 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.87 (0.28), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 5 PHE 0.009 0.002 PHE N 68 TYR 0.015 0.002 TYR G 57 ARG 0.006 0.001 ARG J 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 575 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 22 ASN cc_start: 0.7863 (p0) cc_final: 0.7393 (p0) REVERT: D 34 LEU cc_start: 0.8366 (tp) cc_final: 0.8139 (tp) REVERT: D 44 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7963 (mt) REVERT: D 63 ASN cc_start: 0.8215 (m-40) cc_final: 0.7802 (m-40) REVERT: U 15 LYS cc_start: 0.9092 (mttt) cc_final: 0.8768 (mmtp) REVERT: U 37 LYS cc_start: 0.8178 (ttmt) cc_final: 0.7227 (tptt) REVERT: U 66 LYS cc_start: 0.8563 (tptp) cc_final: 0.6962 (mttt) REVERT: V 37 LYS cc_start: 0.9275 (ttmt) cc_final: 0.7844 (tptt) REVERT: V 47 TYR cc_start: 0.9206 (t80) cc_final: 0.8317 (t80) REVERT: V 49 SER cc_start: 0.8661 (t) cc_final: 0.8250 (p) REVERT: V 51 LEU cc_start: 0.9180 (tp) cc_final: 0.8950 (tp) REVERT: V 53 GLU cc_start: 0.8038 (tp30) cc_final: 0.7765 (mm-30) REVERT: V 77 GLN cc_start: 0.8680 (tp40) cc_final: 0.8051 (tp-100) REVERT: E 15 LYS cc_start: 0.8782 (mmmm) cc_final: 0.8549 (mmmt) REVERT: E 22 ASN cc_start: 0.7632 (p0) cc_final: 0.7038 (p0) REVERT: E 23 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7298 (tp) REVERT: E 32 ASP cc_start: 0.8355 (m-30) cc_final: 0.8037 (m-30) REVERT: E 37 LYS cc_start: 0.8640 (ttmt) cc_final: 0.7401 (tptt) REVERT: E 47 TYR cc_start: 0.8973 (t80) cc_final: 0.8660 (t80) REVERT: E 53 GLU cc_start: 0.8656 (tp30) cc_final: 0.8147 (mm-30) REVERT: E 66 LYS cc_start: 0.8185 (tptp) cc_final: 0.6699 (mttt) REVERT: F 28 THR cc_start: 0.8730 (m) cc_final: 0.8095 (p) REVERT: F 32 ASP cc_start: 0.7818 (m-30) cc_final: 0.7489 (m-30) REVERT: F 34 LEU cc_start: 0.9232 (tp) cc_final: 0.8960 (tt) REVERT: F 37 LYS cc_start: 0.8597 (ttmt) cc_final: 0.7991 (tptt) REVERT: F 39 SER cc_start: 0.8901 (m) cc_final: 0.8248 (t) REVERT: F 47 TYR cc_start: 0.9010 (t80) cc_final: 0.8390 (t80) REVERT: F 49 SER cc_start: 0.9294 (t) cc_final: 0.8910 (p) REVERT: F 53 GLU cc_start: 0.8279 (tp30) cc_final: 0.7711 (mm-30) REVERT: F 66 LYS cc_start: 0.8634 (tptp) cc_final: 0.7297 (mttm) REVERT: G 11 ASP cc_start: 0.8337 (m-30) cc_final: 0.8079 (t0) REVERT: G 33 LYS cc_start: 0.9073 (mtpp) cc_final: 0.8838 (mtpp) REVERT: G 37 LYS cc_start: 0.8466 (ttmt) cc_final: 0.7189 (tptt) REVERT: G 69 LYS cc_start: 0.8775 (tttm) cc_final: 0.8444 (tttt) REVERT: H 28 THR cc_start: 0.8966 (m) cc_final: 0.8294 (p) REVERT: H 32 ASP cc_start: 0.7894 (m-30) cc_final: 0.7602 (m-30) REVERT: H 37 LYS cc_start: 0.8242 (ttmt) cc_final: 0.7078 (tptt) REVERT: H 47 TYR cc_start: 0.9093 (t80) cc_final: 0.7413 (t80) REVERT: H 51 LEU cc_start: 0.9323 (tp) cc_final: 0.8743 (tp) REVERT: I 37 LYS cc_start: 0.8750 (ttmt) cc_final: 0.7379 (tptp) REVERT: I 47 TYR cc_start: 0.9204 (t80) cc_final: 0.8908 (t80) REVERT: J 10 ASP cc_start: 0.8624 (m-30) cc_final: 0.8407 (m-30) REVERT: J 22 ASN cc_start: 0.8107 (p0) cc_final: 0.7551 (p0) REVERT: J 37 LYS cc_start: 0.8885 (ttmt) cc_final: 0.7477 (tptt) REVERT: J 47 TYR cc_start: 0.9204 (t80) cc_final: 0.8490 (t80) REVERT: J 49 SER cc_start: 0.9254 (t) cc_final: 0.8935 (p) REVERT: J 57 TYR cc_start: 0.9108 (t80) cc_final: 0.8881 (t80) REVERT: K 33 LYS cc_start: 0.9198 (mttt) cc_final: 0.8885 (mtpp) REVERT: K 37 LYS cc_start: 0.9032 (ttmt) cc_final: 0.7553 (tptt) REVERT: K 47 TYR cc_start: 0.9186 (t80) cc_final: 0.7718 (t80) REVERT: L 8 TYR cc_start: 0.8592 (t80) cc_final: 0.8335 (t80) REVERT: L 13 SER cc_start: 0.8498 (OUTLIER) cc_final: 0.8190 (t) REVERT: L 26 GLN cc_start: 0.8792 (mt0) cc_final: 0.8081 (tt0) REVERT: L 37 LYS cc_start: 0.8822 (ttmt) cc_final: 0.7132 (tptt) REVERT: L 48 GLN cc_start: 0.8488 (tt0) cc_final: 0.7900 (tt0) REVERT: L 53 GLU cc_start: 0.8240 (tp30) cc_final: 0.7813 (tp30) REVERT: M 22 ASN cc_start: 0.8707 (p0) cc_final: 0.8326 (p0) REVERT: M 28 THR cc_start: 0.8861 (m) cc_final: 0.8152 (p) REVERT: M 31 LEU cc_start: 0.9262 (tp) cc_final: 0.8913 (tp) REVERT: M 32 ASP cc_start: 0.8318 (p0) cc_final: 0.7944 (p0) REVERT: M 37 LYS cc_start: 0.9183 (mtpp) cc_final: 0.8663 (mtpt) REVERT: M 47 TYR cc_start: 0.9178 (t80) cc_final: 0.8534 (t80) REVERT: M 66 LYS cc_start: 0.8560 (tptt) cc_final: 0.8108 (tmtt) REVERT: M 69 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8075 (ttpt) REVERT: N 49 SER cc_start: 0.9478 (m) cc_final: 0.9202 (t) REVERT: N 53 GLU cc_start: 0.8245 (tp30) cc_final: 0.7718 (tp30) REVERT: N 58 ARG cc_start: 0.8048 (mmt180) cc_final: 0.7677 (mmt180) REVERT: O 17 ASP cc_start: 0.7694 (m-30) cc_final: 0.7303 (t0) REVERT: O 22 ASN cc_start: 0.9332 (p0) cc_final: 0.8087 (p0) REVERT: O 25 THR cc_start: 0.8979 (m) cc_final: 0.8374 (p) REVERT: O 28 THR cc_start: 0.8387 (m) cc_final: 0.8094 (p) REVERT: O 33 LYS cc_start: 0.9144 (mttt) cc_final: 0.8417 (mtmm) REVERT: O 49 SER cc_start: 0.9243 (m) cc_final: 0.9007 (t) REVERT: O 52 SER cc_start: 0.9030 (m) cc_final: 0.8694 (t) REVERT: O 59 ASN cc_start: 0.8475 (m-40) cc_final: 0.7890 (m110) REVERT: O 69 LYS cc_start: 0.8125 (tttm) cc_final: 0.7765 (ttmt) REVERT: P 22 ASN cc_start: 0.9300 (p0) cc_final: 0.8885 (p0) REVERT: P 26 GLN cc_start: 0.9226 (tt0) cc_final: 0.8985 (tt0) REVERT: P 69 LYS cc_start: 0.8187 (tttm) cc_final: 0.7724 (ttmt) REVERT: Q 25 THR cc_start: 0.8835 (m) cc_final: 0.8226 (p) REVERT: Q 40 ASP cc_start: 0.8442 (t0) cc_final: 0.7980 (t0) REVERT: Q 54 TYR cc_start: 0.8544 (t80) cc_final: 0.8055 (t80) REVERT: Q 69 LYS cc_start: 0.8414 (tttm) cc_final: 0.7745 (tttt) REVERT: R 22 ASN cc_start: 0.9116 (p0) cc_final: 0.8623 (p0) REVERT: R 29 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8194 (tm-30) REVERT: R 39 SER cc_start: 0.9375 (m) cc_final: 0.8998 (t) REVERT: R 55 ASN cc_start: 0.8876 (t0) cc_final: 0.8482 (t0) REVERT: S 39 SER cc_start: 0.9231 (m) cc_final: 0.8318 (m) REVERT: S 59 ASN cc_start: 0.8551 (m-40) cc_final: 0.8224 (m-40) REVERT: T 22 ASN cc_start: 0.8870 (p0) cc_final: 0.8508 (p0) REVERT: T 25 THR cc_start: 0.8670 (p) cc_final: 0.8303 (t) REVERT: T 39 SER cc_start: 0.9015 (m) cc_final: 0.8741 (p) REVERT: T 48 GLN cc_start: 0.9088 (tm-30) cc_final: 0.8863 (tm-30) REVERT: T 50 LYS cc_start: 0.8887 (mmtt) cc_final: 0.8665 (mmtt) REVERT: T 69 LYS cc_start: 0.6960 (tttm) cc_final: 0.6385 (tttt) outliers start: 52 outliers final: 38 residues processed: 588 average time/residue: 0.2263 time to fit residues: 187.6413 Evaluate side-chains 590 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 548 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 69 LYS Chi-restraints excluded: chain M residue 80 ARG Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 21 ASP Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 65 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 115 optimal weight: 0.0040 chunk 32 optimal weight: 10.0000 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 GLN ** U 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN F 59 ASN J 78 ASN K 24 GLN L 61 GLN L 78 ASN N 48 GLN ** O 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 GLN P 63 ASN R 61 GLN R 63 ASN S 26 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 11837 Z= 0.149 Angle : 0.470 7.674 16112 Z= 0.243 Chirality : 0.036 0.127 1843 Planarity : 0.002 0.018 2109 Dihedral : 3.558 23.660 1596 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.55 % Allowed : 23.05 % Favored : 74.40 % 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: 1.82 (0.22), residues: 1444 helix: 1.85 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.69 (0.29), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 5 PHE 0.004 0.001 PHE L 16 TYR 0.012 0.001 TYR G 47 ARG 0.002 0.000 ARG G 58 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 569 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 34 LEU cc_start: 0.8292 (tp) cc_final: 0.8068 (tp) REVERT: D 44 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7908 (mt) REVERT: D 63 ASN cc_start: 0.7793 (m-40) cc_final: 0.7387 (m-40) REVERT: D 66 LYS cc_start: 0.8943 (tptp) cc_final: 0.7343 (mttt) REVERT: U 15 LYS cc_start: 0.9055 (mttt) cc_final: 0.8772 (mmtp) REVERT: U 37 LYS cc_start: 0.8150 (ttmt) cc_final: 0.7218 (tptp) REVERT: U 66 LYS cc_start: 0.8640 (tptp) cc_final: 0.6565 (mttp) REVERT: V 37 LYS cc_start: 0.9216 (ttmt) cc_final: 0.7755 (tptt) REVERT: V 47 TYR cc_start: 0.9150 (t80) cc_final: 0.8176 (t80) REVERT: V 49 SER cc_start: 0.8639 (t) cc_final: 0.8241 (p) REVERT: V 53 GLU cc_start: 0.8002 (tp30) cc_final: 0.7758 (mm-30) REVERT: V 77 GLN cc_start: 0.8632 (tp40) cc_final: 0.8024 (tp-100) REVERT: E 15 LYS cc_start: 0.8824 (mmmm) cc_final: 0.8615 (mmmt) REVERT: E 22 ASN cc_start: 0.7553 (p0) cc_final: 0.6864 (p0) REVERT: E 23 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7320 (tp) REVERT: E 32 ASP cc_start: 0.8134 (m-30) cc_final: 0.7750 (m-30) REVERT: E 37 LYS cc_start: 0.8661 (ttmt) cc_final: 0.7427 (tptt) REVERT: E 47 TYR cc_start: 0.9024 (t80) cc_final: 0.8694 (t80) REVERT: E 53 GLU cc_start: 0.8592 (tp30) cc_final: 0.8139 (mm-30) REVERT: E 66 LYS cc_start: 0.8112 (tptp) cc_final: 0.6610 (mttt) REVERT: F 28 THR cc_start: 0.8699 (m) cc_final: 0.8099 (p) REVERT: F 32 ASP cc_start: 0.7744 (m-30) cc_final: 0.7414 (m-30) REVERT: F 34 LEU cc_start: 0.9185 (tp) cc_final: 0.8920 (tt) REVERT: F 37 LYS cc_start: 0.8661 (ttmt) cc_final: 0.7978 (tptt) REVERT: F 39 SER cc_start: 0.8827 (m) cc_final: 0.8223 (t) REVERT: F 47 TYR cc_start: 0.8979 (t80) cc_final: 0.8299 (t80) REVERT: F 49 SER cc_start: 0.9255 (t) cc_final: 0.8816 (p) REVERT: F 53 GLU cc_start: 0.8154 (tp30) cc_final: 0.7745 (mm-30) REVERT: F 63 ASN cc_start: 0.9194 (m-40) cc_final: 0.8964 (m110) REVERT: F 66 LYS cc_start: 0.8611 (tptp) cc_final: 0.7597 (ttmt) REVERT: G 33 LYS cc_start: 0.9094 (mtpp) cc_final: 0.8837 (mtpp) REVERT: G 37 LYS cc_start: 0.8394 (ttmt) cc_final: 0.7129 (tptt) REVERT: G 66 LYS cc_start: 0.8923 (tppt) cc_final: 0.8440 (tppt) REVERT: G 69 LYS cc_start: 0.8726 (tttm) cc_final: 0.8426 (tttt) REVERT: H 23 LEU cc_start: 0.8825 (tp) cc_final: 0.8589 (tt) REVERT: H 28 THR cc_start: 0.8955 (m) cc_final: 0.8356 (p) REVERT: H 32 ASP cc_start: 0.7857 (m-30) cc_final: 0.7518 (m-30) REVERT: H 37 LYS cc_start: 0.8095 (ttmt) cc_final: 0.6834 (tptt) REVERT: H 44 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8747 (mt) REVERT: H 47 TYR cc_start: 0.9055 (t80) cc_final: 0.7379 (t80) REVERT: H 51 LEU cc_start: 0.9304 (tp) cc_final: 0.8770 (tp) REVERT: I 37 LYS cc_start: 0.8662 (ttmt) cc_final: 0.7263 (tptp) REVERT: I 47 TYR cc_start: 0.9182 (t80) cc_final: 0.8836 (t80) REVERT: J 17 ASP cc_start: 0.7925 (m-30) cc_final: 0.7673 (m-30) REVERT: J 22 ASN cc_start: 0.8045 (p0) cc_final: 0.7540 (p0) REVERT: J 37 LYS cc_start: 0.8790 (ttmt) cc_final: 0.7456 (tptt) REVERT: J 49 SER cc_start: 0.9259 (t) cc_final: 0.9027 (p) REVERT: K 33 LYS cc_start: 0.9188 (mttt) cc_final: 0.8809 (mtpp) REVERT: K 37 LYS cc_start: 0.8992 (ttmt) cc_final: 0.7507 (tptt) REVERT: K 47 TYR cc_start: 0.9053 (t80) cc_final: 0.7607 (t80) REVERT: L 8 TYR cc_start: 0.8530 (t80) cc_final: 0.8201 (t80) REVERT: L 13 SER cc_start: 0.8714 (t) cc_final: 0.8435 (t) REVERT: L 23 LEU cc_start: 0.8664 (tp) cc_final: 0.8227 (tt) REVERT: L 26 GLN cc_start: 0.8707 (mt0) cc_final: 0.8091 (tt0) REVERT: L 28 THR cc_start: 0.8915 (m) cc_final: 0.8595 (p) REVERT: L 37 LYS cc_start: 0.8735 (ttmt) cc_final: 0.7037 (tptt) REVERT: L 48 GLN cc_start: 0.8317 (tt0) cc_final: 0.7731 (tt0) REVERT: L 53 GLU cc_start: 0.8181 (tp30) cc_final: 0.7787 (tp30) REVERT: L 77 GLN cc_start: 0.8463 (tp-100) cc_final: 0.8039 (tp40) REVERT: M 22 ASN cc_start: 0.8666 (p0) cc_final: 0.8272 (p0) REVERT: M 28 THR cc_start: 0.8833 (m) cc_final: 0.8107 (p) REVERT: M 31 LEU cc_start: 0.9299 (tp) cc_final: 0.8988 (tp) REVERT: M 32 ASP cc_start: 0.8317 (p0) cc_final: 0.7941 (p0) REVERT: M 47 TYR cc_start: 0.9301 (t80) cc_final: 0.8564 (t80) REVERT: M 66 LYS cc_start: 0.8519 (tptt) cc_final: 0.8038 (tmtt) REVERT: N 15 LYS cc_start: 0.8515 (ttmm) cc_final: 0.8176 (ttmm) REVERT: N 31 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8901 (tp) REVERT: N 47 TYR cc_start: 0.8873 (t80) cc_final: 0.7947 (t80) REVERT: N 49 SER cc_start: 0.9438 (m) cc_final: 0.9117 (t) REVERT: N 53 GLU cc_start: 0.8185 (tp30) cc_final: 0.7611 (tp30) REVERT: N 58 ARG cc_start: 0.7919 (mmt180) cc_final: 0.7580 (mmt180) REVERT: O 17 ASP cc_start: 0.7829 (m-30) cc_final: 0.7334 (t0) REVERT: O 22 ASN cc_start: 0.9335 (p0) cc_final: 0.7795 (p0) REVERT: O 25 THR cc_start: 0.8950 (m) cc_final: 0.8366 (p) REVERT: O 28 THR cc_start: 0.8388 (m) cc_final: 0.8088 (p) REVERT: O 33 LYS cc_start: 0.9127 (mttt) cc_final: 0.8374 (mtmm) REVERT: O 49 SER cc_start: 0.9262 (m) cc_final: 0.8984 (t) REVERT: O 59 ASN cc_start: 0.8312 (m-40) cc_final: 0.7866 (m110) REVERT: O 69 LYS cc_start: 0.8185 (tttm) cc_final: 0.7711 (ttmt) REVERT: P 22 ASN cc_start: 0.9270 (p0) cc_final: 0.8866 (p0) REVERT: Q 25 THR cc_start: 0.8579 (m) cc_final: 0.8298 (p) REVERT: Q 40 ASP cc_start: 0.8169 (t0) cc_final: 0.7687 (t0) REVERT: Q 54 TYR cc_start: 0.8455 (t80) cc_final: 0.7966 (t80) REVERT: Q 69 LYS cc_start: 0.8374 (tttm) cc_final: 0.7722 (tttp) REVERT: R 22 ASN cc_start: 0.9069 (p0) cc_final: 0.8753 (p0) REVERT: R 24 GLN cc_start: 0.8085 (pm20) cc_final: 0.7580 (pm20) REVERT: R 39 SER cc_start: 0.9376 (m) cc_final: 0.9080 (t) REVERT: S 39 SER cc_start: 0.9203 (m) cc_final: 0.8199 (m) REVERT: S 59 ASN cc_start: 0.8459 (m-40) cc_final: 0.7718 (m110) REVERT: S 63 ASN cc_start: 0.8524 (m-40) cc_final: 0.8298 (m110) REVERT: T 22 ASN cc_start: 0.8820 (p0) cc_final: 0.8280 (p0) REVERT: T 25 THR cc_start: 0.8587 (p) cc_final: 0.8178 (t) REVERT: T 39 SER cc_start: 0.9082 (m) cc_final: 0.8748 (p) REVERT: T 48 GLN cc_start: 0.9071 (tm-30) cc_final: 0.8476 (tm-30) REVERT: T 50 LYS cc_start: 0.8945 (mmtt) cc_final: 0.8731 (mmtt) REVERT: T 69 LYS cc_start: 0.6934 (tttm) cc_final: 0.6335 (tttt) outliers start: 32 outliers final: 20 residues processed: 576 average time/residue: 0.2111 time to fit residues: 173.2943 Evaluate side-chains 572 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 548 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 80 ARG Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 21 ASP Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 33 LYS Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain S residue 40 ASP Chi-restraints excluded: chain T residue 13 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 10 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 GLN U 59 ASN E 61 GLN F 59 ASN J 78 ASN K 24 GLN L 78 ASN ** O 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 GLN P 26 GLN ** R 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 63 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11837 Z= 0.226 Angle : 0.516 7.010 16112 Z= 0.264 Chirality : 0.039 0.152 1843 Planarity : 0.002 0.019 2109 Dihedral : 3.615 26.405 1596 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.43 % Allowed : 23.29 % Favored : 73.29 % 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: 2.01 (0.22), residues: 1444 helix: 1.96 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.50 (0.32), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 5 PHE 0.010 0.001 PHE I 79 TYR 0.015 0.002 TYR J 47 ARG 0.002 0.000 ARG V 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 552 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 22 ASN cc_start: 0.8061 (p0) cc_final: 0.7829 (p0) REVERT: D 66 LYS cc_start: 0.8874 (tptp) cc_final: 0.7430 (mttt) REVERT: U 15 LYS cc_start: 0.9125 (mttt) cc_final: 0.8867 (mmtp) REVERT: U 37 LYS cc_start: 0.8180 (ttmt) cc_final: 0.7230 (tptt) REVERT: U 66 LYS cc_start: 0.8638 (tptp) cc_final: 0.6577 (mttp) REVERT: V 37 LYS cc_start: 0.8724 (ttmt) cc_final: 0.7479 (tptt) REVERT: V 47 TYR cc_start: 0.9212 (t80) cc_final: 0.8368 (t80) REVERT: V 49 SER cc_start: 0.8638 (t) cc_final: 0.8239 (p) REVERT: V 53 GLU cc_start: 0.8074 (tp30) cc_final: 0.7803 (mm-30) REVERT: V 77 GLN cc_start: 0.8658 (tp40) cc_final: 0.8257 (tp40) REVERT: E 15 LYS cc_start: 0.8865 (mmmm) cc_final: 0.8505 (mmmt) REVERT: E 23 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7851 (tp) REVERT: E 32 ASP cc_start: 0.8148 (m-30) cc_final: 0.7724 (m-30) REVERT: E 37 LYS cc_start: 0.8721 (ttmt) cc_final: 0.7434 (tptt) REVERT: E 47 TYR cc_start: 0.9200 (t80) cc_final: 0.8980 (t80) REVERT: E 53 GLU cc_start: 0.8595 (tp30) cc_final: 0.8109 (mm-30) REVERT: E 66 LYS cc_start: 0.8224 (tptp) cc_final: 0.6693 (mttt) REVERT: F 28 THR cc_start: 0.8702 (m) cc_final: 0.8067 (p) REVERT: F 32 ASP cc_start: 0.7749 (m-30) cc_final: 0.7410 (m-30) REVERT: F 34 LEU cc_start: 0.9214 (tp) cc_final: 0.8942 (tt) REVERT: F 37 LYS cc_start: 0.8656 (ttmt) cc_final: 0.7946 (tptt) REVERT: F 39 SER cc_start: 0.8876 (m) cc_final: 0.8217 (t) REVERT: F 47 TYR cc_start: 0.9027 (t80) cc_final: 0.8380 (t80) REVERT: F 49 SER cc_start: 0.9281 (t) cc_final: 0.8879 (p) REVERT: F 53 GLU cc_start: 0.8304 (tp30) cc_final: 0.7862 (mm-30) REVERT: F 63 ASN cc_start: 0.9233 (m-40) cc_final: 0.9020 (m110) REVERT: F 66 LYS cc_start: 0.8593 (tptp) cc_final: 0.7613 (ttmt) REVERT: G 33 LYS cc_start: 0.9288 (mtpp) cc_final: 0.9061 (mtpp) REVERT: G 37 LYS cc_start: 0.8431 (ttmt) cc_final: 0.7141 (tptt) REVERT: G 66 LYS cc_start: 0.8928 (tppt) cc_final: 0.8684 (tppt) REVERT: G 69 LYS cc_start: 0.8696 (tttm) cc_final: 0.8391 (tttt) REVERT: H 28 THR cc_start: 0.8963 (m) cc_final: 0.8342 (p) REVERT: H 32 ASP cc_start: 0.7940 (m-30) cc_final: 0.7617 (m-30) REVERT: H 37 LYS cc_start: 0.8161 (ttmt) cc_final: 0.6862 (tptt) REVERT: H 47 TYR cc_start: 0.9103 (t80) cc_final: 0.7395 (t80) REVERT: H 51 LEU cc_start: 0.9347 (tp) cc_final: 0.8753 (tp) REVERT: I 37 LYS cc_start: 0.8742 (ttmt) cc_final: 0.7382 (tptp) REVERT: I 47 TYR cc_start: 0.9201 (t80) cc_final: 0.8880 (t80) REVERT: J 17 ASP cc_start: 0.7899 (m-30) cc_final: 0.7571 (m-30) REVERT: J 22 ASN cc_start: 0.8174 (p0) cc_final: 0.7622 (p0) REVERT: J 31 LEU cc_start: 0.8571 (tp) cc_final: 0.8195 (mt) REVERT: J 37 LYS cc_start: 0.8826 (ttmt) cc_final: 0.7447 (tptt) REVERT: J 47 TYR cc_start: 0.9142 (t80) cc_final: 0.8370 (t80) REVERT: J 49 SER cc_start: 0.9235 (t) cc_final: 0.8906 (p) REVERT: K 33 LYS cc_start: 0.9272 (mttt) cc_final: 0.8892 (mtpp) REVERT: K 37 LYS cc_start: 0.9003 (ttmt) cc_final: 0.7483 (tptt) REVERT: K 47 TYR cc_start: 0.9078 (t80) cc_final: 0.7840 (t80) REVERT: L 8 TYR cc_start: 0.8560 (t80) cc_final: 0.8324 (t80) REVERT: L 26 GLN cc_start: 0.8754 (mt0) cc_final: 0.8104 (tt0) REVERT: L 28 THR cc_start: 0.8895 (m) cc_final: 0.8601 (p) REVERT: L 48 GLN cc_start: 0.8434 (tt0) cc_final: 0.7898 (tt0) REVERT: L 53 GLU cc_start: 0.8267 (tp30) cc_final: 0.7837 (tp30) REVERT: L 77 GLN cc_start: 0.8507 (tp-100) cc_final: 0.8097 (tp40) REVERT: M 17 ASP cc_start: 0.8099 (t0) cc_final: 0.7817 (m-30) REVERT: M 22 ASN cc_start: 0.8752 (p0) cc_final: 0.8373 (p0) REVERT: M 28 THR cc_start: 0.8834 (m) cc_final: 0.8069 (p) REVERT: M 31 LEU cc_start: 0.9307 (tp) cc_final: 0.8991 (tp) REVERT: M 32 ASP cc_start: 0.8355 (p0) cc_final: 0.7956 (p0) REVERT: M 37 LYS cc_start: 0.9118 (mtpp) cc_final: 0.8861 (mtpt) REVERT: M 47 TYR cc_start: 0.9305 (t80) cc_final: 0.8661 (t80) REVERT: M 66 LYS cc_start: 0.8594 (tptt) cc_final: 0.8129 (tmtt) REVERT: M 69 LYS cc_start: 0.8596 (tttp) cc_final: 0.7806 (ttpt) REVERT: N 49 SER cc_start: 0.9453 (m) cc_final: 0.9146 (t) REVERT: N 53 GLU cc_start: 0.8199 (tp30) cc_final: 0.7655 (tp30) REVERT: N 58 ARG cc_start: 0.7963 (mmt180) cc_final: 0.7614 (mmt180) REVERT: O 17 ASP cc_start: 0.7703 (m-30) cc_final: 0.7295 (t0) REVERT: O 22 ASN cc_start: 0.9370 (p0) cc_final: 0.8132 (p0) REVERT: O 25 THR cc_start: 0.8951 (m) cc_final: 0.8357 (p) REVERT: O 28 THR cc_start: 0.8378 (m) cc_final: 0.8084 (p) REVERT: O 33 LYS cc_start: 0.9140 (mttt) cc_final: 0.8387 (mtmm) REVERT: O 49 SER cc_start: 0.9262 (m) cc_final: 0.8714 (t) REVERT: O 59 ASN cc_start: 0.8436 (m-40) cc_final: 0.7903 (m110) REVERT: O 69 LYS cc_start: 0.8113 (tttm) cc_final: 0.7595 (ttmt) REVERT: P 22 ASN cc_start: 0.9277 (p0) cc_final: 0.8743 (p0) REVERT: P 28 THR cc_start: 0.8471 (m) cc_final: 0.8083 (p) REVERT: Q 25 THR cc_start: 0.8647 (m) cc_final: 0.8367 (p) REVERT: Q 40 ASP cc_start: 0.8258 (t0) cc_final: 0.7791 (t70) REVERT: Q 49 SER cc_start: 0.9233 (m) cc_final: 0.8667 (t) REVERT: Q 54 TYR cc_start: 0.8522 (t80) cc_final: 0.8030 (t80) REVERT: Q 69 LYS cc_start: 0.8402 (tttm) cc_final: 0.7742 (tttp) REVERT: R 22 ASN cc_start: 0.9137 (p0) cc_final: 0.8607 (p0) REVERT: R 24 GLN cc_start: 0.8088 (pm20) cc_final: 0.7573 (pm20) REVERT: R 29 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8041 (tm-30) REVERT: R 33 LYS cc_start: 0.9133 (ttmt) cc_final: 0.8915 (mtmt) REVERT: R 39 SER cc_start: 0.9422 (m) cc_final: 0.8986 (t) REVERT: S 39 SER cc_start: 0.9217 (m) cc_final: 0.8253 (m) REVERT: S 59 ASN cc_start: 0.8518 (m-40) cc_final: 0.8187 (m-40) REVERT: T 22 ASN cc_start: 0.8924 (p0) cc_final: 0.8523 (p0) REVERT: T 25 THR cc_start: 0.8586 (p) cc_final: 0.8217 (t) REVERT: T 39 SER cc_start: 0.9074 (m) cc_final: 0.8799 (p) REVERT: T 40 ASP cc_start: 0.8226 (t0) cc_final: 0.8021 (t0) REVERT: T 48 GLN cc_start: 0.9097 (tm-30) cc_final: 0.8542 (tm-30) REVERT: T 69 LYS cc_start: 0.7024 (tttm) cc_final: 0.6401 (tttt) outliers start: 43 outliers final: 37 residues processed: 565 average time/residue: 0.2222 time to fit residues: 178.9364 Evaluate side-chains 583 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 545 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 80 ARG Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 21 ASP Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 26 GLN Chi-restraints excluded: chain P residue 29 GLU Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain S residue 49 SER Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 65 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 73 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 108 optimal weight: 0.4980 chunk 71 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 59 optimal weight: 0.2980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 GLN U 59 ASN J 78 ASN K 24 GLN K 55 ASN K 78 ASN L 61 GLN L 78 ASN ** O 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 GLN R 59 ASN R 63 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11837 Z= 0.163 Angle : 0.486 6.700 16112 Z= 0.250 Chirality : 0.036 0.135 1843 Planarity : 0.002 0.018 2109 Dihedral : 3.491 25.105 1596 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.31 % Allowed : 24.88 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.22), residues: 1444 helix: 2.17 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.32 (0.34), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 5 PHE 0.005 0.001 PHE I 79 TYR 0.012 0.001 TYR O 47 ARG 0.002 0.000 ARG R 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 559 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 37 LYS cc_start: 0.8535 (ttmt) cc_final: 0.7437 (tptt) REVERT: U 15 LYS cc_start: 0.9125 (mttt) cc_final: 0.8835 (mmtp) REVERT: U 37 LYS cc_start: 0.8172 (ttmt) cc_final: 0.7243 (tptt) REVERT: U 66 LYS cc_start: 0.8650 (tptp) cc_final: 0.6558 (mttp) REVERT: U 77 GLN cc_start: 0.8938 (tp40) cc_final: 0.8716 (tp40) REVERT: V 37 LYS cc_start: 0.9140 (ttmt) cc_final: 0.7763 (tptt) REVERT: V 47 TYR cc_start: 0.9109 (t80) cc_final: 0.8225 (t80) REVERT: V 49 SER cc_start: 0.8613 (t) cc_final: 0.8176 (p) REVERT: V 53 GLU cc_start: 0.8038 (tp30) cc_final: 0.7778 (mm-30) REVERT: V 77 GLN cc_start: 0.8614 (tp40) cc_final: 0.8262 (tp40) REVERT: E 15 LYS cc_start: 0.8798 (mmmm) cc_final: 0.8508 (mmmt) REVERT: E 22 ASN cc_start: 0.7957 (p0) cc_final: 0.7254 (p0) REVERT: E 23 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7959 (tp) REVERT: E 32 ASP cc_start: 0.8138 (m-30) cc_final: 0.7684 (m-30) REVERT: E 37 LYS cc_start: 0.8736 (ttmt) cc_final: 0.7471 (tptt) REVERT: E 53 GLU cc_start: 0.8559 (tp30) cc_final: 0.8147 (mm-30) REVERT: E 66 LYS cc_start: 0.8376 (tptp) cc_final: 0.6609 (mttt) REVERT: F 28 THR cc_start: 0.8694 (m) cc_final: 0.8071 (p) REVERT: F 32 ASP cc_start: 0.7737 (m-30) cc_final: 0.7400 (m-30) REVERT: F 34 LEU cc_start: 0.9196 (tp) cc_final: 0.8919 (tt) REVERT: F 37 LYS cc_start: 0.8703 (ttmt) cc_final: 0.7990 (tptt) REVERT: F 39 SER cc_start: 0.8804 (m) cc_final: 0.8195 (t) REVERT: F 47 TYR cc_start: 0.8946 (t80) cc_final: 0.8311 (t80) REVERT: F 49 SER cc_start: 0.9258 (t) cc_final: 0.8813 (p) REVERT: F 53 GLU cc_start: 0.8030 (tp30) cc_final: 0.7653 (mm-30) REVERT: F 66 LYS cc_start: 0.8446 (tptp) cc_final: 0.7562 (ttmt) REVERT: G 33 LYS cc_start: 0.9299 (mtpp) cc_final: 0.9065 (mtpp) REVERT: G 37 LYS cc_start: 0.8402 (ttmt) cc_final: 0.7125 (tptt) REVERT: G 66 LYS cc_start: 0.8919 (tppt) cc_final: 0.8613 (tppt) REVERT: G 69 LYS cc_start: 0.8675 (tttm) cc_final: 0.8441 (tttt) REVERT: H 11 ASP cc_start: 0.7967 (m-30) cc_final: 0.7765 (m-30) REVERT: H 23 LEU cc_start: 0.8815 (tp) cc_final: 0.8590 (tt) REVERT: H 28 THR cc_start: 0.8956 (m) cc_final: 0.8341 (p) REVERT: H 32 ASP cc_start: 0.7831 (m-30) cc_final: 0.7494 (m-30) REVERT: H 37 LYS cc_start: 0.8073 (ttmt) cc_final: 0.7009 (tptp) REVERT: H 44 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8776 (mt) REVERT: H 47 TYR cc_start: 0.9075 (t80) cc_final: 0.7360 (t80) REVERT: H 51 LEU cc_start: 0.9318 (tp) cc_final: 0.8792 (tp) REVERT: I 37 LYS cc_start: 0.8684 (ttmt) cc_final: 0.7276 (tptp) REVERT: I 47 TYR cc_start: 0.9168 (t80) cc_final: 0.8852 (t80) REVERT: J 17 ASP cc_start: 0.7912 (m-30) cc_final: 0.7706 (m-30) REVERT: J 22 ASN cc_start: 0.8178 (p0) cc_final: 0.7609 (p0) REVERT: J 37 LYS cc_start: 0.8762 (ttmt) cc_final: 0.7463 (tptt) REVERT: J 47 TYR cc_start: 0.9131 (t80) cc_final: 0.8345 (t80) REVERT: K 33 LYS cc_start: 0.9275 (mttt) cc_final: 0.8879 (mtpp) REVERT: K 37 LYS cc_start: 0.8965 (ttmt) cc_final: 0.7460 (tptt) REVERT: K 47 TYR cc_start: 0.9056 (t80) cc_final: 0.7706 (t80) REVERT: L 8 TYR cc_start: 0.8514 (t80) cc_final: 0.8226 (t80) REVERT: L 23 LEU cc_start: 0.8675 (tp) cc_final: 0.8251 (tt) REVERT: L 26 GLN cc_start: 0.8715 (mt0) cc_final: 0.8073 (tt0) REVERT: L 28 THR cc_start: 0.8885 (m) cc_final: 0.8588 (p) REVERT: L 48 GLN cc_start: 0.8278 (tt0) cc_final: 0.7732 (tt0) REVERT: L 53 GLU cc_start: 0.8181 (tp30) cc_final: 0.7790 (tp30) REVERT: L 77 GLN cc_start: 0.8458 (tp-100) cc_final: 0.8066 (tp40) REVERT: M 17 ASP cc_start: 0.8067 (t0) cc_final: 0.7810 (m-30) REVERT: M 22 ASN cc_start: 0.8689 (p0) cc_final: 0.8330 (p0) REVERT: M 28 THR cc_start: 0.8807 (m) cc_final: 0.8028 (p) REVERT: M 31 LEU cc_start: 0.9307 (tp) cc_final: 0.8999 (tp) REVERT: M 32 ASP cc_start: 0.8390 (p0) cc_final: 0.8031 (p0) REVERT: M 47 TYR cc_start: 0.9274 (t80) cc_final: 0.8627 (t80) REVERT: M 66 LYS cc_start: 0.8592 (tptt) cc_final: 0.8025 (tmtt) REVERT: M 69 LYS cc_start: 0.8576 (tttp) cc_final: 0.7793 (ttpt) REVERT: N 24 GLN cc_start: 0.8589 (mp10) cc_final: 0.8059 (tp40) REVERT: N 49 SER cc_start: 0.9436 (m) cc_final: 0.9095 (t) REVERT: N 53 GLU cc_start: 0.8196 (tp30) cc_final: 0.7715 (tp30) REVERT: N 58 ARG cc_start: 0.7897 (mmt180) cc_final: 0.7524 (mmt180) REVERT: O 15 LYS cc_start: 0.8498 (tppp) cc_final: 0.8279 (tptp) REVERT: O 17 ASP cc_start: 0.7870 (m-30) cc_final: 0.7374 (t0) REVERT: O 22 ASN cc_start: 0.9329 (p0) cc_final: 0.8038 (p0) REVERT: O 25 THR cc_start: 0.9027 (m) cc_final: 0.8420 (p) REVERT: O 28 THR cc_start: 0.8386 (m) cc_final: 0.8067 (p) REVERT: O 33 LYS cc_start: 0.9131 (mttt) cc_final: 0.8379 (mtmm) REVERT: O 49 SER cc_start: 0.9272 (m) cc_final: 0.8730 (t) REVERT: O 59 ASN cc_start: 0.8329 (m-40) cc_final: 0.7939 (m110) REVERT: O 69 LYS cc_start: 0.8064 (tttm) cc_final: 0.7571 (ttmt) REVERT: P 22 ASN cc_start: 0.9248 (p0) cc_final: 0.8605 (p0) REVERT: P 56 LEU cc_start: 0.9338 (mt) cc_final: 0.9132 (mp) REVERT: Q 25 THR cc_start: 0.8607 (m) cc_final: 0.8387 (p) REVERT: Q 40 ASP cc_start: 0.8033 (t0) cc_final: 0.7487 (t0) REVERT: Q 54 TYR cc_start: 0.8523 (t80) cc_final: 0.8064 (t80) REVERT: Q 69 LYS cc_start: 0.8383 (tttm) cc_final: 0.7710 (tttp) REVERT: R 24 GLN cc_start: 0.8075 (pm20) cc_final: 0.7579 (pm20) REVERT: R 29 GLU cc_start: 0.8507 (tm-30) cc_final: 0.7936 (tm-30) REVERT: R 33 LYS cc_start: 0.9123 (ttmt) cc_final: 0.8894 (mtmt) REVERT: R 39 SER cc_start: 0.9285 (m) cc_final: 0.8894 (t) REVERT: R 69 LYS cc_start: 0.8137 (tttm) cc_final: 0.6821 (mttt) REVERT: S 39 SER cc_start: 0.9210 (m) cc_final: 0.8251 (m) REVERT: S 59 ASN cc_start: 0.8453 (m-40) cc_final: 0.7675 (m110) REVERT: T 22 ASN cc_start: 0.8808 (p0) cc_final: 0.8218 (p0) REVERT: T 25 THR cc_start: 0.8527 (p) cc_final: 0.8149 (t) REVERT: T 39 SER cc_start: 0.9085 (m) cc_final: 0.8700 (p) REVERT: T 40 ASP cc_start: 0.8170 (t0) cc_final: 0.7950 (t0) REVERT: T 48 GLN cc_start: 0.9058 (tm-30) cc_final: 0.8504 (tm-30) REVERT: T 50 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8633 (mmmt) REVERT: T 69 LYS cc_start: 0.7002 (tttm) cc_final: 0.6345 (tttt) outliers start: 29 outliers final: 24 residues processed: 568 average time/residue: 0.2166 time to fit residues: 175.1877 Evaluate side-chains 574 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 548 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 21 ASP Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 29 GLU Chi-restraints excluded: chain P residue 65 VAL Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain S residue 40 ASP Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 65 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 0.0170 chunk 81 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 overall best weight: 2.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 GLN G 61 GLN J 78 ASN K 24 GLN L 61 GLN L 78 ASN M 77 GLN ** O 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 GLN P 26 GLN R 63 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11837 Z= 0.189 Angle : 0.500 7.301 16112 Z= 0.255 Chirality : 0.037 0.154 1843 Planarity : 0.002 0.018 2109 Dihedral : 3.491 25.817 1596 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.11 % Allowed : 24.88 % Favored : 72.01 % 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: 2.48 (0.22), residues: 1444 helix: 2.26 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.22 (0.36), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 5 PHE 0.006 0.001 PHE I 79 TYR 0.017 0.001 TYR O 47 ARG 0.003 0.000 ARG Q 58 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 560 time to evaluate : 1.244 Fit side-chains revert: symmetry clash REVERT: D 37 LYS cc_start: 0.8640 (ttmt) cc_final: 0.7539 (tptt) REVERT: U 15 LYS cc_start: 0.9077 (mttt) cc_final: 0.8801 (mmtp) REVERT: U 37 LYS cc_start: 0.8190 (ttmt) cc_final: 0.7250 (tptt) REVERT: U 66 LYS cc_start: 0.8647 (tptp) cc_final: 0.6559 (mttp) REVERT: U 77 GLN cc_start: 0.8907 (tp40) cc_final: 0.8661 (tp40) REVERT: V 37 LYS cc_start: 0.8682 (ttmt) cc_final: 0.7505 (tptt) REVERT: V 47 TYR cc_start: 0.9158 (t80) cc_final: 0.8280 (t80) REVERT: V 49 SER cc_start: 0.8698 (t) cc_final: 0.8273 (p) REVERT: V 53 GLU cc_start: 0.8015 (tp30) cc_final: 0.7749 (mm-30) REVERT: V 77 GLN cc_start: 0.8636 (tp40) cc_final: 0.8286 (tp40) REVERT: E 15 LYS cc_start: 0.8882 (mmmm) cc_final: 0.8623 (mmmt) REVERT: E 22 ASN cc_start: 0.8114 (p0) cc_final: 0.7354 (p0) REVERT: E 23 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7983 (tp) REVERT: E 37 LYS cc_start: 0.8761 (ttmt) cc_final: 0.7467 (tptt) REVERT: E 53 GLU cc_start: 0.8625 (tp30) cc_final: 0.8220 (mm-30) REVERT: E 66 LYS cc_start: 0.8254 (tptp) cc_final: 0.6669 (mttt) REVERT: F 28 THR cc_start: 0.8691 (m) cc_final: 0.8068 (p) REVERT: F 32 ASP cc_start: 0.7741 (m-30) cc_final: 0.7398 (m-30) REVERT: F 34 LEU cc_start: 0.9204 (tp) cc_final: 0.8933 (tt) REVERT: F 37 LYS cc_start: 0.8637 (ttmt) cc_final: 0.7919 (tptt) REVERT: F 39 SER cc_start: 0.8828 (m) cc_final: 0.8180 (t) REVERT: F 47 TYR cc_start: 0.8968 (t80) cc_final: 0.8329 (t80) REVERT: F 49 SER cc_start: 0.9266 (t) cc_final: 0.8816 (p) REVERT: F 53 GLU cc_start: 0.8131 (tp30) cc_final: 0.7710 (mm-30) REVERT: F 63 ASN cc_start: 0.9155 (m-40) cc_final: 0.8824 (m110) REVERT: F 66 LYS cc_start: 0.8446 (tptp) cc_final: 0.7556 (ttmt) REVERT: G 33 LYS cc_start: 0.9114 (mtpp) cc_final: 0.8902 (mtpp) REVERT: G 37 LYS cc_start: 0.8513 (ttmt) cc_final: 0.7207 (tptt) REVERT: G 66 LYS cc_start: 0.8919 (tppt) cc_final: 0.8637 (tppt) REVERT: G 69 LYS cc_start: 0.8669 (tttm) cc_final: 0.8459 (tttt) REVERT: H 28 THR cc_start: 0.8960 (m) cc_final: 0.8389 (p) REVERT: H 32 ASP cc_start: 0.7835 (m-30) cc_final: 0.7504 (m-30) REVERT: H 37 LYS cc_start: 0.8096 (ttmt) cc_final: 0.6800 (tptt) REVERT: H 44 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8748 (mt) REVERT: H 47 TYR cc_start: 0.9101 (t80) cc_final: 0.7378 (t80) REVERT: H 51 LEU cc_start: 0.9347 (tp) cc_final: 0.8753 (tp) REVERT: I 37 LYS cc_start: 0.8684 (ttmt) cc_final: 0.7260 (tptp) REVERT: I 47 TYR cc_start: 0.9164 (t80) cc_final: 0.8835 (t80) REVERT: J 22 ASN cc_start: 0.8239 (p0) cc_final: 0.7640 (p0) REVERT: J 37 LYS cc_start: 0.8798 (ttmt) cc_final: 0.7455 (tptt) REVERT: J 47 TYR cc_start: 0.9204 (t80) cc_final: 0.8437 (t80) REVERT: K 33 LYS cc_start: 0.9277 (mttt) cc_final: 0.8879 (mtpp) REVERT: K 37 LYS cc_start: 0.8963 (ttmt) cc_final: 0.7449 (tptt) REVERT: K 47 TYR cc_start: 0.9057 (t80) cc_final: 0.7795 (t80) REVERT: K 53 GLU cc_start: 0.7717 (tp30) cc_final: 0.7106 (mm-30) REVERT: L 8 TYR cc_start: 0.8467 (t80) cc_final: 0.8260 (t80) REVERT: L 23 LEU cc_start: 0.8515 (tp) cc_final: 0.7994 (tt) REVERT: L 26 GLN cc_start: 0.8783 (mt0) cc_final: 0.8074 (tt0) REVERT: L 28 THR cc_start: 0.8860 (m) cc_final: 0.8589 (p) REVERT: L 48 GLN cc_start: 0.8341 (tt0) cc_final: 0.7792 (tt0) REVERT: L 53 GLU cc_start: 0.8230 (tp30) cc_final: 0.7805 (tp30) REVERT: L 77 GLN cc_start: 0.8507 (tp-100) cc_final: 0.8077 (tp40) REVERT: M 17 ASP cc_start: 0.8065 (t0) cc_final: 0.7822 (m-30) REVERT: M 22 ASN cc_start: 0.8724 (p0) cc_final: 0.8354 (p0) REVERT: M 28 THR cc_start: 0.8801 (m) cc_final: 0.7981 (p) REVERT: M 31 LEU cc_start: 0.9288 (tp) cc_final: 0.8943 (tp) REVERT: M 32 ASP cc_start: 0.8399 (p0) cc_final: 0.8024 (p0) REVERT: M 47 TYR cc_start: 0.9314 (t80) cc_final: 0.8705 (t80) REVERT: M 66 LYS cc_start: 0.8605 (tptt) cc_final: 0.8035 (tmtt) REVERT: M 69 LYS cc_start: 0.8601 (tttp) cc_final: 0.7808 (ttpt) REVERT: N 24 GLN cc_start: 0.8598 (mp10) cc_final: 0.8316 (tp40) REVERT: N 49 SER cc_start: 0.9433 (m) cc_final: 0.9087 (t) REVERT: N 51 LEU cc_start: 0.9096 (tp) cc_final: 0.8798 (tt) REVERT: N 53 GLU cc_start: 0.8193 (tp30) cc_final: 0.7741 (tp30) REVERT: N 58 ARG cc_start: 0.7915 (mmt180) cc_final: 0.7547 (mmt180) REVERT: O 15 LYS cc_start: 0.8665 (tppp) cc_final: 0.8457 (tptp) REVERT: O 17 ASP cc_start: 0.7882 (m-30) cc_final: 0.7349 (t0) REVERT: O 22 ASN cc_start: 0.9319 (p0) cc_final: 0.8123 (p0) REVERT: O 25 THR cc_start: 0.9016 (m) cc_final: 0.8438 (p) REVERT: O 28 THR cc_start: 0.8363 (m) cc_final: 0.8063 (p) REVERT: O 33 LYS cc_start: 0.9137 (mttt) cc_final: 0.8377 (mtmm) REVERT: O 49 SER cc_start: 0.9233 (m) cc_final: 0.8602 (t) REVERT: O 59 ASN cc_start: 0.8205 (m-40) cc_final: 0.7714 (m110) REVERT: O 69 LYS cc_start: 0.8078 (tttm) cc_final: 0.7560 (ttmt) REVERT: P 22 ASN cc_start: 0.9182 (p0) cc_final: 0.8576 (p0) REVERT: Q 25 THR cc_start: 0.8666 (m) cc_final: 0.8458 (p) REVERT: Q 40 ASP cc_start: 0.8082 (t0) cc_final: 0.7629 (t70) REVERT: Q 54 TYR cc_start: 0.8572 (t80) cc_final: 0.8099 (t80) REVERT: Q 69 LYS cc_start: 0.8407 (tttm) cc_final: 0.7956 (ttmt) REVERT: R 24 GLN cc_start: 0.8096 (pm20) cc_final: 0.7574 (pm20) REVERT: R 33 LYS cc_start: 0.9112 (ttmt) cc_final: 0.8822 (mtmt) REVERT: R 39 SER cc_start: 0.9415 (m) cc_final: 0.9058 (t) REVERT: R 51 LEU cc_start: 0.9149 (tp) cc_final: 0.8671 (tt) REVERT: R 69 LYS cc_start: 0.8156 (tttm) cc_final: 0.6822 (mttt) REVERT: S 29 GLU cc_start: 0.7795 (tp30) cc_final: 0.7587 (tp30) REVERT: S 33 LYS cc_start: 0.9000 (mttt) cc_final: 0.8618 (mtmt) REVERT: S 39 SER cc_start: 0.9198 (m) cc_final: 0.8244 (m) REVERT: S 58 ARG cc_start: 0.9007 (mmt180) cc_final: 0.8665 (mmt90) REVERT: S 59 ASN cc_start: 0.8474 (m-40) cc_final: 0.8138 (m-40) REVERT: T 22 ASN cc_start: 0.8906 (p0) cc_final: 0.8503 (p0) REVERT: T 25 THR cc_start: 0.8498 (p) cc_final: 0.8152 (t) REVERT: T 39 SER cc_start: 0.9141 (m) cc_final: 0.8665 (p) REVERT: T 48 GLN cc_start: 0.9065 (tm-30) cc_final: 0.8519 (tm-30) REVERT: T 50 LYS cc_start: 0.8913 (mmtt) cc_final: 0.8621 (mmmt) REVERT: T 69 LYS cc_start: 0.7024 (tttm) cc_final: 0.6380 (tttt) outliers start: 39 outliers final: 32 residues processed: 568 average time/residue: 0.2159 time to fit residues: 174.8735 Evaluate side-chains 586 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 552 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 77 GLN Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 21 ASP Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 26 GLN Chi-restraints excluded: chain P residue 65 VAL Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 65 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 0.9980 chunk 122 optimal weight: 8.9990 chunk 112 optimal weight: 20.0000 chunk 119 optimal weight: 20.0000 chunk 71 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 126 optimal weight: 20.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 GLN G 61 GLN K 24 GLN L 61 GLN ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 78 ASN ** O 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 GLN R 22 ASN R 63 ASN ** S 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 11837 Z= 0.374 Angle : 0.616 8.890 16112 Z= 0.315 Chirality : 0.043 0.157 1843 Planarity : 0.003 0.017 2109 Dihedral : 3.864 30.210 1596 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.75 % Allowed : 24.24 % Favored : 72.01 % 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: 2.11 (0.22), residues: 1444 helix: 2.00 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.13 (0.36), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 5 PHE 0.016 0.002 PHE N 68 TYR 0.033 0.002 TYR E 47 ARG 0.004 0.001 ARG V 58 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 573 time to evaluate : 1.477 Fit side-chains revert: symmetry clash REVERT: D 37 LYS cc_start: 0.8746 (ttmt) cc_final: 0.7701 (tptt) REVERT: D 48 GLN cc_start: 0.8815 (tt0) cc_final: 0.8566 (tt0) REVERT: D 55 ASN cc_start: 0.8623 (t0) cc_final: 0.8019 (t0) REVERT: D 56 LEU cc_start: 0.9053 (mt) cc_final: 0.8815 (mt) REVERT: D 66 LYS cc_start: 0.8775 (tptp) cc_final: 0.7184 (mttt) REVERT: D 77 GLN cc_start: 0.8819 (tp40) cc_final: 0.8617 (tp-100) REVERT: U 37 LYS cc_start: 0.8302 (ttmt) cc_final: 0.7270 (tptt) REVERT: U 66 LYS cc_start: 0.8538 (tptp) cc_final: 0.6873 (mttt) REVERT: U 77 GLN cc_start: 0.8966 (tp40) cc_final: 0.8719 (tp40) REVERT: V 37 LYS cc_start: 0.8845 (ttmt) cc_final: 0.7925 (tptt) REVERT: V 49 SER cc_start: 0.8625 (t) cc_final: 0.8212 (p) REVERT: V 53 GLU cc_start: 0.8280 (tp30) cc_final: 0.8076 (mm-30) REVERT: V 77 GLN cc_start: 0.8702 (tp40) cc_final: 0.8012 (tp-100) REVERT: E 15 LYS cc_start: 0.8970 (mmmm) cc_final: 0.8696 (mmmt) REVERT: E 21 ASP cc_start: 0.7734 (m-30) cc_final: 0.7497 (m-30) REVERT: E 22 ASN cc_start: 0.8372 (p0) cc_final: 0.7744 (p0) REVERT: E 23 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7499 (tp) REVERT: E 37 LYS cc_start: 0.8772 (ttmt) cc_final: 0.7350 (tptt) REVERT: E 53 GLU cc_start: 0.8699 (tp30) cc_final: 0.8203 (mm-30) REVERT: E 66 LYS cc_start: 0.8446 (tptp) cc_final: 0.6942 (mttt) REVERT: F 28 THR cc_start: 0.8730 (m) cc_final: 0.8518 (p) REVERT: F 34 LEU cc_start: 0.9232 (tp) cc_final: 0.8964 (tt) REVERT: F 37 LYS cc_start: 0.8794 (ttmt) cc_final: 0.7983 (tptt) REVERT: F 39 SER cc_start: 0.8908 (m) cc_final: 0.8270 (t) REVERT: F 47 TYR cc_start: 0.9141 (t80) cc_final: 0.8650 (t80) REVERT: F 49 SER cc_start: 0.9359 (t) cc_final: 0.8983 (p) REVERT: F 51 LEU cc_start: 0.9230 (tp) cc_final: 0.8942 (tp) REVERT: F 63 ASN cc_start: 0.9202 (m-40) cc_final: 0.8901 (m110) REVERT: F 66 LYS cc_start: 0.8609 (tptp) cc_final: 0.7576 (ttmt) REVERT: G 33 LYS cc_start: 0.9090 (mtpp) cc_final: 0.8885 (mtpp) REVERT: G 37 LYS cc_start: 0.8475 (ttmt) cc_final: 0.7143 (tptt) REVERT: G 66 LYS cc_start: 0.8924 (tppt) cc_final: 0.8645 (tppt) REVERT: G 69 LYS cc_start: 0.8609 (tttm) cc_final: 0.8294 (tttt) REVERT: H 28 THR cc_start: 0.9009 (m) cc_final: 0.8307 (p) REVERT: H 32 ASP cc_start: 0.7935 (m-30) cc_final: 0.7651 (m-30) REVERT: H 37 LYS cc_start: 0.8380 (ttmt) cc_final: 0.7081 (tptt) REVERT: I 37 LYS cc_start: 0.8776 (ttmt) cc_final: 0.7365 (tptp) REVERT: I 47 TYR cc_start: 0.9043 (t80) cc_final: 0.8797 (t80) REVERT: J 17 ASP cc_start: 0.7900 (m-30) cc_final: 0.7440 (m-30) REVERT: J 22 ASN cc_start: 0.8444 (p0) cc_final: 0.7809 (p0) REVERT: J 37 LYS cc_start: 0.8877 (ttmt) cc_final: 0.7377 (tptt) REVERT: J 47 TYR cc_start: 0.9294 (t80) cc_final: 0.8541 (t80) REVERT: K 33 LYS cc_start: 0.9217 (mttt) cc_final: 0.8825 (mtpp) REVERT: K 37 LYS cc_start: 0.9018 (ttmt) cc_final: 0.7500 (tptt) REVERT: K 47 TYR cc_start: 0.9113 (t80) cc_final: 0.7743 (t80) REVERT: K 53 GLU cc_start: 0.7635 (tp30) cc_final: 0.7068 (mm-30) REVERT: L 8 TYR cc_start: 0.8591 (t80) cc_final: 0.8341 (t80) REVERT: L 26 GLN cc_start: 0.8825 (mt0) cc_final: 0.8119 (tt0) REVERT: L 28 THR cc_start: 0.8905 (m) cc_final: 0.8636 (p) REVERT: L 48 GLN cc_start: 0.8629 (tt0) cc_final: 0.8072 (tt0) REVERT: L 50 LYS cc_start: 0.8615 (mmtt) cc_final: 0.7922 (mmtp) REVERT: L 53 GLU cc_start: 0.8282 (tp30) cc_final: 0.7816 (tp30) REVERT: L 77 GLN cc_start: 0.8644 (tp-100) cc_final: 0.8141 (tp40) REVERT: M 17 ASP cc_start: 0.8154 (t0) cc_final: 0.7878 (m-30) REVERT: M 22 ASN cc_start: 0.8875 (p0) cc_final: 0.8502 (p0) REVERT: M 28 THR cc_start: 0.8809 (m) cc_final: 0.7982 (p) REVERT: M 31 LEU cc_start: 0.9293 (tp) cc_final: 0.8944 (tp) REVERT: M 32 ASP cc_start: 0.8251 (p0) cc_final: 0.7860 (p0) REVERT: M 47 TYR cc_start: 0.9207 (t80) cc_final: 0.8587 (t80) REVERT: M 66 LYS cc_start: 0.8632 (tptt) cc_final: 0.8106 (tmtt) REVERT: M 69 LYS cc_start: 0.8674 (tttp) cc_final: 0.7901 (ttpt) REVERT: N 24 GLN cc_start: 0.8625 (mp10) cc_final: 0.8368 (tp40) REVERT: N 49 SER cc_start: 0.9470 (m) cc_final: 0.9180 (t) REVERT: N 51 LEU cc_start: 0.9152 (tp) cc_final: 0.8693 (tt) REVERT: N 53 GLU cc_start: 0.8199 (tp30) cc_final: 0.7757 (tp30) REVERT: N 58 ARG cc_start: 0.8085 (mmt180) cc_final: 0.7689 (mmt180) REVERT: O 15 LYS cc_start: 0.8701 (tppp) cc_final: 0.8474 (tptp) REVERT: O 17 ASP cc_start: 0.7795 (m-30) cc_final: 0.7348 (t0) REVERT: O 22 ASN cc_start: 0.9370 (p0) cc_final: 0.8097 (p0) REVERT: O 25 THR cc_start: 0.9060 (m) cc_final: 0.8435 (p) REVERT: O 28 THR cc_start: 0.8361 (m) cc_final: 0.8027 (p) REVERT: O 33 LYS cc_start: 0.9118 (mttt) cc_final: 0.8341 (mtmm) REVERT: O 49 SER cc_start: 0.9251 (m) cc_final: 0.8680 (t) REVERT: O 59 ASN cc_start: 0.8339 (m-40) cc_final: 0.7832 (m110) REVERT: O 69 LYS cc_start: 0.8169 (tttm) cc_final: 0.7625 (ttmt) REVERT: P 22 ASN cc_start: 0.9233 (p0) cc_final: 0.8497 (p0) REVERT: Q 25 THR cc_start: 0.8841 (m) cc_final: 0.8524 (p) REVERT: Q 40 ASP cc_start: 0.8258 (t0) cc_final: 0.7698 (t0) REVERT: Q 49 SER cc_start: 0.9073 (m) cc_final: 0.8823 (t) REVERT: Q 54 TYR cc_start: 0.8751 (t80) cc_final: 0.8444 (t80) REVERT: Q 69 LYS cc_start: 0.8471 (tttm) cc_final: 0.7771 (tttt) REVERT: R 33 LYS cc_start: 0.9126 (ttmt) cc_final: 0.8874 (mtmt) REVERT: R 39 SER cc_start: 0.9315 (m) cc_final: 0.9111 (t) REVERT: R 51 LEU cc_start: 0.9171 (tp) cc_final: 0.8826 (tt) REVERT: R 69 LYS cc_start: 0.8122 (tttm) cc_final: 0.7277 (ttmt) REVERT: S 29 GLU cc_start: 0.7829 (tp30) cc_final: 0.7623 (tp30) REVERT: S 33 LYS cc_start: 0.8979 (mttt) cc_final: 0.8604 (mtmt) REVERT: S 39 SER cc_start: 0.9227 (m) cc_final: 0.8282 (m) REVERT: S 58 ARG cc_start: 0.9043 (mmt180) cc_final: 0.8747 (mmt90) REVERT: S 59 ASN cc_start: 0.8554 (m-40) cc_final: 0.8232 (m-40) REVERT: T 22 ASN cc_start: 0.8926 (p0) cc_final: 0.8340 (p0) REVERT: T 25 THR cc_start: 0.8542 (p) cc_final: 0.8224 (t) REVERT: T 39 SER cc_start: 0.9105 (m) cc_final: 0.8756 (p) REVERT: T 40 ASP cc_start: 0.8246 (t0) cc_final: 0.8042 (t0) REVERT: T 48 GLN cc_start: 0.9101 (tm-30) cc_final: 0.8565 (tm-30) REVERT: T 69 LYS cc_start: 0.7094 (tttm) cc_final: 0.6465 (tttt) outliers start: 47 outliers final: 42 residues processed: 587 average time/residue: 0.2257 time to fit residues: 189.0513 Evaluate side-chains 606 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 563 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 21 ASP Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 65 VAL Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 17 ASP Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 40 ASP Chi-restraints excluded: chain S residue 49 SER Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 65 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 105 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 112 optimal weight: 20.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 GLN M 77 GLN N 78 ASN ** O 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11837 Z= 0.276 Angle : 0.565 7.455 16112 Z= 0.292 Chirality : 0.040 0.151 1843 Planarity : 0.003 0.024 2109 Dihedral : 3.815 28.741 1596 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.35 % Allowed : 25.36 % Favored : 71.29 % 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: 2.18 (0.22), residues: 1444 helix: 2.04 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.10 (0.37), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 5 PHE 0.011 0.001 PHE N 68 TYR 0.028 0.002 TYR E 47 ARG 0.003 0.000 ARG D 58 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 565 time to evaluate : 1.352 Fit side-chains revert: symmetry clash REVERT: D 37 LYS cc_start: 0.8429 (ttmt) cc_final: 0.7634 (tptt) REVERT: D 77 GLN cc_start: 0.8792 (tp40) cc_final: 0.8566 (tp-100) REVERT: U 37 LYS cc_start: 0.8304 (ttmt) cc_final: 0.7269 (tptt) REVERT: U 66 LYS cc_start: 0.8508 (tptp) cc_final: 0.6796 (mttt) REVERT: U 77 GLN cc_start: 0.8969 (tp40) cc_final: 0.8766 (tp40) REVERT: V 37 LYS cc_start: 0.8783 (ttmt) cc_final: 0.7927 (tptt) REVERT: V 49 SER cc_start: 0.8654 (t) cc_final: 0.8207 (p) REVERT: V 53 GLU cc_start: 0.8073 (tp30) cc_final: 0.7767 (mm-30) REVERT: V 77 GLN cc_start: 0.8674 (tp40) cc_final: 0.7992 (tp-100) REVERT: E 15 LYS cc_start: 0.8958 (mmmm) cc_final: 0.8685 (mmmt) REVERT: E 21 ASP cc_start: 0.7876 (m-30) cc_final: 0.7559 (m-30) REVERT: E 22 ASN cc_start: 0.8380 (p0) cc_final: 0.7813 (p0) REVERT: E 23 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8166 (tp) REVERT: E 37 LYS cc_start: 0.8805 (ttmt) cc_final: 0.7489 (tptt) REVERT: E 53 GLU cc_start: 0.8657 (tp30) cc_final: 0.8169 (mm-30) REVERT: E 66 LYS cc_start: 0.8443 (tptp) cc_final: 0.7007 (mttt) REVERT: F 34 LEU cc_start: 0.9223 (tp) cc_final: 0.8950 (tt) REVERT: F 37 LYS cc_start: 0.8804 (ttmt) cc_final: 0.7970 (tptt) REVERT: F 39 SER cc_start: 0.8906 (m) cc_final: 0.8239 (t) REVERT: F 47 TYR cc_start: 0.9111 (t80) cc_final: 0.8554 (t80) REVERT: F 49 SER cc_start: 0.9294 (t) cc_final: 0.8877 (p) REVERT: F 51 LEU cc_start: 0.9208 (tp) cc_final: 0.8860 (tp) REVERT: F 53 GLU cc_start: 0.8270 (tp30) cc_final: 0.7876 (mm-30) REVERT: F 63 ASN cc_start: 0.9187 (m-40) cc_final: 0.8911 (m110) REVERT: F 66 LYS cc_start: 0.8612 (tptp) cc_final: 0.7515 (ttmt) REVERT: G 33 LYS cc_start: 0.9287 (mtpp) cc_final: 0.9081 (mtpp) REVERT: G 37 LYS cc_start: 0.8444 (ttmt) cc_final: 0.7119 (tptt) REVERT: G 66 LYS cc_start: 0.8893 (tppt) cc_final: 0.8664 (tppt) REVERT: G 69 LYS cc_start: 0.8615 (tttm) cc_final: 0.8337 (tttt) REVERT: H 28 THR cc_start: 0.9036 (m) cc_final: 0.8493 (p) REVERT: H 32 ASP cc_start: 0.7840 (m-30) cc_final: 0.7558 (m-30) REVERT: H 37 LYS cc_start: 0.8635 (ttmt) cc_final: 0.7063 (tptt) REVERT: H 47 TYR cc_start: 0.9151 (t80) cc_final: 0.7346 (t80) REVERT: I 37 LYS cc_start: 0.8724 (ttmt) cc_final: 0.7264 (tptp) REVERT: I 47 TYR cc_start: 0.9020 (t80) cc_final: 0.8768 (t80) REVERT: J 17 ASP cc_start: 0.7894 (m-30) cc_final: 0.7498 (m-30) REVERT: J 22 ASN cc_start: 0.8638 (p0) cc_final: 0.8017 (p0) REVERT: J 37 LYS cc_start: 0.8802 (ttmt) cc_final: 0.7260 (tptt) REVERT: J 47 TYR cc_start: 0.9273 (t80) cc_final: 0.8459 (t80) REVERT: K 37 LYS cc_start: 0.8998 (ttmt) cc_final: 0.7469 (tptt) REVERT: K 47 TYR cc_start: 0.9075 (t80) cc_final: 0.7806 (t80) REVERT: K 53 GLU cc_start: 0.7749 (tp30) cc_final: 0.7185 (mm-30) REVERT: L 26 GLN cc_start: 0.8840 (mt0) cc_final: 0.8126 (tt0) REVERT: L 28 THR cc_start: 0.8888 (m) cc_final: 0.8629 (p) REVERT: L 48 GLN cc_start: 0.8491 (tt0) cc_final: 0.7934 (tt0) REVERT: L 50 LYS cc_start: 0.8608 (mmtt) cc_final: 0.7879 (mmtp) REVERT: L 53 GLU cc_start: 0.8269 (tp30) cc_final: 0.7827 (tp30) REVERT: L 77 GLN cc_start: 0.8459 (tp-100) cc_final: 0.8176 (tp40) REVERT: M 17 ASP cc_start: 0.8123 (t0) cc_final: 0.7863 (m-30) REVERT: M 22 ASN cc_start: 0.8882 (p0) cc_final: 0.8517 (p0) REVERT: M 28 THR cc_start: 0.8821 (m) cc_final: 0.7941 (p) REVERT: M 31 LEU cc_start: 0.9290 (tp) cc_final: 0.8931 (tp) REVERT: M 32 ASP cc_start: 0.8286 (p0) cc_final: 0.7929 (p0) REVERT: M 47 TYR cc_start: 0.9182 (t80) cc_final: 0.8589 (t80) REVERT: M 66 LYS cc_start: 0.8602 (tptt) cc_final: 0.8080 (tmtt) REVERT: M 69 LYS cc_start: 0.8576 (tttp) cc_final: 0.7830 (ttpt) REVERT: N 23 LEU cc_start: 0.9044 (tp) cc_final: 0.8489 (tp) REVERT: N 24 GLN cc_start: 0.8625 (mp10) cc_final: 0.8078 (tp40) REVERT: N 49 SER cc_start: 0.9466 (m) cc_final: 0.9188 (t) REVERT: N 50 LYS cc_start: 0.8988 (mmtt) cc_final: 0.8692 (mmmt) REVERT: N 58 ARG cc_start: 0.8043 (mmt180) cc_final: 0.7656 (mmt180) REVERT: O 17 ASP cc_start: 0.7795 (m-30) cc_final: 0.7320 (t0) REVERT: O 22 ASN cc_start: 0.9345 (p0) cc_final: 0.8100 (p0) REVERT: O 25 THR cc_start: 0.9036 (m) cc_final: 0.8474 (p) REVERT: O 28 THR cc_start: 0.8375 (m) cc_final: 0.8072 (p) REVERT: O 33 LYS cc_start: 0.9103 (mttt) cc_final: 0.8369 (mtmm) REVERT: O 47 TYR cc_start: 0.8851 (t80) cc_final: 0.8544 (t80) REVERT: O 49 SER cc_start: 0.9260 (m) cc_final: 0.8657 (t) REVERT: O 59 ASN cc_start: 0.8271 (m-40) cc_final: 0.7708 (m110) REVERT: O 69 LYS cc_start: 0.8142 (tttm) cc_final: 0.7591 (ttmt) REVERT: P 22 ASN cc_start: 0.9262 (p0) cc_final: 0.8557 (p0) REVERT: P 57 TYR cc_start: 0.9204 (t80) cc_final: 0.8962 (t80) REVERT: Q 25 THR cc_start: 0.8813 (m) cc_final: 0.8529 (p) REVERT: Q 40 ASP cc_start: 0.8188 (t0) cc_final: 0.7649 (t0) REVERT: Q 49 SER cc_start: 0.9272 (m) cc_final: 0.8837 (t) REVERT: Q 54 TYR cc_start: 0.8668 (t80) cc_final: 0.8361 (t80) REVERT: Q 69 LYS cc_start: 0.8447 (tttm) cc_final: 0.7721 (tttt) REVERT: R 24 GLN cc_start: 0.8119 (pm20) cc_final: 0.7565 (pm20) REVERT: R 33 LYS cc_start: 0.9118 (ttmt) cc_final: 0.8888 (ttmt) REVERT: R 39 SER cc_start: 0.9482 (m) cc_final: 0.9241 (t) REVERT: R 51 LEU cc_start: 0.9136 (tp) cc_final: 0.8646 (tt) REVERT: R 69 LYS cc_start: 0.8104 (tttm) cc_final: 0.7245 (ttmt) REVERT: S 26 GLN cc_start: 0.9005 (tt0) cc_final: 0.8676 (tt0) REVERT: S 33 LYS cc_start: 0.8968 (mttt) cc_final: 0.8630 (mtmt) REVERT: S 39 SER cc_start: 0.9200 (m) cc_final: 0.8618 (p) REVERT: S 58 ARG cc_start: 0.9032 (mmt180) cc_final: 0.8736 (mmt90) REVERT: S 59 ASN cc_start: 0.8486 (m-40) cc_final: 0.8155 (m-40) REVERT: T 22 ASN cc_start: 0.8966 (p0) cc_final: 0.8562 (p0) REVERT: T 25 THR cc_start: 0.8493 (p) cc_final: 0.8227 (t) REVERT: T 39 SER cc_start: 0.9036 (m) cc_final: 0.8821 (p) REVERT: T 48 GLN cc_start: 0.9088 (tm-30) cc_final: 0.8545 (tm-30) REVERT: T 69 LYS cc_start: 0.7085 (tttm) cc_final: 0.6462 (tttt) outliers start: 42 outliers final: 41 residues processed: 577 average time/residue: 0.2065 time to fit residues: 169.1935 Evaluate side-chains 600 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 558 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain I residue 49 SER Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 77 GLN Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 21 ASP Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 33 LYS Chi-restraints excluded: chain P residue 65 VAL Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 40 ASP Chi-restraints excluded: chain S residue 49 SER Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 65 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 105 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 GLN N 78 ASN ** O 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.112704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.096015 restraints weight = 17692.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.099182 restraints weight = 9586.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.101301 restraints weight = 6290.348| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.200 11837 Z= 0.310 Angle : 0.828 59.200 16112 Z= 0.468 Chirality : 0.041 0.503 1843 Planarity : 0.003 0.023 2109 Dihedral : 3.804 28.723 1596 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.91 % Allowed : 25.44 % Favored : 70.65 % Cbeta Deviations : 0.07 % 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: 2.18 (0.22), residues: 1444 helix: 2.04 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.10 (0.37), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 5 PHE 0.010 0.001 PHE N 68 TYR 0.025 0.002 TYR E 47 ARG 0.003 0.000 ARG Q 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3066.13 seconds wall clock time: 55 minutes 55.26 seconds (3355.26 seconds total)