Starting phenix.real_space_refine on Tue Mar 19 14:32:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o4u_3746/03_2024/5o4u_3746.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o4u_3746/03_2024/5o4u_3746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o4u_3746/03_2024/5o4u_3746.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o4u_3746/03_2024/5o4u_3746.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o4u_3746/03_2024/5o4u_3746.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o4u_3746/03_2024/5o4u_3746.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 15600 2.51 5 N 4064 2.21 5 O 4848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24528 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "B" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "C" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "D" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "E" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "F" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "G" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "H" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "I" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "J" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "K" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "L" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "M" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "N" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "O" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Chain: "P" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1533 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 7, 'TRANS': 199} Time building chain proxies: 12.48, per 1000 atoms: 0.51 Number of scatterers: 24528 At special positions: 0 Unit cell: (112, 114.24, 198.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 4848 8.00 N 4064 7.00 C 15600 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: 10.74 Conformation dependent library (CDL) restraints added in 5.1 seconds 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5952 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 55 sheets defined 23.8% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'A' and resid 6 through 53 removed outlier: 3.734A pdb=" N GLY A 10 " --> pdb=" O ALA A 6 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A 11 " --> pdb=" O VAL A 7 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU A 12 " --> pdb=" O GLY A 8 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS A 39 " --> pdb=" O TYR A 35 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A 53 " --> pdb=" O GLN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 128 removed outlier: 3.770A pdb=" N TRP A 127 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 28 removed outlier: 3.940A pdb=" N VAL B 19 " --> pdb=" O PHE B 15 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 20 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 53 removed outlier: 3.656A pdb=" N TYR B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR B 47 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR B 48 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL B 51 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 53 " --> pdb=" O GLN B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'C' and resid 7 through 53 removed outlier: 3.808A pdb=" N THR C 11 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N LEU C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 20 " --> pdb=" O ILE C 16 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU C 29 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN C 31 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA C 42 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR C 48 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL C 51 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 53 " --> pdb=" O GLN C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 92 removed outlier: 3.771A pdb=" N THR C 92 " --> pdb=" O LEU C 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 53 removed outlier: 4.095A pdb=" N LEU D 12 " --> pdb=" O GLY D 8 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU D 20 " --> pdb=" O ILE D 16 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN D 37 " --> pdb=" O SER D 33 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLN D 38 " --> pdb=" O GLY D 34 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS D 39 " --> pdb=" O TYR D 35 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR D 47 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N THR D 48 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER D 53 " --> pdb=" O GLN D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 128 removed outlier: 3.834A pdb=" N TRP D 127 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN D 128 " --> pdb=" O THR D 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 124 through 128' Processing helix chain 'E' and resid 7 through 53 removed outlier: 3.586A pdb=" N THR E 11 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER E 53 " --> pdb=" O GLN E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 128 removed outlier: 3.674A pdb=" N TRP E 127 " --> pdb=" O SER E 124 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN E 128 " --> pdb=" O THR E 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 124 through 128' Processing helix chain 'F' and resid 9 through 25 removed outlier: 3.682A pdb=" N VAL F 19 " --> pdb=" O PHE F 15 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL F 24 " --> pdb=" O LEU F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 38 removed outlier: 3.937A pdb=" N GLN F 38 " --> pdb=" O GLY F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 53 removed outlier: 3.942A pdb=" N THR F 47 " --> pdb=" O THR F 43 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR F 48 " --> pdb=" O GLY F 44 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN F 49 " --> pdb=" O ARG F 45 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL F 51 " --> pdb=" O THR F 47 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER F 53 " --> pdb=" O GLN F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 128 removed outlier: 3.592A pdb=" N TRP F 127 " --> pdb=" O SER F 124 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN F 128 " --> pdb=" O THR F 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 124 through 128' Processing helix chain 'G' and resid 7 through 25 removed outlier: 3.616A pdb=" N LEU G 20 " --> pdb=" O ILE G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 52 removed outlier: 3.634A pdb=" N LEU G 36 " --> pdb=" O THR G 32 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN G 37 " --> pdb=" O SER G 33 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA G 42 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG G 45 " --> pdb=" O GLN G 41 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N THR G 48 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL G 51 " --> pdb=" O THR G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 128 removed outlier: 3.684A pdb=" N TRP G 127 " --> pdb=" O SER G 124 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN G 128 " --> pdb=" O THR G 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 124 through 128' Processing helix chain 'H' and resid 9 through 25 removed outlier: 3.759A pdb=" N VAL H 14 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE H 15 " --> pdb=" O THR H 11 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL H 19 " --> pdb=" O PHE H 15 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU H 20 " --> pdb=" O ILE H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 53 removed outlier: 3.583A pdb=" N TYR H 35 " --> pdb=" O GLN H 31 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU H 36 " --> pdb=" O THR H 32 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA H 42 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR H 47 " --> pdb=" O THR H 43 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL H 51 " --> pdb=" O THR H 47 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER H 53 " --> pdb=" O GLN H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 128 removed outlier: 3.819A pdb=" N TRP H 127 " --> pdb=" O SER H 124 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN H 128 " --> pdb=" O THR H 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 124 through 128' Processing helix chain 'I' and resid 7 through 45 removed outlier: 3.560A pdb=" N THR I 11 " --> pdb=" O VAL I 7 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LEU I 12 " --> pdb=" O GLY I 8 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE I 13 " --> pdb=" O ILE I 9 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL I 19 " --> pdb=" O PHE I 15 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU I 20 " --> pdb=" O ILE I 16 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU I 29 " --> pdb=" O ALA I 25 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER I 33 " --> pdb=" O LEU I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 53 removed outlier: 4.223A pdb=" N VAL I 51 " --> pdb=" O THR I 47 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER I 53 " --> pdb=" O GLN I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 128 removed outlier: 3.705A pdb=" N TRP I 127 " --> pdb=" O SER I 124 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN I 128 " --> pdb=" O THR I 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 124 through 128' Processing helix chain 'J' and resid 7 through 27 removed outlier: 3.788A pdb=" N ILE J 16 " --> pdb=" O LEU J 12 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA J 17 " --> pdb=" O ILE J 13 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET J 18 " --> pdb=" O VAL J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 53 removed outlier: 3.510A pdb=" N TYR J 35 " --> pdb=" O GLN J 31 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU J 36 " --> pdb=" O THR J 32 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN J 37 " --> pdb=" O SER J 33 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA J 42 " --> pdb=" O GLN J 38 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR J 43 " --> pdb=" O LYS J 39 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU J 46 " --> pdb=" O ALA J 42 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR J 48 " --> pdb=" O GLY J 44 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER J 53 " --> pdb=" O GLN J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 128 removed outlier: 3.929A pdb=" N TRP J 127 " --> pdb=" O SER J 124 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN J 128 " --> pdb=" O THR J 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 124 through 128' Processing helix chain 'K' and resid 9 through 53 removed outlier: 3.569A pdb=" N ILE K 13 " --> pdb=" O ILE K 9 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE K 15 " --> pdb=" O THR K 11 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER K 33 " --> pdb=" O LEU K 29 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER K 53 " --> pdb=" O GLN K 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 41 removed outlier: 3.583A pdb=" N LEU L 20 " --> pdb=" O ILE L 16 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN L 38 " --> pdb=" O GLY L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 53 removed outlier: 3.570A pdb=" N ARG L 45 " --> pdb=" O GLN L 41 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU L 46 " --> pdb=" O ALA L 42 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR L 47 " --> pdb=" O THR L 43 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR L 48 " --> pdb=" O GLY L 44 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL L 51 " --> pdb=" O THR L 47 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER L 53 " --> pdb=" O GLN L 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 28 removed outlier: 3.624A pdb=" N VAL M 24 " --> pdb=" O LEU M 20 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL M 28 " --> pdb=" O VAL M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 30 through 53 removed outlier: 3.576A pdb=" N LEU M 36 " --> pdb=" O THR M 32 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN M 37 " --> pdb=" O SER M 33 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLN M 38 " --> pdb=" O GLY M 34 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS M 39 " --> pdb=" O TYR M 35 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA M 42 " --> pdb=" O GLN M 38 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG M 45 " --> pdb=" O GLN M 41 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR M 48 " --> pdb=" O GLY M 44 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL M 51 " --> pdb=" O THR M 47 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER M 53 " --> pdb=" O GLN M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 124 through 128 removed outlier: 3.839A pdb=" N TRP M 127 " --> pdb=" O SER M 124 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASN M 128 " --> pdb=" O THR M 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 124 through 128' Processing helix chain 'N' and resid 7 through 30 removed outlier: 3.702A pdb=" N THR N 11 " --> pdb=" O VAL N 7 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU N 12 " --> pdb=" O GLY N 8 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE N 13 " --> pdb=" O ILE N 9 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL N 28 " --> pdb=" O VAL N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 53 removed outlier: 4.038A pdb=" N GLN N 37 " --> pdb=" O SER N 33 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLN N 38 " --> pdb=" O GLY N 34 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS N 39 " --> pdb=" O TYR N 35 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER N 40 " --> pdb=" O LEU N 36 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA N 42 " --> pdb=" O GLN N 38 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR N 43 " --> pdb=" O LYS N 39 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG N 45 " --> pdb=" O GLN N 41 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR N 48 " --> pdb=" O GLY N 44 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL N 51 " --> pdb=" O THR N 47 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER N 53 " --> pdb=" O GLN N 49 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 28 removed outlier: 4.557A pdb=" N LEU O 12 " --> pdb=" O GLY O 8 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL O 28 " --> pdb=" O VAL O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 50 removed outlier: 3.724A pdb=" N SER O 33 " --> pdb=" O LEU O 29 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA O 42 " --> pdb=" O GLN O 38 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR O 43 " --> pdb=" O LYS O 39 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR O 47 " --> pdb=" O THR O 43 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N THR O 48 " --> pdb=" O GLY O 44 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN O 49 " --> pdb=" O ARG O 45 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 53 removed outlier: 3.501A pdb=" N ILE P 16 " --> pdb=" O LEU P 12 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA P 42 " --> pdb=" O GLN P 38 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU P 46 " --> pdb=" O ALA P 42 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N THR P 48 " --> pdb=" O GLY P 44 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL P 51 " --> pdb=" O THR P 47 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER P 53 " --> pdb=" O GLN P 49 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 57 removed outlier: 3.540A pdb=" N SER A 79 " --> pdb=" O LYS A 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 96 Processing sheet with id=AA3, first strand: chain 'A' and resid 106 through 107 removed outlier: 7.188A pdb=" N LYS A 106 " --> pdb=" O PHE A 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 147 removed outlier: 3.614A pdb=" N ASP A 147 " --> pdb=" O TYR A 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 55 through 61 removed outlier: 5.272A pdb=" N VAL B 57 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N SER B 79 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N SER B 59 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR B 77 " --> pdb=" O SER B 59 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS B 164 " --> pdb=" O ASN B 133 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASN B 133 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LYS B 106 " --> pdb=" O PHE B 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 55 through 61 removed outlier: 5.272A pdb=" N VAL B 57 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N SER B 79 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N SER B 59 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR B 77 " --> pdb=" O SER B 59 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 158 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 139 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 87 through 88 removed outlier: 3.634A pdb=" N ILE B 87 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR B 150 " --> pdb=" O ASP B 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 94 through 96 Processing sheet with id=AA9, first strand: chain 'C' and resid 55 through 57 removed outlier: 3.656A pdb=" N SER C 79 " --> pdb=" O LYS C 56 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE C 158 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU C 139 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LYS C 164 " --> pdb=" O ASN C 133 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN C 133 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LYS C 106 " --> pdb=" O PHE C 134 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N ILE C 136 " --> pdb=" O LYS C 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 93 through 96 removed outlier: 3.673A pdb=" N ARG C 93 " --> pdb=" O ILE C 187 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE C 182 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE C 196 " --> pdb=" O GLY C 184 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 146 through 147 removed outlier: 3.510A pdb=" N ASP C 147 " --> pdb=" O TYR C 150 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 55 through 61 removed outlier: 3.543A pdb=" N SER D 79 " --> pdb=" O LYS D 56 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR D 77 " --> pdb=" O LEU D 58 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N VAL D 60 " --> pdb=" O ALA D 75 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALA D 75 " --> pdb=" O VAL D 60 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE D 158 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 139 " --> pdb=" O ILE D 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 87 through 88 removed outlier: 3.996A pdb=" N ILE D 87 " --> pdb=" O LEU D 153 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 92 through 96 Processing sheet with id=AB6, first strand: chain 'D' and resid 106 through 107 removed outlier: 6.985A pdb=" N LYS D 106 " --> pdb=" O PHE D 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 55 through 61 removed outlier: 3.941A pdb=" N TYR E 77 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N VAL E 60 " --> pdb=" O ALA E 75 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ALA E 75 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LYS E 164 " --> pdb=" O ASN E 133 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN E 133 " --> pdb=" O LYS E 164 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LYS E 106 " --> pdb=" O PHE E 134 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N ILE E 136 " --> pdb=" O LYS E 106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 87 through 88 removed outlier: 3.903A pdb=" N ILE E 87 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU E 153 " --> pdb=" O ILE E 87 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR E 150 " --> pdb=" O ASP E 147 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP E 147 " --> pdb=" O TYR E 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 93 through 96 removed outlier: 3.569A pdb=" N ARG E 93 " --> pdb=" O ILE E 187 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 55 through 61 removed outlier: 5.298A pdb=" N VAL F 57 " --> pdb=" O SER F 79 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N SER F 79 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N SER F 59 " --> pdb=" O TYR F 77 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N TYR F 77 " --> pdb=" O SER F 59 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 87 through 88 removed outlier: 3.710A pdb=" N TYR F 150 " --> pdb=" O ASP F 147 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP F 147 " --> pdb=" O TYR F 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 93 through 97 Processing sheet with id=AC4, first strand: chain 'F' and resid 106 through 107 removed outlier: 7.010A pdb=" N LYS F 106 " --> pdb=" O PHE F 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'G' and resid 55 through 61 removed outlier: 5.243A pdb=" N VAL G 57 " --> pdb=" O SER G 79 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N SER G 79 " --> pdb=" O VAL G 57 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N SER G 59 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR G 77 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYS G 164 " --> pdb=" O ASN G 133 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN G 133 " --> pdb=" O LYS G 164 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N PHE G 134 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N LYS G 106 " --> pdb=" O PHE G 134 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ILE G 136 " --> pdb=" O LYS G 106 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG G 93 " --> pdb=" O ILE G 187 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE G 187 " --> pdb=" O ARG G 93 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 87 through 88 removed outlier: 3.520A pdb=" N ILE G 87 " --> pdb=" O LEU G 153 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 55 through 57 removed outlier: 7.310A pdb=" N LYS H 106 " --> pdb=" O PHE H 134 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N ILE H 136 " --> pdb=" O LYS H 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 87 through 88 removed outlier: 3.532A pdb=" N ILE H 87 " --> pdb=" O LEU H 153 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP H 147 " --> pdb=" O TYR H 150 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 93 through 96 removed outlier: 3.535A pdb=" N ARG H 93 " --> pdb=" O ILE H 187 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 55 through 57 removed outlier: 3.525A pdb=" N SER I 79 " --> pdb=" O LYS I 56 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 87 through 88 removed outlier: 3.585A pdb=" N ILE I 87 " --> pdb=" O LEU I 153 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 93 through 96 removed outlier: 3.801A pdb=" N ARG I 93 " --> pdb=" O ILE I 187 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE I 187 " --> pdb=" O ARG I 93 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 55 through 61 removed outlier: 3.551A pdb=" N LEU J 58 " --> pdb=" O TYR J 77 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR J 77 " --> pdb=" O LEU J 58 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL J 60 " --> pdb=" O ALA J 75 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA J 75 " --> pdb=" O VAL J 60 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 87 through 88 Processing sheet with id=AD6, first strand: chain 'J' and resid 133 through 134 removed outlier: 7.522A pdb=" N PHE J 134 " --> pdb=" O VAL J 104 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LYS J 106 " --> pdb=" O PHE J 134 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL J 94 " --> pdb=" O LEU J 105 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG J 93 " --> pdb=" O ILE J 187 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE J 187 " --> pdb=" O ARG J 93 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE J 182 " --> pdb=" O PHE J 198 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 55 through 61 removed outlier: 3.766A pdb=" N LEU K 58 " --> pdb=" O TYR K 77 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR K 77 " --> pdb=" O LEU K 58 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL K 60 " --> pdb=" O ALA K 75 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA K 75 " --> pdb=" O VAL K 60 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 87 through 88 removed outlier: 3.667A pdb=" N ASP K 147 " --> pdb=" O TYR K 150 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 93 through 96 removed outlier: 3.744A pdb=" N ILE K 187 " --> pdb=" O ARG K 93 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 106 through 107 removed outlier: 6.962A pdb=" N LYS K 106 " --> pdb=" O PHE K 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'L' and resid 55 through 57 removed outlier: 4.912A pdb=" N LYS L 164 " --> pdb=" O ASN L 133 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASN L 133 " --> pdb=" O LYS L 164 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LYS L 106 " --> pdb=" O PHE L 134 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N ILE L 136 " --> pdb=" O LYS L 106 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 87 through 88 removed outlier: 3.739A pdb=" N ILE L 87 " --> pdb=" O LEU L 153 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 93 through 96 removed outlier: 3.575A pdb=" N ARG L 93 " --> pdb=" O ILE L 187 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE L 187 " --> pdb=" O ARG L 93 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 55 through 57 removed outlier: 3.542A pdb=" N SER M 79 " --> pdb=" O LYS M 56 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 87 through 88 removed outlier: 4.015A pdb=" N ILE M 87 " --> pdb=" O LEU M 153 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 93 through 96 removed outlier: 3.816A pdb=" N ARG M 93 " --> pdb=" O ILE M 187 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE M 187 " --> pdb=" O ARG M 93 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 55 through 57 Processing sheet with id=AE9, first strand: chain 'N' and resid 87 through 88 removed outlier: 3.866A pdb=" N ILE N 87 " --> pdb=" O LEU N 153 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 93 through 96 removed outlier: 3.708A pdb=" N ARG N 93 " --> pdb=" O ILE N 187 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 106 through 107 removed outlier: 7.156A pdb=" N LYS N 106 " --> pdb=" O PHE N 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'O' and resid 55 through 61 removed outlier: 5.117A pdb=" N VAL O 57 " --> pdb=" O SER O 79 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N SER O 79 " --> pdb=" O VAL O 57 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N SER O 59 " --> pdb=" O TYR O 77 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TYR O 77 " --> pdb=" O SER O 59 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE O 158 " --> pdb=" O LEU O 139 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU O 139 " --> pdb=" O ILE O 158 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 93 through 96 removed outlier: 3.513A pdb=" N ARG O 93 " --> pdb=" O ILE O 187 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE O 187 " --> pdb=" O ARG O 93 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 106 through 107 removed outlier: 7.113A pdb=" N LYS O 106 " --> pdb=" O PHE O 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'O' and resid 146 through 147 removed outlier: 3.582A pdb=" N ASP O 147 " --> pdb=" O TYR O 150 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'P' and resid 55 through 56 Processing sheet with id=AF8, first strand: chain 'P' and resid 87 through 88 removed outlier: 3.606A pdb=" N ILE P 87 " --> pdb=" O LEU P 153 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P' and resid 93 through 96 removed outlier: 3.683A pdb=" N ARG P 93 " --> pdb=" O ILE P 187 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'P' and resid 106 through 107 removed outlier: 6.888A pdb=" N LYS P 106 " --> pdb=" O PHE P 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 801 hydrogen bonds defined for protein. 2244 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: 7.66 Time building geometry restraints manager: 11.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6332 1.33 - 1.45: 4024 1.45 - 1.57: 14492 1.57 - 1.69: 0 1.69 - 1.80: 32 Bond restraints: 24880 Sorted by residual: bond pdb=" N VAL L 7 " pdb=" CA VAL L 7 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.22e-02 6.72e+03 6.73e+00 bond pdb=" CG1 ILE D 182 " pdb=" CD1 ILE D 182 " ideal model delta sigma weight residual 1.513 1.413 0.100 3.90e-02 6.57e+02 6.52e+00 bond pdb=" CA VAL J 7 " pdb=" C VAL J 7 " ideal model delta sigma weight residual 1.523 1.555 -0.032 1.27e-02 6.20e+03 6.17e+00 bond pdb=" N VAL J 7 " pdb=" CA VAL J 7 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.19e-02 7.06e+03 6.03e+00 bond pdb=" CA VAL L 7 " pdb=" C VAL L 7 " ideal model delta sigma weight residual 1.526 1.557 -0.031 1.32e-02 5.74e+03 5.35e+00 ... (remaining 24875 not shown) Histogram of bond angle deviations from ideal: 99.15 - 106.11: 472 106.11 - 113.07: 13809 113.07 - 120.04: 8303 120.04 - 127.00: 11131 127.00 - 133.96: 189 Bond angle restraints: 33904 Sorted by residual: angle pdb=" N VAL J 7 " pdb=" CA VAL J 7 " pdb=" C VAL J 7 " ideal model delta sigma weight residual 110.62 125.95 -15.33 1.02e+00 9.61e-01 2.26e+02 angle pdb=" N VAL G 7 " pdb=" CA VAL G 7 " pdb=" C VAL G 7 " ideal model delta sigma weight residual 110.62 121.27 -10.65 1.02e+00 9.61e-01 1.09e+02 angle pdb=" N VAL M 7 " pdb=" CA VAL M 7 " pdb=" C VAL M 7 " ideal model delta sigma weight residual 110.62 119.37 -8.75 1.02e+00 9.61e-01 7.37e+01 angle pdb=" N VAL B 7 " pdb=" CA VAL B 7 " pdb=" C VAL B 7 " ideal model delta sigma weight residual 113.43 106.79 6.64 1.09e+00 8.42e-01 3.71e+01 angle pdb=" N SER H 40 " pdb=" CA SER H 40 " pdb=" C SER H 40 " ideal model delta sigma weight residual 111.28 117.34 -6.06 1.09e+00 8.42e-01 3.09e+01 ... (remaining 33899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.93: 13346 13.93 - 27.86: 1099 27.86 - 41.78: 272 41.78 - 55.71: 50 55.71 - 69.64: 1 Dihedral angle restraints: 14768 sinusoidal: 5408 harmonic: 9360 Sorted by residual: dihedral pdb=" CA VAL D 208 " pdb=" C VAL D 208 " pdb=" N ILE D 209 " pdb=" CA ILE D 209 " ideal model delta harmonic sigma weight residual -180.00 -146.49 -33.51 0 5.00e+00 4.00e-02 4.49e+01 dihedral pdb=" CA VAL G 208 " pdb=" C VAL G 208 " pdb=" N ILE G 209 " pdb=" CA ILE G 209 " ideal model delta harmonic sigma weight residual 180.00 -148.49 -31.51 0 5.00e+00 4.00e-02 3.97e+01 dihedral pdb=" CA GLU L 207 " pdb=" C GLU L 207 " pdb=" N VAL L 208 " pdb=" CA VAL L 208 " ideal model delta harmonic sigma weight residual -180.00 -148.67 -31.33 0 5.00e+00 4.00e-02 3.93e+01 ... (remaining 14765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 3649 0.103 - 0.206: 451 0.206 - 0.309: 71 0.309 - 0.412: 20 0.412 - 0.515: 17 Chirality restraints: 4208 Sorted by residual: chirality pdb=" CB ILE B 182 " pdb=" CA ILE B 182 " pdb=" CG1 ILE B 182 " pdb=" CG2 ILE B 182 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.52 2.00e-01 2.50e+01 6.64e+00 chirality pdb=" CB ILE E 182 " pdb=" CA ILE E 182 " pdb=" CG1 ILE E 182 " pdb=" CG2 ILE E 182 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.80e+00 chirality pdb=" CB ILE M 182 " pdb=" CA ILE M 182 " pdb=" CG1 ILE M 182 " pdb=" CG2 ILE M 182 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.67e+00 ... (remaining 4205 not shown) Planarity restraints: 4320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 200 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO C 201 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO C 201 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 201 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 22 " -0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C ALA D 22 " 0.059 2.00e-02 2.50e+03 pdb=" O ALA D 22 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA D 23 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR J 200 " 0.052 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PRO J 201 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO J 201 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO J 201 " 0.042 5.00e-02 4.00e+02 ... (remaining 4317 not shown) Histogram of nonbonded interaction distances: 0.59 - 1.45: 5 1.45 - 2.31: 51 2.31 - 3.17: 21768 3.17 - 4.04: 61959 4.04 - 4.90: 109146 Warning: very small nonbonded interaction distances. Nonbonded interactions: 192929 Sorted by model distance: nonbonded pdb=" CA GLY K 34 " pdb=" NE2 GLN K 37 " model vdw 0.586 3.520 nonbonded pdb=" O GLY K 34 " pdb=" OE1 GLN K 37 " model vdw 0.830 3.040 nonbonded pdb=" C GLY K 34 " pdb=" NE2 GLN K 37 " model vdw 1.185 3.350 nonbonded pdb=" NZ LYS B 39 " pdb=" CG2 THR B 43 " model vdw 1.227 3.540 nonbonded pdb=" O GLY K 34 " pdb=" CD GLN K 37 " model vdw 1.291 3.270 ... (remaining 192924 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 0.350 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: 0.020 Extract box with map and model: 3.300 Check model and map are aligned: 0.370 Set scattering table: 0.330 Process input model: 65.760 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.180 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 24880 Z= 0.455 Angle : 1.258 15.334 33904 Z= 0.723 Chirality : 0.080 0.515 4208 Planarity : 0.008 0.102 4320 Dihedral : 11.284 69.640 8816 Min Nonbonded Distance : 0.586 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.26 % Favored : 82.74 % Rotamer: Outliers : 1.75 % Allowed : 6.55 % Favored : 91.70 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.67 (0.12), residues: 3280 helix: -1.82 (0.20), residues: 592 sheet: -3.91 (0.14), residues: 752 loop : -3.29 (0.12), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.007 TRP J 127 HIS 0.010 0.003 HIS F 113 PHE 0.033 0.005 PHE E 121 TYR 0.030 0.003 TYR D 112 ARG 0.006 0.001 ARG F 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1152 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 1105 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 THR cc_start: 0.8123 (p) cc_final: 0.7586 (m) REVERT: A 105 LEU cc_start: 0.9265 (mm) cc_final: 0.8871 (mm) REVERT: A 110 THR cc_start: 0.7053 (p) cc_final: 0.6719 (t) REVERT: A 155 LYS cc_start: 0.7322 (ptpt) cc_final: 0.7018 (tptt) REVERT: A 200 THR cc_start: 0.8248 (m) cc_final: 0.7739 (p) REVERT: B 49 GLN cc_start: 0.6468 (mt0) cc_final: 0.6088 (mm-40) REVERT: B 204 TYR cc_start: 0.6842 (p90) cc_final: 0.6589 (p90) REVERT: C 46 GLU cc_start: 0.6349 (mt-10) cc_final: 0.6109 (mt-10) REVERT: C 60 VAL cc_start: 0.9106 (t) cc_final: 0.8850 (m) REVERT: C 150 TYR cc_start: 0.7934 (m-80) cc_final: 0.7566 (m-10) REVERT: D 31 GLN cc_start: 0.6084 (tt0) cc_final: 0.5685 (tt0) REVERT: D 105 LEU cc_start: 0.8285 (mm) cc_final: 0.7982 (mm) REVERT: D 172 PHE cc_start: 0.8555 (m-10) cc_final: 0.8157 (m-10) REVERT: D 177 PRO cc_start: 0.8999 (Cg_endo) cc_final: 0.8781 (Cg_exo) REVERT: D 200 THR cc_start: 0.8561 (m) cc_final: 0.7875 (p) REVERT: E 105 LEU cc_start: 0.8017 (mm) cc_final: 0.7521 (mm) REVERT: E 110 THR cc_start: 0.8051 (p) cc_final: 0.7429 (t) REVERT: E 150 TYR cc_start: 0.7200 (m-80) cc_final: 0.6904 (m-80) REVERT: E 176 ILE cc_start: 0.8307 (pt) cc_final: 0.7802 (mt) REVERT: E 185 LYS cc_start: 0.8121 (ptmt) cc_final: 0.7838 (pttp) REVERT: E 200 THR cc_start: 0.8555 (m) cc_final: 0.7876 (p) REVERT: F 112 TYR cc_start: 0.7066 (m-80) cc_final: 0.6830 (m-10) REVERT: G 158 ILE cc_start: 0.8934 (mt) cc_final: 0.8656 (mm) REVERT: H 55 ILE cc_start: 0.8683 (mt) cc_final: 0.8406 (mm) REVERT: H 93 ARG cc_start: 0.7584 (mmt-90) cc_final: 0.5988 (mtt180) REVERT: H 139 LEU cc_start: 0.8440 (pp) cc_final: 0.8177 (pp) REVERT: H 158 ILE cc_start: 0.8296 (mt) cc_final: 0.7912 (tt) REVERT: H 185 LYS cc_start: 0.8513 (ptmt) cc_final: 0.8153 (pttm) REVERT: I 64 THR cc_start: 0.6745 (t) cc_final: 0.6512 (t) REVERT: I 66 SER cc_start: 0.7580 (m) cc_final: 0.6804 (p) REVERT: I 110 THR cc_start: 0.6804 (p) cc_final: 0.6528 (t) REVERT: I 158 ILE cc_start: 0.8710 (mt) cc_final: 0.8074 (tp) REVERT: I 200 THR cc_start: 0.8414 (m) cc_final: 0.8189 (t) REVERT: I 204 TYR cc_start: 0.6419 (p90) cc_final: 0.5958 (p90) REVERT: J 16 ILE cc_start: 0.9165 (mt) cc_final: 0.8949 (mt) REVERT: J 18 MET cc_start: 0.5327 (ttt) cc_final: 0.4477 (ptp) REVERT: J 35 TYR cc_start: 0.6011 (t80) cc_final: 0.5578 (t80) REVERT: J 56 LYS cc_start: 0.7885 (pttp) cc_final: 0.7670 (ptpp) REVERT: J 202 SER cc_start: 0.7587 (t) cc_final: 0.7349 (m) REVERT: K 56 LYS cc_start: 0.8535 (pttp) cc_final: 0.8277 (pttm) REVERT: K 210 GLU cc_start: 0.8515 (pm20) cc_final: 0.7987 (pm20) REVERT: L 35 TYR cc_start: 0.6806 (t80) cc_final: 0.6011 (t80) REVERT: L 36 LEU cc_start: 0.7463 (mt) cc_final: 0.6914 (mt) REVERT: L 56 LYS cc_start: 0.8238 (pttp) cc_final: 0.7973 (pttm) REVERT: L 183 THR cc_start: 0.8156 (m) cc_final: 0.7781 (p) REVERT: L 202 SER cc_start: 0.5846 (p) cc_final: 0.5175 (p) REVERT: M 73 LYS cc_start: 0.8131 (mtmt) cc_final: 0.7904 (mtmm) REVERT: M 92 THR cc_start: 0.8435 (m) cc_final: 0.8167 (m) REVERT: M 155 LYS cc_start: 0.6981 (ptpt) cc_final: 0.6724 (ptmt) REVERT: M 179 ARG cc_start: 0.6798 (ttp-110) cc_final: 0.6333 (ptp90) REVERT: M 183 THR cc_start: 0.8364 (m) cc_final: 0.8081 (m) REVERT: M 200 THR cc_start: 0.8033 (m) cc_final: 0.7708 (p) REVERT: N 31 GLN cc_start: 0.6073 (tt0) cc_final: 0.5840 (tt0) REVERT: N 55 ILE cc_start: 0.8436 (mt) cc_final: 0.8100 (mm) REVERT: N 73 LYS cc_start: 0.8185 (mtmt) cc_final: 0.7720 (mtmm) REVERT: N 155 LYS cc_start: 0.6859 (ptpt) cc_final: 0.6053 (tmtt) REVERT: O 9 ILE cc_start: 0.5793 (mp) cc_final: 0.5474 (mp) REVERT: O 160 VAL cc_start: 0.8578 (t) cc_final: 0.8221 (t) REVERT: O 199 THR cc_start: 0.7726 (p) cc_final: 0.7447 (t) REVERT: P 18 MET cc_start: 0.5297 (ttt) cc_final: 0.4562 (ttm) REVERT: P 66 SER cc_start: 0.7391 (m) cc_final: 0.6669 (t) REVERT: P 140 GLN cc_start: 0.6617 (tt0) cc_final: 0.5801 (mm110) REVERT: P 172 PHE cc_start: 0.7058 (m-10) cc_final: 0.6160 (m-80) outliers start: 47 outliers final: 25 residues processed: 1126 average time/residue: 0.3312 time to fit residues: 593.8837 Evaluate side-chains 857 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 832 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 270 optimal weight: 5.9990 chunk 242 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 163 optimal weight: 0.8980 chunk 129 optimal weight: 7.9990 chunk 250 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 152 optimal weight: 0.6980 chunk 186 optimal weight: 6.9990 chunk 290 optimal weight: 3.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 GLN ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN D 91 ASN D 133 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 ASN E 133 ASN E 140 GLN E 144 ASN ** F 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN I 102 GLN ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 140 GLN J 31 GLN J 41 GLN K 81 ASN K 91 ASN ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 140 GLN K 149 ASN ** L 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 140 GLN M 31 GLN ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 131 ASN M 133 ASN M 149 ASN ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN N 91 ASN N 149 ASN ** O 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 102 GLN ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 149 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24880 Z= 0.285 Angle : 0.773 9.455 33904 Z= 0.411 Chirality : 0.054 0.419 4208 Planarity : 0.006 0.074 4320 Dihedral : 7.623 29.140 3456 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.82 % Favored : 84.18 % Rotamer: Outliers : 0.52 % Allowed : 7.51 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.13), residues: 3280 helix: -0.89 (0.18), residues: 704 sheet: -3.16 (0.17), residues: 576 loop : -3.49 (0.12), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP J 127 HIS 0.007 0.002 HIS E 113 PHE 0.032 0.003 PHE C 198 TYR 0.015 0.002 TYR M 70 ARG 0.003 0.001 ARG D 179 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 945 time to evaluate : 2.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.9312 (mm) cc_final: 0.9027 (mm) REVERT: A 131 ASN cc_start: 0.6950 (m-40) cc_final: 0.6738 (m-40) REVERT: A 153 LEU cc_start: 0.7876 (mt) cc_final: 0.7655 (mt) REVERT: A 155 LYS cc_start: 0.7524 (ptpt) cc_final: 0.6710 (tptt) REVERT: A 200 THR cc_start: 0.8257 (m) cc_final: 0.7794 (p) REVERT: B 49 GLN cc_start: 0.6720 (mt0) cc_final: 0.6293 (mm-40) REVERT: B 73 LYS cc_start: 0.7998 (tttt) cc_final: 0.7228 (tttt) REVERT: B 97 SER cc_start: 0.6895 (p) cc_final: 0.6666 (p) REVERT: B 182 ILE cc_start: 0.9459 (tp) cc_final: 0.8911 (tt) REVERT: C 105 LEU cc_start: 0.8757 (mm) cc_final: 0.8435 (mm) REVERT: C 178 PRO cc_start: 0.8210 (Cg_exo) cc_final: 0.7745 (Cg_endo) REVERT: D 105 LEU cc_start: 0.8176 (mm) cc_final: 0.7900 (mm) REVERT: D 108 GLU cc_start: 0.5766 (tp30) cc_final: 0.5497 (tp30) REVERT: D 132 THR cc_start: 0.8715 (m) cc_final: 0.8324 (m) REVERT: D 133 ASN cc_start: 0.8489 (m-40) cc_final: 0.7488 (m-40) REVERT: D 172 PHE cc_start: 0.8706 (m-10) cc_final: 0.8293 (m-80) REVERT: D 200 THR cc_start: 0.8395 (m) cc_final: 0.7650 (p) REVERT: E 105 LEU cc_start: 0.7927 (mm) cc_final: 0.7092 (mm) REVERT: E 110 THR cc_start: 0.8085 (p) cc_final: 0.7416 (t) REVERT: E 143 ASP cc_start: 0.7961 (t0) cc_final: 0.7668 (t0) REVERT: E 176 ILE cc_start: 0.8205 (pt) cc_final: 0.7909 (mt) REVERT: E 185 LYS cc_start: 0.8136 (ptmt) cc_final: 0.7515 (pttm) REVERT: E 186 VAL cc_start: 0.9156 (t) cc_final: 0.8609 (m) REVERT: E 200 THR cc_start: 0.8574 (m) cc_final: 0.7975 (p) REVERT: F 112 TYR cc_start: 0.7249 (m-80) cc_final: 0.6965 (m-80) REVERT: G 158 ILE cc_start: 0.8847 (mt) cc_final: 0.8624 (mm) REVERT: H 127 TRP cc_start: 0.8418 (m100) cc_final: 0.8087 (m100) REVERT: H 139 LEU cc_start: 0.8274 (pp) cc_final: 0.8016 (pp) REVERT: H 185 LYS cc_start: 0.8453 (ptmt) cc_final: 0.8077 (pttm) REVERT: H 200 THR cc_start: 0.8590 (m) cc_final: 0.8020 (p) REVERT: I 66 SER cc_start: 0.7235 (m) cc_final: 0.6701 (p) REVERT: I 112 TYR cc_start: 0.7872 (m-80) cc_final: 0.7141 (m-80) REVERT: I 158 ILE cc_start: 0.8717 (mt) cc_final: 0.8108 (tp) REVERT: J 18 MET cc_start: 0.5226 (ttt) cc_final: 0.4265 (ptp) REVERT: J 35 TYR cc_start: 0.5899 (t80) cc_final: 0.5330 (t80) REVERT: J 36 LEU cc_start: 0.7370 (mm) cc_final: 0.7161 (mm) REVERT: J 93 ARG cc_start: 0.8122 (mpt90) cc_final: 0.6504 (mmt180) REVERT: J 127 TRP cc_start: 0.6850 (m100) cc_final: 0.6553 (m100) REVERT: J 161 ILE cc_start: 0.8420 (mt) cc_final: 0.7995 (mp) REVERT: K 56 LYS cc_start: 0.8556 (pttp) cc_final: 0.8303 (pttt) REVERT: L 28 VAL cc_start: 0.7777 (t) cc_final: 0.7493 (t) REVERT: L 56 LYS cc_start: 0.8142 (pttp) cc_final: 0.7559 (ptpp) REVERT: M 48 THR cc_start: 0.7624 (p) cc_final: 0.7369 (p) REVERT: M 73 LYS cc_start: 0.8063 (mtmt) cc_final: 0.7835 (mtmm) REVERT: M 133 ASN cc_start: 0.8203 (m-40) cc_final: 0.7668 (m-40) REVERT: M 172 PHE cc_start: 0.8218 (m-80) cc_final: 0.5791 (t80) REVERT: M 182 ILE cc_start: 0.8879 (tp) cc_final: 0.8427 (tt) REVERT: M 200 THR cc_start: 0.8190 (m) cc_final: 0.7963 (p) REVERT: N 73 LYS cc_start: 0.7996 (mtmt) cc_final: 0.7285 (mtmm) REVERT: N 106 LYS cc_start: 0.7263 (ttpp) cc_final: 0.6776 (tttt) REVERT: N 112 TYR cc_start: 0.7627 (m-80) cc_final: 0.7324 (m-80) REVERT: O 41 GLN cc_start: 0.6183 (mt0) cc_final: 0.5900 (mt0) REVERT: O 197 GLU cc_start: 0.6246 (tt0) cc_final: 0.5858 (tt0) REVERT: P 18 MET cc_start: 0.5099 (ttt) cc_final: 0.4592 (ttm) REVERT: P 33 SER cc_start: 0.7748 (p) cc_final: 0.6933 (p) REVERT: P 66 SER cc_start: 0.7215 (m) cc_final: 0.6412 (t) REVERT: P 132 THR cc_start: 0.8220 (m) cc_final: 0.7894 (m) REVERT: P 140 GLN cc_start: 0.6586 (tt0) cc_final: 0.5711 (mm110) REVERT: P 164 LYS cc_start: 0.7781 (ttpt) cc_final: 0.7512 (ttpt) outliers start: 14 outliers final: 4 residues processed: 952 average time/residue: 0.3140 time to fit residues: 484.3286 Evaluate side-chains 819 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 815 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 161 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 241 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 80 optimal weight: 100.0000 chunk 291 optimal weight: 8.9990 chunk 314 optimal weight: 6.9990 chunk 259 optimal weight: 20.0000 chunk 288 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 233 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 113 HIS A 140 GLN ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN D 91 ASN D 113 HIS ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN ** F 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 GLN ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 140 GLN K 91 ASN ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 149 ASN L 49 GLN L 140 GLN ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 91 ASN M 149 ASN ** N 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 102 GLN ** N 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 102 GLN P 41 GLN ** P 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24880 Z= 0.289 Angle : 0.751 9.961 33904 Z= 0.398 Chirality : 0.054 0.374 4208 Planarity : 0.006 0.062 4320 Dihedral : 7.264 28.993 3456 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.07 % Favored : 82.93 % Rotamer: Outliers : 0.33 % Allowed : 7.29 % Favored : 92.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.13), residues: 3280 helix: -0.25 (0.19), residues: 704 sheet: -2.95 (0.18), residues: 576 loop : -3.45 (0.12), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP G 127 HIS 0.009 0.002 HIS D 113 PHE 0.027 0.003 PHE C 198 TYR 0.023 0.002 TYR O 112 ARG 0.004 0.001 ARG F 93 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 915 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.6490 (OUTLIER) cc_final: 0.4906 (mp10) REVERT: A 131 ASN cc_start: 0.6803 (m-40) cc_final: 0.6362 (m-40) REVERT: A 133 ASN cc_start: 0.8534 (m110) cc_final: 0.7537 (m-40) REVERT: A 155 LYS cc_start: 0.7422 (ptpt) cc_final: 0.6852 (tptt) REVERT: A 171 VAL cc_start: 0.8409 (p) cc_final: 0.7921 (t) REVERT: A 174 LYS cc_start: 0.6885 (mptt) cc_final: 0.6471 (mmtp) REVERT: A 200 THR cc_start: 0.8260 (m) cc_final: 0.7816 (p) REVERT: B 49 GLN cc_start: 0.6723 (mt0) cc_final: 0.6341 (mm-40) REVERT: B 182 ILE cc_start: 0.9386 (tp) cc_final: 0.9120 (tt) REVERT: B 202 SER cc_start: 0.7337 (m) cc_final: 0.7100 (m) REVERT: C 105 LEU cc_start: 0.8832 (mm) cc_final: 0.8534 (mm) REVERT: C 178 PRO cc_start: 0.8095 (Cg_exo) cc_final: 0.7793 (Cg_endo) REVERT: C 212 GLN cc_start: 0.7232 (tt0) cc_final: 0.6539 (tt0) REVERT: D 20 LEU cc_start: 0.7928 (mm) cc_final: 0.7584 (mm) REVERT: D 105 LEU cc_start: 0.8298 (mm) cc_final: 0.8028 (mm) REVERT: D 108 GLU cc_start: 0.5703 (tp30) cc_final: 0.5398 (tp30) REVERT: D 132 THR cc_start: 0.8764 (m) cc_final: 0.8289 (m) REVERT: D 133 ASN cc_start: 0.8435 (m-40) cc_final: 0.7143 (m-40) REVERT: D 172 PHE cc_start: 0.8722 (m-10) cc_final: 0.8251 (m-80) REVERT: D 181 LYS cc_start: 0.6831 (tptp) cc_final: 0.6583 (tptp) REVERT: D 200 THR cc_start: 0.8473 (m) cc_final: 0.7675 (p) REVERT: E 105 LEU cc_start: 0.7899 (mm) cc_final: 0.7327 (mm) REVERT: E 143 ASP cc_start: 0.7912 (t0) cc_final: 0.7652 (t0) REVERT: E 179 ARG cc_start: 0.6477 (ptp-110) cc_final: 0.5771 (mtm110) REVERT: E 185 LYS cc_start: 0.8135 (ptmt) cc_final: 0.7400 (pttm) REVERT: E 186 VAL cc_start: 0.9175 (t) cc_final: 0.8698 (m) REVERT: E 200 THR cc_start: 0.8558 (m) cc_final: 0.8135 (p) REVERT: F 114 LYS cc_start: 0.7734 (tptp) cc_final: 0.7516 (tptt) REVERT: G 36 LEU cc_start: 0.6475 (mt) cc_final: 0.6243 (mt) REVERT: G 55 ILE cc_start: 0.7983 (mt) cc_final: 0.7730 (mt) REVERT: G 81 ASN cc_start: 0.8272 (m-40) cc_final: 0.7789 (m110) REVERT: G 95 VAL cc_start: 0.8914 (t) cc_final: 0.8608 (m) REVERT: G 144 ASN cc_start: 0.8146 (m-40) cc_final: 0.7936 (m-40) REVERT: H 37 GLN cc_start: 0.7227 (tm-30) cc_final: 0.6973 (tm-30) REVERT: H 105 LEU cc_start: 0.8681 (mm) cc_final: 0.8252 (mm) REVERT: H 127 TRP cc_start: 0.8402 (m100) cc_final: 0.8078 (m100) REVERT: H 139 LEU cc_start: 0.8608 (pp) cc_final: 0.8370 (pp) REVERT: H 185 LYS cc_start: 0.8539 (ptmt) cc_final: 0.8101 (pttm) REVERT: H 200 THR cc_start: 0.8650 (m) cc_final: 0.8001 (p) REVERT: I 37 GLN cc_start: 0.5630 (tm-30) cc_final: 0.5388 (tm-30) REVERT: I 48 THR cc_start: 0.7081 (p) cc_final: 0.6813 (p) REVERT: I 66 SER cc_start: 0.7430 (m) cc_final: 0.6853 (p) REVERT: I 112 TYR cc_start: 0.8252 (m-80) cc_final: 0.7532 (m-80) REVERT: I 158 ILE cc_start: 0.8779 (mt) cc_final: 0.8138 (tp) REVERT: I 172 PHE cc_start: 0.7878 (m-80) cc_final: 0.5655 (t80) REVERT: J 18 MET cc_start: 0.4891 (ttt) cc_final: 0.4142 (ptp) REVERT: J 35 TYR cc_start: 0.5809 (t80) cc_final: 0.5431 (t80) REVERT: J 161 ILE cc_start: 0.8408 (mt) cc_final: 0.8073 (mp) REVERT: J 208 VAL cc_start: 0.9024 (t) cc_final: 0.8556 (t) REVERT: L 202 SER cc_start: 0.6291 (p) cc_final: 0.6086 (m) REVERT: M 48 THR cc_start: 0.7741 (p) cc_final: 0.7403 (p) REVERT: M 73 LYS cc_start: 0.8084 (mtmt) cc_final: 0.7870 (mtmm) REVERT: M 133 ASN cc_start: 0.8228 (m-40) cc_final: 0.7751 (m-40) REVERT: M 172 PHE cc_start: 0.8059 (m-80) cc_final: 0.5804 (t80) REVERT: M 179 ARG cc_start: 0.6908 (ttp80) cc_final: 0.6387 (ptp90) REVERT: M 182 ILE cc_start: 0.9021 (tp) cc_final: 0.8450 (tt) REVERT: M 200 THR cc_start: 0.8323 (m) cc_final: 0.8097 (p) REVERT: N 73 LYS cc_start: 0.8120 (mtmt) cc_final: 0.7190 (mtmm) REVERT: N 94 VAL cc_start: 0.9345 (p) cc_final: 0.9115 (p) REVERT: N 102 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7381 (mm-40) REVERT: N 106 LYS cc_start: 0.6980 (ttpp) cc_final: 0.6749 (tttt) REVERT: N 172 PHE cc_start: 0.7575 (m-80) cc_final: 0.5124 (t80) REVERT: O 109 LYS cc_start: 0.5913 (mttt) cc_final: 0.5582 (mttt) REVERT: P 18 MET cc_start: 0.5004 (ttt) cc_final: 0.4702 (ttm) REVERT: P 66 SER cc_start: 0.7203 (m) cc_final: 0.6417 (t) REVERT: P 79 SER cc_start: 0.8949 (t) cc_final: 0.8583 (p) REVERT: P 132 THR cc_start: 0.8234 (m) cc_final: 0.7759 (m) REVERT: P 140 GLN cc_start: 0.6655 (tt0) cc_final: 0.5634 (mm110) REVERT: P 174 LYS cc_start: 0.6313 (mttp) cc_final: 0.5150 (mmtm) outliers start: 9 outliers final: 2 residues processed: 922 average time/residue: 0.3114 time to fit residues: 464.0688 Evaluate side-chains 805 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 801 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 287 optimal weight: 20.0000 chunk 218 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 138 optimal weight: 0.0570 chunk 195 optimal weight: 5.9990 chunk 292 optimal weight: 6.9990 chunk 309 optimal weight: 8.9990 chunk 152 optimal weight: 4.9990 chunk 276 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 102 GLN A 140 GLN ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN D 148 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 ASN ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 149 ASN N 91 ASN ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 41 GLN ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 24880 Z= 0.303 Angle : 0.746 9.490 33904 Z= 0.395 Chirality : 0.055 0.423 4208 Planarity : 0.006 0.064 4320 Dihedral : 7.090 29.029 3456 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.65 % Favored : 82.35 % Rotamer: Outliers : 0.33 % Allowed : 5.13 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.13), residues: 3280 helix: 0.16 (0.19), residues: 704 sheet: -2.58 (0.17), residues: 672 loop : -3.55 (0.12), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP J 127 HIS 0.017 0.003 HIS D 113 PHE 0.026 0.003 PHE C 198 TYR 0.017 0.002 TYR G 204 ARG 0.003 0.001 ARG F 93 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 890 time to evaluate : 2.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 LYS cc_start: 0.7401 (ptpt) cc_final: 0.6919 (tptt) REVERT: A 171 VAL cc_start: 0.8515 (p) cc_final: 0.8105 (t) REVERT: A 174 LYS cc_start: 0.6887 (mptt) cc_final: 0.6287 (mmtp) REVERT: A 200 THR cc_start: 0.8234 (m) cc_final: 0.7812 (p) REVERT: B 182 ILE cc_start: 0.9398 (tp) cc_final: 0.9047 (tt) REVERT: B 202 SER cc_start: 0.7189 (m) cc_final: 0.6921 (m) REVERT: C 105 LEU cc_start: 0.8851 (mm) cc_final: 0.8538 (mm) REVERT: C 178 PRO cc_start: 0.8110 (Cg_exo) cc_final: 0.7845 (Cg_endo) REVERT: C 212 GLN cc_start: 0.7223 (tt0) cc_final: 0.6437 (tt0) REVERT: D 18 MET cc_start: 0.4976 (tmm) cc_final: 0.4553 (tmm) REVERT: D 20 LEU cc_start: 0.7792 (mm) cc_final: 0.7550 (mm) REVERT: D 105 LEU cc_start: 0.8333 (mm) cc_final: 0.8068 (mm) REVERT: D 108 GLU cc_start: 0.5793 (tp30) cc_final: 0.5466 (tp30) REVERT: D 132 THR cc_start: 0.8745 (m) cc_final: 0.8394 (m) REVERT: D 133 ASN cc_start: 0.8486 (m-40) cc_final: 0.7245 (m-40) REVERT: D 172 PHE cc_start: 0.8785 (m-80) cc_final: 0.8261 (m-80) REVERT: D 200 THR cc_start: 0.8590 (m) cc_final: 0.7834 (p) REVERT: E 105 LEU cc_start: 0.7875 (mm) cc_final: 0.7218 (mm) REVERT: E 185 LYS cc_start: 0.8197 (ptmt) cc_final: 0.7411 (pttm) REVERT: E 186 VAL cc_start: 0.9038 (t) cc_final: 0.8571 (m) REVERT: G 55 ILE cc_start: 0.7956 (mt) cc_final: 0.7754 (mt) REVERT: G 81 ASN cc_start: 0.8390 (m-40) cc_final: 0.7664 (m110) REVERT: G 95 VAL cc_start: 0.8881 (t) cc_final: 0.8619 (m) REVERT: H 18 MET cc_start: 0.4410 (mmm) cc_final: 0.4021 (mmm) REVERT: H 37 GLN cc_start: 0.7207 (tm-30) cc_final: 0.6985 (tm-30) REVERT: H 105 LEU cc_start: 0.8682 (mm) cc_final: 0.8227 (mm) REVERT: H 185 LYS cc_start: 0.8528 (ptmt) cc_final: 0.7936 (pttm) REVERT: H 200 THR cc_start: 0.8639 (m) cc_final: 0.7939 (p) REVERT: I 18 MET cc_start: 0.4765 (ttt) cc_final: 0.4527 (ttp) REVERT: I 37 GLN cc_start: 0.5476 (tm-30) cc_final: 0.5070 (tm-30) REVERT: I 66 SER cc_start: 0.7345 (m) cc_final: 0.6868 (p) REVERT: I 112 TYR cc_start: 0.8340 (m-80) cc_final: 0.7762 (m-80) REVERT: I 158 ILE cc_start: 0.8829 (mt) cc_final: 0.8191 (mm) REVERT: I 172 PHE cc_start: 0.7738 (m-80) cc_final: 0.5620 (t80) REVERT: I 181 LYS cc_start: 0.8367 (ttmm) cc_final: 0.8159 (tttt) REVERT: J 13 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7568 (mt) REVERT: J 18 MET cc_start: 0.4623 (ttt) cc_final: 0.4209 (mtm) REVERT: J 35 TYR cc_start: 0.5918 (t80) cc_final: 0.5530 (t80) REVERT: J 55 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7203 (mp) REVERT: J 56 LYS cc_start: 0.8064 (pttp) cc_final: 0.7794 (ptpt) REVERT: J 78 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8929 (mt) REVERT: K 106 LYS cc_start: 0.6654 (tttt) cc_final: 0.6327 (tttt) REVERT: L 163 VAL cc_start: 0.8574 (t) cc_final: 0.8228 (m) REVERT: L 183 THR cc_start: 0.8095 (m) cc_final: 0.7767 (p) REVERT: L 202 SER cc_start: 0.6544 (p) cc_final: 0.6158 (m) REVERT: M 48 THR cc_start: 0.7834 (p) cc_final: 0.7510 (p) REVERT: M 73 LYS cc_start: 0.8054 (mtmt) cc_final: 0.7838 (mtmm) REVERT: M 106 LYS cc_start: 0.7327 (ttpp) cc_final: 0.7114 (tttt) REVERT: M 133 ASN cc_start: 0.8179 (m-40) cc_final: 0.7591 (m-40) REVERT: M 150 TYR cc_start: 0.8602 (m-80) cc_final: 0.8393 (m-80) REVERT: M 179 ARG cc_start: 0.6923 (ttp80) cc_final: 0.6446 (ptp90) REVERT: M 182 ILE cc_start: 0.9101 (tp) cc_final: 0.8700 (tt) REVERT: M 200 THR cc_start: 0.8443 (m) cc_final: 0.8178 (p) REVERT: N 18 MET cc_start: 0.6234 (mtm) cc_final: 0.6033 (mtm) REVERT: N 73 LYS cc_start: 0.8109 (mtmt) cc_final: 0.7243 (mtmm) REVERT: N 106 LYS cc_start: 0.7170 (ttpp) cc_final: 0.6915 (tttt) REVERT: N 132 THR cc_start: 0.8348 (m) cc_final: 0.8105 (m) REVERT: N 172 PHE cc_start: 0.7828 (m-80) cc_final: 0.5417 (t80) REVERT: O 41 GLN cc_start: 0.6302 (mt0) cc_final: 0.6044 (mt0) REVERT: O 98 ASN cc_start: 0.8137 (t0) cc_final: 0.7776 (t0) REVERT: O 202 SER cc_start: 0.6580 (m) cc_final: 0.4227 (m) REVERT: P 18 MET cc_start: 0.4885 (ttt) cc_final: 0.4474 (mtm) REVERT: P 20 LEU cc_start: 0.6885 (mt) cc_final: 0.6589 (mt) REVERT: P 66 SER cc_start: 0.7016 (m) cc_final: 0.6155 (t) REVERT: P 69 THR cc_start: 0.6985 (m) cc_final: 0.6354 (m) REVERT: P 79 SER cc_start: 0.9082 (t) cc_final: 0.8468 (p) REVERT: P 106 LYS cc_start: 0.6903 (tptp) cc_final: 0.6587 (tptp) REVERT: P 132 THR cc_start: 0.8070 (m) cc_final: 0.7647 (m) REVERT: P 140 GLN cc_start: 0.6729 (tt0) cc_final: 0.5739 (mm110) REVERT: P 174 LYS cc_start: 0.6244 (mttp) cc_final: 0.5367 (mmtm) outliers start: 9 outliers final: 1 residues processed: 897 average time/residue: 0.3144 time to fit residues: 459.0911 Evaluate side-chains 781 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 777 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 257 optimal weight: 10.0000 chunk 175 optimal weight: 0.0570 chunk 4 optimal weight: 2.9990 chunk 230 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 chunk 263 optimal weight: 4.9990 chunk 213 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 277 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 overall best weight: 4.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 GLN ** C 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN D 91 ASN E 31 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 ASN ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 ASN K 91 ASN ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 140 GLN K 148 GLN ** L 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 91 ASN ** M 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 ASN O 102 GLN ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 24880 Z= 0.352 Angle : 0.781 9.684 33904 Z= 0.415 Chirality : 0.056 0.442 4208 Planarity : 0.006 0.076 4320 Dihedral : 7.212 30.464 3456 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.57 % Favored : 81.43 % Rotamer: Outliers : 0.11 % Allowed : 6.29 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.13), residues: 3280 helix: 0.35 (0.19), residues: 704 sheet: -2.45 (0.18), residues: 672 loop : -3.56 (0.12), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.005 TRP J 127 HIS 0.009 0.003 HIS E 113 PHE 0.029 0.003 PHE J 198 TYR 0.019 0.002 TYR A 112 ARG 0.007 0.001 ARG O 179 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 898 time to evaluate : 2.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASN cc_start: 0.7015 (m-40) cc_final: 0.6704 (m-40) REVERT: A 155 LYS cc_start: 0.7503 (ptpt) cc_final: 0.6920 (tptt) REVERT: A 174 LYS cc_start: 0.7001 (mptt) cc_final: 0.6533 (mmtp) REVERT: A 200 THR cc_start: 0.8136 (m) cc_final: 0.7697 (p) REVERT: A 204 TYR cc_start: 0.6568 (p90) cc_final: 0.6160 (p90) REVERT: B 109 LYS cc_start: 0.6694 (mtmt) cc_final: 0.6468 (mtmt) REVERT: B 158 ILE cc_start: 0.8452 (mt) cc_final: 0.8246 (mt) REVERT: B 182 ILE cc_start: 0.9360 (tp) cc_final: 0.9027 (tt) REVERT: B 202 SER cc_start: 0.6943 (m) cc_final: 0.6440 (m) REVERT: C 68 LYS cc_start: 0.5430 (mmtm) cc_final: 0.5177 (mmtm) REVERT: C 105 LEU cc_start: 0.8916 (mm) cc_final: 0.8492 (mm) REVERT: C 155 LYS cc_start: 0.7449 (ptpp) cc_final: 0.6960 (ptpp) REVERT: C 178 PRO cc_start: 0.8197 (Cg_exo) cc_final: 0.7936 (Cg_endo) REVERT: D 55 ILE cc_start: 0.8047 (mt) cc_final: 0.7649 (mt) REVERT: D 105 LEU cc_start: 0.8402 (mm) cc_final: 0.8191 (mm) REVERT: D 132 THR cc_start: 0.8880 (m) cc_final: 0.8499 (m) REVERT: D 172 PHE cc_start: 0.8861 (m-80) cc_final: 0.8358 (m-80) REVERT: D 200 THR cc_start: 0.8457 (m) cc_final: 0.7736 (p) REVERT: E 143 ASP cc_start: 0.7906 (t0) cc_final: 0.7619 (t0) REVERT: E 179 ARG cc_start: 0.5978 (ptp90) cc_final: 0.5669 (mtm110) REVERT: E 185 LYS cc_start: 0.8271 (ptmt) cc_final: 0.7482 (pttm) REVERT: E 186 VAL cc_start: 0.8974 (t) cc_final: 0.8721 (m) REVERT: E 200 THR cc_start: 0.8607 (m) cc_final: 0.8140 (p) REVERT: F 106 LYS cc_start: 0.7627 (ttpt) cc_final: 0.7211 (tmmt) REVERT: F 132 THR cc_start: 0.8875 (p) cc_final: 0.8628 (p) REVERT: G 81 ASN cc_start: 0.8408 (m-40) cc_final: 0.7613 (m110) REVERT: G 95 VAL cc_start: 0.8920 (t) cc_final: 0.8598 (m) REVERT: G 200 THR cc_start: 0.8594 (m) cc_final: 0.8023 (p) REVERT: H 18 MET cc_start: 0.4434 (mmm) cc_final: 0.3991 (mmm) REVERT: H 37 GLN cc_start: 0.7398 (tm-30) cc_final: 0.6985 (tm-30) REVERT: H 105 LEU cc_start: 0.8684 (mm) cc_final: 0.8267 (mm) REVERT: H 185 LYS cc_start: 0.8655 (ptmt) cc_final: 0.7944 (pttm) REVERT: H 200 THR cc_start: 0.8671 (m) cc_final: 0.7940 (p) REVERT: I 48 THR cc_start: 0.6698 (p) cc_final: 0.6444 (p) REVERT: I 66 SER cc_start: 0.7517 (m) cc_final: 0.7004 (p) REVERT: I 112 TYR cc_start: 0.8418 (m-80) cc_final: 0.7871 (m-80) REVERT: I 158 ILE cc_start: 0.8867 (mt) cc_final: 0.8222 (mm) REVERT: I 172 PHE cc_start: 0.7717 (m-80) cc_final: 0.5502 (t80) REVERT: J 18 MET cc_start: 0.4843 (ttt) cc_final: 0.4087 (ptp) REVERT: J 35 TYR cc_start: 0.6121 (t80) cc_final: 0.5779 (t80) REVERT: J 208 VAL cc_start: 0.9036 (t) cc_final: 0.8722 (t) REVERT: J 210 GLU cc_start: 0.8492 (pm20) cc_final: 0.8251 (pm20) REVERT: K 106 LYS cc_start: 0.6714 (tttt) cc_final: 0.6413 (tttt) REVERT: L 163 VAL cc_start: 0.8671 (t) cc_final: 0.8398 (m) REVERT: L 196 ILE cc_start: 0.8827 (pt) cc_final: 0.8595 (pt) REVERT: L 202 SER cc_start: 0.6553 (p) cc_final: 0.6269 (m) REVERT: M 48 THR cc_start: 0.7965 (p) cc_final: 0.7677 (p) REVERT: M 73 LYS cc_start: 0.8109 (mtmt) cc_final: 0.7881 (mtmm) REVERT: M 98 ASN cc_start: 0.5278 (t0) cc_final: 0.4995 (t0) REVERT: M 106 LYS cc_start: 0.7548 (ttpp) cc_final: 0.7234 (tttt) REVERT: M 133 ASN cc_start: 0.8322 (m-40) cc_final: 0.7730 (m-40) REVERT: M 179 ARG cc_start: 0.6987 (ttp80) cc_final: 0.6481 (ptp90) REVERT: M 182 ILE cc_start: 0.8946 (tp) cc_final: 0.8388 (tt) REVERT: M 200 THR cc_start: 0.8592 (m) cc_final: 0.8343 (p) REVERT: N 69 THR cc_start: 0.6999 (m) cc_final: 0.5951 (m) REVERT: N 73 LYS cc_start: 0.7960 (mtmt) cc_final: 0.7170 (mtmm) REVERT: N 106 LYS cc_start: 0.7318 (ttpp) cc_final: 0.7019 (tttt) REVERT: N 132 THR cc_start: 0.8128 (m) cc_final: 0.7920 (m) REVERT: N 172 PHE cc_start: 0.7762 (m-80) cc_final: 0.5465 (t80) REVERT: O 41 GLN cc_start: 0.6078 (mt0) cc_final: 0.5829 (mt0) REVERT: O 98 ASN cc_start: 0.8099 (t0) cc_final: 0.7874 (t0) REVERT: P 18 MET cc_start: 0.4707 (ttt) cc_final: 0.4323 (mtm) REVERT: P 20 LEU cc_start: 0.6928 (mt) cc_final: 0.6700 (mt) REVERT: P 69 THR cc_start: 0.6876 (m) cc_final: 0.6455 (m) REVERT: P 79 SER cc_start: 0.8945 (t) cc_final: 0.8611 (p) REVERT: P 132 THR cc_start: 0.8184 (m) cc_final: 0.7747 (m) REVERT: P 140 GLN cc_start: 0.7053 (tt0) cc_final: 0.5864 (mm110) outliers start: 3 outliers final: 0 residues processed: 899 average time/residue: 0.3232 time to fit residues: 468.0263 Evaluate side-chains 774 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 774 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 104 optimal weight: 4.9990 chunk 278 optimal weight: 20.0000 chunk 61 optimal weight: 0.9990 chunk 181 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 309 optimal weight: 5.9990 chunk 257 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 162 optimal weight: 0.2980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN H 31 GLN ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 140 GLN ** J 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 133 ASN ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 GLN L 81 ASN ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 ASN M 149 ASN ** O 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 148 GLN ** P 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 81 ASN P 133 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24880 Z= 0.222 Angle : 0.725 9.108 33904 Z= 0.379 Chirality : 0.055 0.422 4208 Planarity : 0.005 0.075 4320 Dihedral : 6.784 27.897 3456 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.00 % Favored : 85.00 % Rotamer: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.14), residues: 3280 helix: 0.58 (0.19), residues: 736 sheet: -2.51 (0.16), residues: 752 loop : -3.46 (0.13), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 127 HIS 0.008 0.002 HIS D 113 PHE 0.020 0.003 PHE A 172 TYR 0.019 0.001 TYR G 204 ARG 0.005 0.001 ARG B 179 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 885 time to evaluate : 2.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASN cc_start: 0.6367 (m-40) cc_final: 0.5967 (m-40) REVERT: A 155 LYS cc_start: 0.7637 (ptpt) cc_final: 0.6912 (tptt) REVERT: A 174 LYS cc_start: 0.6691 (mptt) cc_final: 0.6268 (mmtp) REVERT: A 200 THR cc_start: 0.8014 (m) cc_final: 0.7610 (p) REVERT: B 109 LYS cc_start: 0.6728 (mtmt) cc_final: 0.6375 (mtmt) REVERT: B 176 ILE cc_start: 0.8242 (mt) cc_final: 0.7981 (mt) REVERT: B 182 ILE cc_start: 0.9277 (tp) cc_final: 0.8881 (tt) REVERT: B 202 SER cc_start: 0.7111 (m) cc_final: 0.6694 (m) REVERT: C 48 THR cc_start: 0.5902 (p) cc_final: 0.5674 (p) REVERT: C 105 LEU cc_start: 0.8640 (mm) cc_final: 0.8320 (mm) REVERT: C 155 LYS cc_start: 0.7441 (ptpp) cc_final: 0.6872 (ptpp) REVERT: C 199 THR cc_start: 0.7684 (p) cc_final: 0.7452 (p) REVERT: D 28 VAL cc_start: 0.8065 (t) cc_final: 0.7840 (t) REVERT: D 132 THR cc_start: 0.8647 (m) cc_final: 0.8289 (m) REVERT: D 172 PHE cc_start: 0.8647 (m-80) cc_final: 0.8091 (m-80) REVERT: D 200 THR cc_start: 0.8455 (m) cc_final: 0.7728 (p) REVERT: E 105 LEU cc_start: 0.7719 (mm) cc_final: 0.7223 (mm) REVERT: E 143 ASP cc_start: 0.7880 (t0) cc_final: 0.7602 (t0) REVERT: E 185 LYS cc_start: 0.8131 (ptmt) cc_final: 0.7329 (pttm) REVERT: F 106 LYS cc_start: 0.7537 (ttpt) cc_final: 0.7192 (tmmt) REVERT: F 132 THR cc_start: 0.8724 (p) cc_final: 0.8414 (p) REVERT: G 81 ASN cc_start: 0.8315 (m-40) cc_final: 0.7605 (m110) REVERT: G 181 LYS cc_start: 0.8014 (tppp) cc_final: 0.6713 (tppt) REVERT: G 189 GLU cc_start: 0.4996 (tt0) cc_final: 0.4502 (tt0) REVERT: G 200 THR cc_start: 0.8754 (m) cc_final: 0.8163 (p) REVERT: H 105 LEU cc_start: 0.8706 (mm) cc_final: 0.8164 (mm) REVERT: H 185 LYS cc_start: 0.8464 (ptmt) cc_final: 0.7870 (pttm) REVERT: H 200 THR cc_start: 0.8582 (m) cc_final: 0.7926 (p) REVERT: I 64 THR cc_start: 0.6351 (t) cc_final: 0.5741 (t) REVERT: I 66 SER cc_start: 0.7477 (m) cc_final: 0.7044 (p) REVERT: I 112 TYR cc_start: 0.8253 (m-80) cc_final: 0.7765 (m-80) REVERT: I 158 ILE cc_start: 0.8792 (mt) cc_final: 0.8198 (mm) REVERT: I 172 PHE cc_start: 0.6785 (m-80) cc_final: 0.5761 (t80) REVERT: I 204 TYR cc_start: 0.5782 (p90) cc_final: 0.5231 (p90) REVERT: J 18 MET cc_start: 0.4677 (ttt) cc_final: 0.4258 (mtm) REVERT: J 35 TYR cc_start: 0.5918 (t80) cc_final: 0.5545 (t80) REVERT: J 56 LYS cc_start: 0.8306 (ptpt) cc_final: 0.7439 (ptpt) REVERT: J 208 VAL cc_start: 0.9015 (t) cc_final: 0.8761 (t) REVERT: J 210 GLU cc_start: 0.8133 (pm20) cc_final: 0.7848 (pm20) REVERT: K 56 LYS cc_start: 0.8761 (pttt) cc_final: 0.8548 (pttt) REVERT: L 105 LEU cc_start: 0.8326 (mm) cc_final: 0.8038 (mm) REVERT: L 202 SER cc_start: 0.6684 (p) cc_final: 0.6420 (m) REVERT: M 73 LYS cc_start: 0.7948 (mtmt) cc_final: 0.7700 (mtmm) REVERT: M 105 LEU cc_start: 0.8324 (mm) cc_final: 0.8067 (mm) REVERT: M 106 LYS cc_start: 0.7481 (ttpp) cc_final: 0.7220 (tttt) REVERT: M 133 ASN cc_start: 0.8164 (m110) cc_final: 0.7335 (m-40) REVERT: M 200 THR cc_start: 0.8495 (m) cc_final: 0.8245 (p) REVERT: N 132 THR cc_start: 0.8032 (m) cc_final: 0.7726 (m) REVERT: N 172 PHE cc_start: 0.7611 (m-80) cc_final: 0.5674 (t80) REVERT: P 18 MET cc_start: 0.4822 (ttt) cc_final: 0.4246 (mtp) REVERT: P 20 LEU cc_start: 0.6914 (mt) cc_final: 0.6540 (mt) REVERT: P 66 SER cc_start: 0.6962 (m) cc_final: 0.6256 (t) REVERT: P 132 THR cc_start: 0.8216 (m) cc_final: 0.7627 (m) REVERT: P 140 GLN cc_start: 0.6744 (tt0) cc_final: 0.5690 (mm110) outliers start: 0 outliers final: 0 residues processed: 885 average time/residue: 0.3136 time to fit residues: 452.9193 Evaluate side-chains 773 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 773 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 298 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 176 optimal weight: 0.4980 chunk 226 optimal weight: 8.9990 chunk 175 optimal weight: 0.1980 chunk 260 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 308 optimal weight: 5.9990 chunk 193 optimal weight: 0.9980 chunk 188 optimal weight: 4.9990 chunk 142 optimal weight: 10.0000 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN D 91 ASN ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 113 HIS ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 140 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 91 ASN ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 41 GLN O 102 GLN O 131 ASN ** O 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 133 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 24880 Z= 0.272 Angle : 0.739 9.376 33904 Z= 0.389 Chirality : 0.056 0.458 4208 Planarity : 0.006 0.074 4320 Dihedral : 6.717 29.276 3456 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.07 % Favored : 82.93 % Rotamer: Outliers : 0.04 % Allowed : 3.76 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.14), residues: 3280 helix: 0.70 (0.19), residues: 736 sheet: -2.24 (0.18), residues: 672 loop : -3.48 (0.12), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP J 127 HIS 0.013 0.003 HIS I 113 PHE 0.031 0.003 PHE P 190 TYR 0.019 0.002 TYR B 204 ARG 0.005 0.001 ARG B 179 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 867 time to evaluate : 2.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASN cc_start: 0.6429 (m-40) cc_final: 0.6000 (m-40) REVERT: A 155 LYS cc_start: 0.7682 (ptpt) cc_final: 0.7181 (tptt) REVERT: A 174 LYS cc_start: 0.6845 (mptt) cc_final: 0.6328 (mmtp) REVERT: A 200 THR cc_start: 0.8093 (m) cc_final: 0.7651 (p) REVERT: B 182 ILE cc_start: 0.9304 (tp) cc_final: 0.8963 (tt) REVERT: B 202 SER cc_start: 0.7220 (m) cc_final: 0.6838 (m) REVERT: C 105 LEU cc_start: 0.8844 (mm) cc_final: 0.8501 (mm) REVERT: C 155 LYS cc_start: 0.7400 (ptpp) cc_final: 0.7029 (ptpp) REVERT: C 178 PRO cc_start: 0.8254 (Cg_exo) cc_final: 0.7952 (Cg_endo) REVERT: C 199 THR cc_start: 0.7705 (p) cc_final: 0.7491 (p) REVERT: D 105 LEU cc_start: 0.8211 (mm) cc_final: 0.8010 (mm) REVERT: D 132 THR cc_start: 0.8433 (m) cc_final: 0.8231 (m) REVERT: D 172 PHE cc_start: 0.8583 (m-80) cc_final: 0.8104 (m-80) REVERT: D 200 THR cc_start: 0.8460 (m) cc_final: 0.7723 (p) REVERT: E 73 LYS cc_start: 0.7795 (mtmt) cc_final: 0.7441 (mtpt) REVERT: E 105 LEU cc_start: 0.7741 (mm) cc_final: 0.7186 (mm) REVERT: E 143 ASP cc_start: 0.7772 (t0) cc_final: 0.7554 (t0) REVERT: E 185 LYS cc_start: 0.8190 (ptmt) cc_final: 0.7370 (pttm) REVERT: F 106 LYS cc_start: 0.7535 (ttpt) cc_final: 0.7221 (tmmt) REVERT: F 204 TYR cc_start: 0.5950 (p90) cc_final: 0.5257 (p90) REVERT: G 55 ILE cc_start: 0.8101 (mt) cc_final: 0.7785 (mt) REVERT: G 81 ASN cc_start: 0.8268 (m-40) cc_final: 0.7585 (m110) REVERT: G 181 LYS cc_start: 0.7963 (tppp) cc_final: 0.6704 (tppt) REVERT: G 200 THR cc_start: 0.8743 (m) cc_final: 0.8162 (p) REVERT: H 105 LEU cc_start: 0.8666 (mm) cc_final: 0.8123 (mm) REVERT: H 185 LYS cc_start: 0.8466 (ptmt) cc_final: 0.7910 (pttm) REVERT: H 200 THR cc_start: 0.8613 (m) cc_final: 0.7855 (p) REVERT: I 66 SER cc_start: 0.7536 (m) cc_final: 0.7137 (p) REVERT: I 112 TYR cc_start: 0.8374 (m-80) cc_final: 0.7766 (m-80) REVERT: I 158 ILE cc_start: 0.8805 (mt) cc_final: 0.8169 (mm) REVERT: I 172 PHE cc_start: 0.7021 (m-80) cc_final: 0.5732 (t80) REVERT: J 18 MET cc_start: 0.4735 (ttt) cc_final: 0.4068 (ptp) REVERT: J 35 TYR cc_start: 0.5954 (t80) cc_final: 0.5718 (t80) REVERT: L 105 LEU cc_start: 0.8345 (mm) cc_final: 0.8045 (mm) REVERT: L 179 ARG cc_start: 0.7320 (mtt-85) cc_final: 0.6750 (mtt-85) REVERT: L 202 SER cc_start: 0.6388 (p) cc_final: 0.5689 (p) REVERT: M 48 THR cc_start: 0.7998 (p) cc_final: 0.7677 (p) REVERT: M 73 LYS cc_start: 0.7997 (mtmt) cc_final: 0.7778 (mtmm) REVERT: M 106 LYS cc_start: 0.7463 (ttpp) cc_final: 0.7247 (tttt) REVERT: M 133 ASN cc_start: 0.8244 (m110) cc_final: 0.7508 (m-40) REVERT: M 172 PHE cc_start: 0.7067 (m-10) cc_final: 0.6531 (t80) REVERT: M 179 ARG cc_start: 0.6783 (ttp80) cc_final: 0.6309 (ptp90) REVERT: M 200 THR cc_start: 0.8529 (m) cc_final: 0.8249 (p) REVERT: N 132 THR cc_start: 0.8000 (m) cc_final: 0.7706 (m) REVERT: N 133 ASN cc_start: 0.7759 (m-40) cc_final: 0.7468 (m-40) REVERT: N 172 PHE cc_start: 0.7623 (m-80) cc_final: 0.5555 (t80) REVERT: N 200 THR cc_start: 0.8410 (m) cc_final: 0.8137 (p) REVERT: O 41 GLN cc_start: 0.6263 (mt0) cc_final: 0.6055 (mt0) REVERT: O 60 VAL cc_start: 0.8804 (m) cc_final: 0.8537 (p) REVERT: O 109 LYS cc_start: 0.5931 (mttt) cc_final: 0.5377 (mttt) REVERT: P 18 MET cc_start: 0.4747 (ttt) cc_final: 0.4112 (mtp) REVERT: P 20 LEU cc_start: 0.6903 (mt) cc_final: 0.6610 (mt) REVERT: P 140 GLN cc_start: 0.6648 (tt0) cc_final: 0.5769 (mm110) REVERT: P 172 PHE cc_start: 0.7170 (m-80) cc_final: 0.5232 (t80) outliers start: 1 outliers final: 1 residues processed: 868 average time/residue: 0.3338 time to fit residues: 476.5271 Evaluate side-chains 761 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 760 time to evaluate : 2.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 190 optimal weight: 10.0000 chunk 123 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 92 optimal weight: 0.4980 chunk 60 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 196 optimal weight: 0.9990 chunk 210 optimal weight: 20.0000 chunk 152 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 242 optimal weight: 0.9980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN D 133 ASN ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 ASN G 128 ASN ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN M 41 GLN ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 49 GLN P 133 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24880 Z= 0.242 Angle : 0.737 8.870 33904 Z= 0.386 Chirality : 0.056 0.459 4208 Planarity : 0.006 0.076 4320 Dihedral : 6.615 28.461 3456 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.07 % Favored : 83.93 % Rotamer: Outliers : 0.04 % Allowed : 2.01 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.14), residues: 3280 helix: 0.82 (0.19), residues: 736 sheet: -2.13 (0.18), residues: 672 loop : -3.46 (0.12), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP D 127 HIS 0.011 0.002 HIS O 113 PHE 0.024 0.003 PHE G 134 TYR 0.016 0.001 TYR A 150 ARG 0.006 0.001 ARG B 179 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 867 time to evaluate : 2.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASN cc_start: 0.6337 (m-40) cc_final: 0.5908 (m-40) REVERT: A 153 LEU cc_start: 0.8045 (mt) cc_final: 0.7808 (mt) REVERT: A 155 LYS cc_start: 0.7764 (ptpt) cc_final: 0.7118 (tptt) REVERT: A 174 LYS cc_start: 0.6890 (mptt) cc_final: 0.6310 (mmtp) REVERT: A 200 THR cc_start: 0.8100 (m) cc_final: 0.7647 (p) REVERT: B 200 THR cc_start: 0.8766 (m) cc_final: 0.8085 (p) REVERT: B 202 SER cc_start: 0.7202 (m) cc_final: 0.6789 (m) REVERT: C 48 THR cc_start: 0.6125 (p) cc_final: 0.5326 (p) REVERT: C 56 LYS cc_start: 0.8163 (ptpp) cc_final: 0.7813 (ptpp) REVERT: C 105 LEU cc_start: 0.8822 (mm) cc_final: 0.8474 (mm) REVERT: C 155 LYS cc_start: 0.7499 (ptpp) cc_final: 0.6985 (ptpp) REVERT: C 198 PHE cc_start: 0.8409 (p90) cc_final: 0.7963 (p90) REVERT: D 28 VAL cc_start: 0.7987 (t) cc_final: 0.7775 (t) REVERT: D 31 GLN cc_start: 0.5558 (tt0) cc_final: 0.5345 (tt0) REVERT: D 105 LEU cc_start: 0.8045 (mm) cc_final: 0.7812 (mm) REVERT: D 132 THR cc_start: 0.8540 (m) cc_final: 0.8314 (m) REVERT: D 172 PHE cc_start: 0.8461 (m-80) cc_final: 0.8015 (m-80) REVERT: D 200 THR cc_start: 0.8406 (m) cc_final: 0.7634 (p) REVERT: E 105 LEU cc_start: 0.7534 (mm) cc_final: 0.7206 (mm) REVERT: E 143 ASP cc_start: 0.7928 (t0) cc_final: 0.7674 (t0) REVERT: E 185 LYS cc_start: 0.8209 (ptmt) cc_final: 0.7384 (pttm) REVERT: F 106 LYS cc_start: 0.7324 (ttpt) cc_final: 0.7044 (tmmt) REVERT: F 132 THR cc_start: 0.8298 (p) cc_final: 0.7905 (p) REVERT: G 55 ILE cc_start: 0.8118 (mt) cc_final: 0.7649 (mt) REVERT: G 81 ASN cc_start: 0.8130 (m110) cc_final: 0.7539 (m110) REVERT: G 200 THR cc_start: 0.8678 (m) cc_final: 0.8134 (p) REVERT: H 37 GLN cc_start: 0.7071 (tm-30) cc_final: 0.6790 (tm-30) REVERT: H 105 LEU cc_start: 0.8578 (mm) cc_final: 0.8130 (mm) REVERT: H 185 LYS cc_start: 0.8369 (ptmt) cc_final: 0.7813 (pttm) REVERT: H 200 THR cc_start: 0.8513 (m) cc_final: 0.7784 (p) REVERT: I 48 THR cc_start: 0.6440 (p) cc_final: 0.6217 (p) REVERT: I 64 THR cc_start: 0.6316 (t) cc_final: 0.5849 (t) REVERT: I 66 SER cc_start: 0.7403 (m) cc_final: 0.7044 (p) REVERT: I 112 TYR cc_start: 0.8410 (m-80) cc_final: 0.7939 (m-80) REVERT: I 158 ILE cc_start: 0.8820 (mt) cc_final: 0.8243 (mm) REVERT: I 172 PHE cc_start: 0.7004 (m-80) cc_final: 0.5393 (t80) REVERT: I 204 TYR cc_start: 0.5784 (p90) cc_final: 0.5292 (p90) REVERT: J 18 MET cc_start: 0.4820 (ttt) cc_final: 0.4102 (ptp) REVERT: J 35 TYR cc_start: 0.5902 (t80) cc_final: 0.5662 (t80) REVERT: J 56 LYS cc_start: 0.8424 (ptpt) cc_final: 0.7777 (ptpt) REVERT: J 210 GLU cc_start: 0.8196 (pm20) cc_final: 0.7864 (pm20) REVERT: K 36 LEU cc_start: 0.6498 (mp) cc_final: 0.6270 (mp) REVERT: K 49 GLN cc_start: 0.6447 (mt0) cc_final: 0.5942 (mp10) REVERT: K 68 LYS cc_start: 0.7098 (mmmt) cc_final: 0.6530 (mmtp) REVERT: L 105 LEU cc_start: 0.8335 (mm) cc_final: 0.8096 (mm) REVERT: L 109 LYS cc_start: 0.8091 (mppt) cc_final: 0.7767 (mppt) REVERT: L 179 ARG cc_start: 0.7304 (mtt-85) cc_final: 0.6748 (mtt-85) REVERT: L 202 SER cc_start: 0.6452 (p) cc_final: 0.5775 (p) REVERT: M 73 LYS cc_start: 0.7956 (mtmt) cc_final: 0.7660 (mtmm) REVERT: M 133 ASN cc_start: 0.8059 (m110) cc_final: 0.7345 (m-40) REVERT: M 179 ARG cc_start: 0.6656 (ttp80) cc_final: 0.6319 (ptp90) REVERT: M 183 THR cc_start: 0.7857 (m) cc_final: 0.7599 (m) REVERT: M 200 THR cc_start: 0.8563 (m) cc_final: 0.8319 (p) REVERT: N 172 PHE cc_start: 0.7570 (m-80) cc_final: 0.5608 (t80) REVERT: N 200 THR cc_start: 0.8379 (m) cc_final: 0.8113 (p) REVERT: O 155 LYS cc_start: 0.6755 (ptpp) cc_final: 0.6404 (ptpp) REVERT: P 18 MET cc_start: 0.4691 (ttt) cc_final: 0.4041 (mtp) REVERT: P 20 LEU cc_start: 0.6920 (mt) cc_final: 0.6636 (mt) REVERT: P 66 SER cc_start: 0.7142 (m) cc_final: 0.6453 (t) REVERT: P 140 GLN cc_start: 0.6917 (tt0) cc_final: 0.5742 (mm110) REVERT: P 172 PHE cc_start: 0.7052 (m-80) cc_final: 0.5328 (t80) REVERT: P 174 LYS cc_start: 0.6448 (ttmt) cc_final: 0.4821 (tppt) outliers start: 1 outliers final: 0 residues processed: 868 average time/residue: 0.3089 time to fit residues: 437.9495 Evaluate side-chains 767 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 767 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 280 optimal weight: 7.9990 chunk 295 optimal weight: 1.9990 chunk 269 optimal weight: 7.9990 chunk 287 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 225 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 259 optimal weight: 3.9990 chunk 271 optimal weight: 10.0000 chunk 286 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN C 38 GLN D 133 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 41 GLN O 102 GLN ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 148 GLN P 133 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 24880 Z= 0.323 Angle : 0.774 9.713 33904 Z= 0.408 Chirality : 0.057 0.508 4208 Planarity : 0.006 0.081 4320 Dihedral : 6.763 28.864 3456 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.71 % Favored : 82.29 % Rotamer: Outliers : 0.04 % Allowed : 1.41 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.14), residues: 3280 helix: 0.80 (0.19), residues: 736 sheet: -1.99 (0.18), residues: 672 loop : -3.47 (0.12), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.005 TRP F 127 HIS 0.021 0.003 HIS G 113 PHE 0.031 0.003 PHE J 198 TYR 0.021 0.002 TYR G 107 ARG 0.012 0.001 ARG J 93 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 843 time to evaluate : 2.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 THR cc_start: 0.7066 (p) cc_final: 0.6802 (t) REVERT: A 131 ASN cc_start: 0.6486 (m-40) cc_final: 0.6035 (m-40) REVERT: A 153 LEU cc_start: 0.8013 (mt) cc_final: 0.7680 (mt) REVERT: A 155 LYS cc_start: 0.7786 (ptpt) cc_final: 0.7155 (tptt) REVERT: A 174 LYS cc_start: 0.7043 (mptt) cc_final: 0.6584 (mmtp) REVERT: A 200 THR cc_start: 0.8254 (m) cc_final: 0.7768 (p) REVERT: B 73 LYS cc_start: 0.7906 (tppp) cc_final: 0.7621 (tptt) REVERT: B 158 ILE cc_start: 0.8478 (mt) cc_final: 0.8237 (mt) REVERT: B 200 THR cc_start: 0.8894 (m) cc_final: 0.8118 (p) REVERT: B 202 SER cc_start: 0.7260 (m) cc_final: 0.6984 (m) REVERT: C 49 GLN cc_start: 0.4835 (mm-40) cc_final: 0.4587 (mm-40) REVERT: C 105 LEU cc_start: 0.8919 (mm) cc_final: 0.8565 (mm) REVERT: D 105 LEU cc_start: 0.8185 (mm) cc_final: 0.7967 (mm) REVERT: D 132 THR cc_start: 0.8820 (m) cc_final: 0.8543 (m) REVERT: D 172 PHE cc_start: 0.8622 (m-80) cc_final: 0.8123 (m-80) REVERT: D 200 THR cc_start: 0.8524 (m) cc_final: 0.7638 (p) REVERT: E 73 LYS cc_start: 0.7715 (mtmt) cc_final: 0.7298 (mtpt) REVERT: E 185 LYS cc_start: 0.8206 (ptmt) cc_final: 0.7394 (pttm) REVERT: F 132 THR cc_start: 0.8641 (p) cc_final: 0.8388 (p) REVERT: F 162 THR cc_start: 0.7998 (m) cc_final: 0.7739 (m) REVERT: G 55 ILE cc_start: 0.8076 (mt) cc_final: 0.7643 (mt) REVERT: G 81 ASN cc_start: 0.8379 (m110) cc_final: 0.7676 (m110) REVERT: G 200 THR cc_start: 0.8608 (m) cc_final: 0.8125 (p) REVERT: H 37 GLN cc_start: 0.7136 (tm-30) cc_final: 0.6846 (tm-30) REVERT: H 105 LEU cc_start: 0.8687 (mm) cc_final: 0.8285 (mm) REVERT: H 185 LYS cc_start: 0.8488 (ptmt) cc_final: 0.7929 (pttm) REVERT: I 48 THR cc_start: 0.6338 (p) cc_final: 0.6103 (p) REVERT: I 64 THR cc_start: 0.6706 (t) cc_final: 0.6391 (t) REVERT: I 66 SER cc_start: 0.7563 (m) cc_final: 0.7169 (p) REVERT: I 158 ILE cc_start: 0.8839 (mt) cc_final: 0.8289 (mm) REVERT: I 172 PHE cc_start: 0.7363 (m-80) cc_final: 0.5652 (t80) REVERT: I 204 TYR cc_start: 0.5762 (p90) cc_final: 0.5170 (p90) REVERT: J 18 MET cc_start: 0.4997 (ttt) cc_final: 0.4144 (ptp) REVERT: J 35 TYR cc_start: 0.6053 (t80) cc_final: 0.5789 (t80) REVERT: K 36 LEU cc_start: 0.6472 (mp) cc_final: 0.6252 (mp) REVERT: K 49 GLN cc_start: 0.6391 (mt0) cc_final: 0.5862 (mp10) REVERT: K 68 LYS cc_start: 0.6973 (mmmt) cc_final: 0.6661 (mmtp) REVERT: L 47 THR cc_start: 0.7000 (p) cc_final: 0.6629 (p) REVERT: L 73 LYS cc_start: 0.7092 (tppt) cc_final: 0.6292 (tptm) REVERT: L 179 ARG cc_start: 0.7381 (mtt-85) cc_final: 0.6886 (mtt-85) REVERT: L 202 SER cc_start: 0.6759 (p) cc_final: 0.6552 (m) REVERT: M 73 LYS cc_start: 0.8072 (mtmt) cc_final: 0.7711 (mtmm) REVERT: M 106 LYS cc_start: 0.7641 (ttpp) cc_final: 0.7390 (tttt) REVERT: M 133 ASN cc_start: 0.8251 (m110) cc_final: 0.7615 (m-40) REVERT: M 179 ARG cc_start: 0.6798 (ttp80) cc_final: 0.6447 (ptp90) REVERT: M 200 THR cc_start: 0.8554 (m) cc_final: 0.8297 (p) REVERT: N 132 THR cc_start: 0.7990 (m) cc_final: 0.7759 (m) REVERT: N 172 PHE cc_start: 0.7718 (m-80) cc_final: 0.5648 (t80) REVERT: N 200 THR cc_start: 0.8397 (m) cc_final: 0.8110 (p) REVERT: O 41 GLN cc_start: 0.6281 (mt0) cc_final: 0.6060 (mt0) REVERT: P 18 MET cc_start: 0.4796 (ttt) cc_final: 0.4123 (mtp) REVERT: P 20 LEU cc_start: 0.7023 (mt) cc_final: 0.6684 (mt) REVERT: P 66 SER cc_start: 0.7200 (m) cc_final: 0.6505 (t) REVERT: P 140 GLN cc_start: 0.7140 (tt0) cc_final: 0.5883 (mm110) REVERT: P 172 PHE cc_start: 0.7145 (m-80) cc_final: 0.5333 (t80) outliers start: 1 outliers final: 1 residues processed: 843 average time/residue: 0.3065 time to fit residues: 421.9502 Evaluate side-chains 740 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 739 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 188 optimal weight: 0.3980 chunk 303 optimal weight: 2.9990 chunk 185 optimal weight: 5.9990 chunk 144 optimal weight: 7.9990 chunk 211 optimal weight: 0.9980 chunk 318 optimal weight: 9.9990 chunk 293 optimal weight: 0.6980 chunk 253 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 196 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN ** J 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 91 ASN ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 133 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24880 Z= 0.249 Angle : 0.760 9.496 33904 Z= 0.397 Chirality : 0.057 0.492 4208 Planarity : 0.006 0.081 4320 Dihedral : 6.635 28.327 3456 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.37 % Favored : 84.63 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.14), residues: 3280 helix: 0.91 (0.19), residues: 736 sheet: -2.09 (0.17), residues: 752 loop : -3.43 (0.13), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.005 TRP F 127 HIS 0.008 0.002 HIS O 113 PHE 0.027 0.003 PHE J 198 TYR 0.032 0.001 TYR L 35 ARG 0.010 0.001 ARG H 179 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6560 Ramachandran restraints generated. 3280 Oldfield, 0 Emsley, 3280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 833 time to evaluate : 2.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 THR cc_start: 0.7004 (p) cc_final: 0.6702 (t) REVERT: A 131 ASN cc_start: 0.6342 (m-40) cc_final: 0.5934 (m-40) REVERT: A 153 LEU cc_start: 0.8082 (mt) cc_final: 0.7835 (mt) REVERT: A 155 LYS cc_start: 0.7840 (ptpt) cc_final: 0.7123 (tptt) REVERT: A 174 LYS cc_start: 0.6919 (mptt) cc_final: 0.6378 (mmtp) REVERT: A 200 THR cc_start: 0.8151 (m) cc_final: 0.7699 (p) REVERT: B 73 LYS cc_start: 0.7982 (tppp) cc_final: 0.7768 (tptm) REVERT: B 200 THR cc_start: 0.8820 (m) cc_final: 0.8114 (p) REVERT: B 202 SER cc_start: 0.7201 (m) cc_final: 0.6847 (m) REVERT: C 56 LYS cc_start: 0.8311 (ptpp) cc_final: 0.7977 (ptpp) REVERT: C 105 LEU cc_start: 0.8900 (mm) cc_final: 0.8584 (mm) REVERT: D 105 LEU cc_start: 0.8044 (mm) cc_final: 0.7782 (mm) REVERT: D 132 THR cc_start: 0.8713 (m) cc_final: 0.8474 (m) REVERT: D 172 PHE cc_start: 0.8426 (m-80) cc_final: 0.8012 (m-80) REVERT: D 200 THR cc_start: 0.8440 (m) cc_final: 0.7809 (p) REVERT: E 143 ASP cc_start: 0.7906 (t0) cc_final: 0.7592 (t0) REVERT: E 185 LYS cc_start: 0.8195 (ptmt) cc_final: 0.7363 (pttm) REVERT: F 200 THR cc_start: 0.7962 (m) cc_final: 0.7378 (p) REVERT: G 55 ILE cc_start: 0.8167 (mt) cc_final: 0.7811 (mt) REVERT: G 81 ASN cc_start: 0.8150 (m110) cc_final: 0.7506 (m110) REVERT: G 96 LEU cc_start: 0.8580 (tt) cc_final: 0.8255 (tt) REVERT: G 200 THR cc_start: 0.8574 (m) cc_final: 0.8074 (p) REVERT: H 37 GLN cc_start: 0.7248 (tm-30) cc_final: 0.6967 (tm-30) REVERT: H 105 LEU cc_start: 0.8569 (mm) cc_final: 0.8187 (mm) REVERT: H 185 LYS cc_start: 0.8413 (ptmt) cc_final: 0.7833 (pttm) REVERT: H 200 THR cc_start: 0.8550 (m) cc_final: 0.7815 (p) REVERT: I 48 THR cc_start: 0.6402 (p) cc_final: 0.6040 (p) REVERT: I 64 THR cc_start: 0.6290 (t) cc_final: 0.5856 (t) REVERT: I 66 SER cc_start: 0.7349 (m) cc_final: 0.6979 (p) REVERT: I 73 LYS cc_start: 0.7513 (tptp) cc_final: 0.7161 (tptp) REVERT: I 158 ILE cc_start: 0.8814 (mt) cc_final: 0.8284 (mm) REVERT: I 172 PHE cc_start: 0.7235 (m-80) cc_final: 0.5642 (t80) REVERT: I 204 TYR cc_start: 0.5790 (p90) cc_final: 0.5264 (p90) REVERT: J 18 MET cc_start: 0.5066 (ttt) cc_final: 0.4206 (ptp) REVERT: J 35 TYR cc_start: 0.5927 (t80) cc_final: 0.5713 (t80) REVERT: J 208 VAL cc_start: 0.9050 (t) cc_final: 0.8718 (t) REVERT: J 210 GLU cc_start: 0.8208 (pm20) cc_final: 0.7817 (pm20) REVERT: K 49 GLN cc_start: 0.6124 (mt0) cc_final: 0.5598 (mp10) REVERT: K 68 LYS cc_start: 0.6798 (mmmt) cc_final: 0.6306 (mmtp) REVERT: L 47 THR cc_start: 0.7198 (p) cc_final: 0.6829 (p) REVERT: L 105 LEU cc_start: 0.8332 (mm) cc_final: 0.7930 (mm) REVERT: L 109 LYS cc_start: 0.8018 (mppt) cc_final: 0.7574 (mppt) REVERT: L 179 ARG cc_start: 0.7309 (mtt-85) cc_final: 0.6871 (mtt-85) REVERT: M 98 ASN cc_start: 0.5692 (t0) cc_final: 0.5265 (m-40) REVERT: M 105 LEU cc_start: 0.8254 (mm) cc_final: 0.8035 (mm) REVERT: M 106 LYS cc_start: 0.7581 (ttpp) cc_final: 0.7290 (tttt) REVERT: M 179 ARG cc_start: 0.6734 (ttp80) cc_final: 0.6470 (ptp90) REVERT: M 200 THR cc_start: 0.8619 (m) cc_final: 0.8305 (p) REVERT: N 72 GLU cc_start: 0.6164 (pm20) cc_final: 0.5955 (pm20) REVERT: N 132 THR cc_start: 0.8006 (m) cc_final: 0.7751 (m) REVERT: N 172 PHE cc_start: 0.7625 (m-80) cc_final: 0.5587 (t80) REVERT: N 200 THR cc_start: 0.8333 (m) cc_final: 0.8085 (p) REVERT: O 41 GLN cc_start: 0.5905 (mt0) cc_final: 0.5643 (mt0) REVERT: O 43 THR cc_start: 0.7968 (p) cc_final: 0.7763 (t) REVERT: P 18 MET cc_start: 0.4880 (ttt) cc_final: 0.4058 (mtp) REVERT: P 20 LEU cc_start: 0.6962 (mt) cc_final: 0.6640 (mt) REVERT: P 66 SER cc_start: 0.7064 (m) cc_final: 0.6398 (t) REVERT: P 132 THR cc_start: 0.7905 (m) cc_final: 0.7615 (m) REVERT: P 140 GLN cc_start: 0.6796 (tt0) cc_final: 0.5985 (mm110) REVERT: P 172 PHE cc_start: 0.7090 (m-80) cc_final: 0.5373 (t80) outliers start: 0 outliers final: 0 residues processed: 833 average time/residue: 0.3103 time to fit residues: 424.7793 Evaluate side-chains 725 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 725 time to evaluate : 2.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 201 optimal weight: 0.9990 chunk 270 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 234 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 254 optimal weight: 0.0370 chunk 106 optimal weight: 0.0970 chunk 261 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN D 133 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 102 GLN O 212 GLN P 133 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.188735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.179231 restraints weight = 32107.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.181411 restraints weight = 21387.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.182886 restraints weight = 15112.322| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 24880 Z= 0.217 Angle : 0.721 11.137 33904 Z= 0.375 Chirality : 0.054 0.427 4208 Planarity : 0.006 0.081 4320 Dihedral : 6.312 29.061 3456 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.16 % Favored : 83.84 % Rotamer: Outliers : 0.04 % Allowed : 0.52 % Favored : 99.44 % 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: -2.91 (0.14), residues: 3280 helix: 1.09 (0.19), residues: 736 sheet: -1.98 (0.18), residues: 752 loop : -3.40 (0.13), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP F 127 HIS 0.010 0.002 HIS I 113 PHE 0.024 0.002 PHE O 198 TYR 0.031 0.001 TYR L 35 ARG 0.008 0.001 ARG H 179 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7193.62 seconds wall clock time: 129 minutes 31.76 seconds (7771.76 seconds total)