Starting phenix.real_space_refine on Sat Jan 20 04:35:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e0f_8946/01_2024/6e0f_8946.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e0f_8946/01_2024/6e0f_8946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e0f_8946/01_2024/6e0f_8946.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e0f_8946/01_2024/6e0f_8946.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e0f_8946/01_2024/6e0f_8946.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e0f_8946/01_2024/6e0f_8946.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.014 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 80 5.16 5 C 8700 2.51 5 N 2320 2.21 5 O 2550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13650 Number of models: 1 Model: "" Number of chains: 10 Chain: "J" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1365 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 7, 'TRANS': 166} Chain: "A" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1365 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 7, 'TRANS': 166} Chain: "I" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1365 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 7, 'TRANS': 166} Chain: "E" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1365 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 7, 'TRANS': 166} Chain: "G" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1365 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 7, 'TRANS': 166} Chain: "F" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1365 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 7, 'TRANS': 166} Chain: "B" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1365 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 7, 'TRANS': 166} Chain: "C" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1365 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 7, 'TRANS': 166} Chain: "D" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1365 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 7, 'TRANS': 166} Chain: "H" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1365 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 7, 'TRANS': 166} Time building chain proxies: 7.79, per 1000 atoms: 0.57 Number of scatterers: 13650 At special positions: 0 Unit cell: (133, 135, 61, 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 80 16.00 O 2550 8.00 N 2320 7.00 C 8700 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: 5.66 Conformation dependent library (CDL) restraints added in 2.5 seconds 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 15 sheets defined 27.6% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.623A pdb=" N LYS J 64 " --> pdb=" O ASN J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'J' and resid 82 through 90 removed outlier: 4.199A pdb=" N PHE J 88 " --> pdb=" O GLU J 84 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER J 89 " --> pdb=" O ILE J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 97 removed outlier: 3.634A pdb=" N GLU J 96 " --> pdb=" O HIS J 92 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS J 97 " --> pdb=" O ALA J 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 92 through 97' Processing helix chain 'J' and resid 109 through 119 Processing helix chain 'J' and resid 181 through 198 removed outlier: 3.961A pdb=" N LEU J 189 " --> pdb=" O ALA J 185 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN J 193 " --> pdb=" O LEU J 189 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN J 198 " --> pdb=" O TYR J 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 64 removed outlier: 3.622A pdb=" N LYS A 64 " --> pdb=" O ASN A 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 82 through 90 removed outlier: 4.200A pdb=" N PHE A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.633A pdb=" N GLU A 96 " --> pdb=" O HIS A 92 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 92 through 97' Processing helix chain 'A' and resid 109 through 119 Processing helix chain 'A' and resid 181 through 198 removed outlier: 3.961A pdb=" N LEU A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN A 198 " --> pdb=" O TYR A 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.623A pdb=" N LYS I 64 " --> pdb=" O ASN I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'I' and resid 82 through 90 removed outlier: 4.198A pdb=" N PHE I 88 " --> pdb=" O GLU I 84 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER I 89 " --> pdb=" O ILE I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 97 removed outlier: 3.633A pdb=" N GLU I 96 " --> pdb=" O HIS I 92 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS I 97 " --> pdb=" O ALA I 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 92 through 97' Processing helix chain 'I' and resid 109 through 119 Processing helix chain 'I' and resid 181 through 198 removed outlier: 3.960A pdb=" N LEU I 189 " --> pdb=" O ALA I 185 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN I 193 " --> pdb=" O LEU I 189 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN I 198 " --> pdb=" O TYR I 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 64 removed outlier: 3.623A pdb=" N LYS E 64 " --> pdb=" O ASN E 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 64' Processing helix chain 'E' and resid 82 through 90 removed outlier: 4.199A pdb=" N PHE E 88 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER E 89 " --> pdb=" O ILE E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 97 removed outlier: 3.634A pdb=" N GLU E 96 " --> pdb=" O HIS E 92 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS E 97 " --> pdb=" O ALA E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 97' Processing helix chain 'E' and resid 109 through 119 Processing helix chain 'E' and resid 181 through 198 removed outlier: 3.961A pdb=" N LEU E 189 " --> pdb=" O ALA E 185 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN E 198 " --> pdb=" O TYR E 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 removed outlier: 3.623A pdb=" N LYS G 64 " --> pdb=" O ASN G 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 64' Processing helix chain 'G' and resid 82 through 90 removed outlier: 4.199A pdb=" N PHE G 88 " --> pdb=" O GLU G 84 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER G 89 " --> pdb=" O ILE G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 removed outlier: 3.634A pdb=" N GLU G 96 " --> pdb=" O HIS G 92 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS G 97 " --> pdb=" O ALA G 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 92 through 97' Processing helix chain 'G' and resid 109 through 119 Processing helix chain 'G' and resid 181 through 198 removed outlier: 3.960A pdb=" N LEU G 189 " --> pdb=" O ALA G 185 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN G 193 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN G 198 " --> pdb=" O TYR G 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 64 removed outlier: 3.622A pdb=" N LYS F 64 " --> pdb=" O ASN F 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 61 through 64' Processing helix chain 'F' and resid 82 through 90 removed outlier: 4.199A pdb=" N PHE F 88 " --> pdb=" O GLU F 84 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER F 89 " --> pdb=" O ILE F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 97 removed outlier: 3.634A pdb=" N GLU F 96 " --> pdb=" O HIS F 92 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS F 97 " --> pdb=" O ALA F 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 92 through 97' Processing helix chain 'F' and resid 109 through 119 Processing helix chain 'F' and resid 181 through 198 removed outlier: 3.960A pdb=" N LEU F 189 " --> pdb=" O ALA F 185 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN F 193 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN F 198 " --> pdb=" O TYR F 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 64 removed outlier: 3.623A pdb=" N LYS B 64 " --> pdb=" O ASN B 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 64' Processing helix chain 'B' and resid 82 through 90 removed outlier: 4.198A pdb=" N PHE B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 97 removed outlier: 3.634A pdb=" N GLU B 96 " --> pdb=" O HIS B 92 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 92 through 97' Processing helix chain 'B' and resid 109 through 119 Processing helix chain 'B' and resid 181 through 198 removed outlier: 3.960A pdb=" N LEU B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN B 198 " --> pdb=" O TYR B 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.622A pdb=" N LYS C 64 " --> pdb=" O ASN C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 82 through 90 removed outlier: 4.199A pdb=" N PHE C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER C 89 " --> pdb=" O ILE C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 removed outlier: 3.633A pdb=" N GLU C 96 " --> pdb=" O HIS C 92 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS C 97 " --> pdb=" O ALA C 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 92 through 97' Processing helix chain 'C' and resid 109 through 119 Processing helix chain 'C' and resid 181 through 198 removed outlier: 3.960A pdb=" N LEU C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN C 198 " --> pdb=" O TYR C 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 removed outlier: 3.623A pdb=" N LYS D 64 " --> pdb=" O ASN D 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 64' Processing helix chain 'D' and resid 82 through 90 removed outlier: 4.199A pdb=" N PHE D 88 " --> pdb=" O GLU D 84 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER D 89 " --> pdb=" O ILE D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 97 removed outlier: 3.634A pdb=" N GLU D 96 " --> pdb=" O HIS D 92 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 92 through 97' Processing helix chain 'D' and resid 109 through 119 Processing helix chain 'D' and resid 181 through 198 removed outlier: 3.961A pdb=" N LEU D 189 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN D 193 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN D 198 " --> pdb=" O TYR D 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.622A pdb=" N LYS H 64 " --> pdb=" O ASN H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 82 through 90 removed outlier: 4.198A pdb=" N PHE H 88 " --> pdb=" O GLU H 84 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER H 89 " --> pdb=" O ILE H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 97 removed outlier: 3.633A pdb=" N GLU H 96 " --> pdb=" O HIS H 92 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS H 97 " --> pdb=" O ALA H 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 92 through 97' Processing helix chain 'H' and resid 109 through 119 Processing helix chain 'H' and resid 181 through 198 removed outlier: 3.960A pdb=" N LEU H 189 " --> pdb=" O ALA H 185 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN H 193 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN H 198 " --> pdb=" O TYR H 194 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 54 through 59 Processing sheet with id=AA2, first strand: chain 'J' and resid 100 through 105 removed outlier: 6.251A pdb=" N TYR J 67 " --> pdb=" O GLN J 101 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL J 103 " --> pdb=" O TYR J 67 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL J 69 " --> pdb=" O VAL J 103 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL J 105 " --> pdb=" O VAL J 69 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N PHE J 71 " --> pdb=" O VAL J 105 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TYR A 67 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL A 103 " --> pdb=" O TYR A 67 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL A 69 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL A 105 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N PHE A 71 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 59 Processing sheet with id=AA4, first strand: chain 'I' and resid 54 through 59 Processing sheet with id=AA5, first strand: chain 'I' and resid 100 through 105 removed outlier: 6.251A pdb=" N TYR I 67 " --> pdb=" O GLN I 101 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL I 103 " --> pdb=" O TYR I 67 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL I 69 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL I 105 " --> pdb=" O VAL I 69 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N PHE I 71 " --> pdb=" O VAL I 105 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TYR E 67 " --> pdb=" O GLN E 101 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL E 103 " --> pdb=" O TYR E 67 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL E 69 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL E 105 " --> pdb=" O VAL E 69 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N PHE E 71 " --> pdb=" O VAL E 105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 54 through 59 Processing sheet with id=AA7, first strand: chain 'G' and resid 54 through 59 Processing sheet with id=AA8, first strand: chain 'G' and resid 100 through 105 removed outlier: 6.251A pdb=" N TYR G 67 " --> pdb=" O GLN G 101 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL G 103 " --> pdb=" O TYR G 67 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL G 69 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL G 105 " --> pdb=" O VAL G 69 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N PHE G 71 " --> pdb=" O VAL G 105 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TYR C 67 " --> pdb=" O GLN C 101 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL C 103 " --> pdb=" O TYR C 67 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL C 69 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL C 105 " --> pdb=" O VAL C 69 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N PHE C 71 " --> pdb=" O VAL C 105 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 54 through 59 Processing sheet with id=AB1, first strand: chain 'F' and resid 100 through 105 removed outlier: 6.251A pdb=" N TYR F 67 " --> pdb=" O GLN F 101 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL F 103 " --> pdb=" O TYR F 67 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL F 69 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL F 105 " --> pdb=" O VAL F 69 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N PHE F 71 " --> pdb=" O VAL F 105 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TYR B 67 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL B 103 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL B 69 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL B 105 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N PHE B 71 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 54 through 59 Processing sheet with id=AB3, first strand: chain 'C' and resid 54 through 59 Processing sheet with id=AB4, first strand: chain 'D' and resid 54 through 59 Processing sheet with id=AB5, first strand: chain 'D' and resid 100 through 105 removed outlier: 6.251A pdb=" N TYR D 67 " --> pdb=" O GLN D 101 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL D 103 " --> pdb=" O TYR D 67 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL D 69 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL D 105 " --> pdb=" O VAL D 69 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N PHE D 71 " --> pdb=" O VAL D 105 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TYR H 67 " --> pdb=" O GLN H 101 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL H 103 " --> pdb=" O TYR H 67 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL H 69 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL H 105 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N PHE H 71 " --> pdb=" O VAL H 105 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 54 through 59 410 hydrogen bonds defined for protein. 1140 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.77 Time building geometry restraints manager: 5.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4480 1.34 - 1.46: 2581 1.46 - 1.57: 6739 1.57 - 1.69: 0 1.69 - 1.81: 130 Bond restraints: 13930 Sorted by residual: bond pdb=" CB PHE D 71 " pdb=" CG PHE D 71 " ideal model delta sigma weight residual 1.502 1.435 0.067 2.30e-02 1.89e+03 8.55e+00 bond pdb=" CB PHE H 71 " pdb=" CG PHE H 71 " ideal model delta sigma weight residual 1.502 1.435 0.067 2.30e-02 1.89e+03 8.52e+00 bond pdb=" CB PHE E 71 " pdb=" CG PHE E 71 " ideal model delta sigma weight residual 1.502 1.435 0.067 2.30e-02 1.89e+03 8.49e+00 bond pdb=" CB PHE J 71 " pdb=" CG PHE J 71 " ideal model delta sigma weight residual 1.502 1.435 0.067 2.30e-02 1.89e+03 8.45e+00 bond pdb=" CB PHE F 71 " pdb=" CG PHE F 71 " ideal model delta sigma weight residual 1.502 1.435 0.067 2.30e-02 1.89e+03 8.41e+00 ... (remaining 13925 not shown) Histogram of bond angle deviations from ideal: 97.90 - 105.11: 271 105.11 - 112.31: 6741 112.31 - 119.52: 4953 119.52 - 126.73: 6765 126.73 - 133.94: 130 Bond angle restraints: 18860 Sorted by residual: angle pdb=" N VAL F 38 " pdb=" CA VAL F 38 " pdb=" CB VAL F 38 " ideal model delta sigma weight residual 112.08 105.85 6.23 1.68e+00 3.54e-01 1.37e+01 angle pdb=" N VAL A 38 " pdb=" CA VAL A 38 " pdb=" CB VAL A 38 " ideal model delta sigma weight residual 112.08 105.88 6.20 1.68e+00 3.54e-01 1.36e+01 angle pdb=" N VAL I 38 " pdb=" CA VAL I 38 " pdb=" CB VAL I 38 " ideal model delta sigma weight residual 112.08 105.89 6.19 1.68e+00 3.54e-01 1.36e+01 angle pdb=" N VAL C 38 " pdb=" CA VAL C 38 " pdb=" CB VAL C 38 " ideal model delta sigma weight residual 112.08 105.89 6.19 1.68e+00 3.54e-01 1.36e+01 angle pdb=" N VAL J 38 " pdb=" CA VAL J 38 " pdb=" CB VAL J 38 " ideal model delta sigma weight residual 112.08 105.90 6.18 1.68e+00 3.54e-01 1.35e+01 ... (remaining 18855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.34: 7092 9.34 - 18.69: 958 18.69 - 28.03: 210 28.03 - 37.38: 50 37.38 - 46.72: 40 Dihedral angle restraints: 8350 sinusoidal: 3310 harmonic: 5040 Sorted by residual: dihedral pdb=" CA ARG G 121 " pdb=" C ARG G 121 " pdb=" N LYS G 122 " pdb=" CA LYS G 122 " ideal model delta harmonic sigma weight residual -180.00 -159.56 -20.44 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ARG F 121 " pdb=" C ARG F 121 " pdb=" N LYS F 122 " pdb=" CA LYS F 122 " ideal model delta harmonic sigma weight residual -180.00 -159.56 -20.44 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ARG C 121 " pdb=" C ARG C 121 " pdb=" N LYS C 122 " pdb=" CA LYS C 122 " ideal model delta harmonic sigma weight residual -180.00 -159.57 -20.43 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 8347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1294 0.054 - 0.108: 598 0.108 - 0.162: 168 0.162 - 0.215: 20 0.215 - 0.269: 20 Chirality restraints: 2100 Sorted by residual: chirality pdb=" CA TYR G 33 " pdb=" N TYR G 33 " pdb=" C TYR G 33 " pdb=" CB TYR G 33 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA TYR H 33 " pdb=" N TYR H 33 " pdb=" C TYR H 33 " pdb=" CB TYR H 33 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA TYR E 33 " pdb=" N TYR E 33 " pdb=" C TYR E 33 " pdb=" CB TYR E 33 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 2097 not shown) Planarity restraints: 2460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 116 " 0.023 2.00e-02 2.50e+03 1.61e-02 6.45e+00 pdb=" CG TRP F 116 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP F 116 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP F 116 " -0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP F 116 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 116 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP F 116 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 116 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 116 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP F 116 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 116 " -0.024 2.00e-02 2.50e+03 1.60e-02 6.43e+00 pdb=" CG TRP G 116 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP G 116 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP G 116 " 0.012 2.00e-02 2.50e+03 pdb=" NE1 TRP G 116 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP G 116 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP G 116 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 116 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 116 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP G 116 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 116 " 0.023 2.00e-02 2.50e+03 1.60e-02 6.41e+00 pdb=" CG TRP B 116 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 116 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP B 116 " -0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP B 116 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 116 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 116 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 116 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 116 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 116 " 0.000 2.00e-02 2.50e+03 ... (remaining 2457 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 137 2.58 - 3.16: 11462 3.16 - 3.74: 20443 3.74 - 4.32: 31323 4.32 - 4.90: 48905 Nonbonded interactions: 112270 Sorted by model distance: nonbonded pdb=" O ARG E 34 " pdb=" OG1 THR E 35 " model vdw 1.999 2.440 nonbonded pdb=" O ARG J 34 " pdb=" OG1 THR J 35 " model vdw 1.999 2.440 nonbonded pdb=" O ARG I 34 " pdb=" OG1 THR I 35 " model vdw 1.999 2.440 nonbonded pdb=" O ARG D 34 " pdb=" OG1 THR D 35 " model vdw 1.999 2.440 nonbonded pdb=" O ARG A 34 " pdb=" OG1 THR A 35 " model vdw 1.999 2.440 ... (remaining 112265 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' } 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: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.070 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 38.010 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.080 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 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 : 0.010 0.067 13930 Z= 0.681 Angle : 1.010 7.971 18860 Z= 0.571 Chirality : 0.068 0.269 2100 Planarity : 0.006 0.048 2460 Dihedral : 9.643 46.720 5110 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.14 % Favored : 91.28 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % 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: -4.79 (0.16), residues: 1720 helix: -4.51 (0.09), residues: 500 sheet: -2.48 (0.23), residues: 390 loop : -2.53 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.010 TRP F 116 HIS 0.009 0.003 HIS H 113 PHE 0.023 0.006 PHE I 160 TYR 0.029 0.003 TYR B 67 ARG 0.002 0.000 ARG I 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 616 time to evaluate : 1.530 Fit side-chains REVERT: A 169 ARG cc_start: 0.8375 (mmm-85) cc_final: 0.8073 (mtt-85) REVERT: I 100 THR cc_start: 0.9030 (t) cc_final: 0.8811 (m) REVERT: I 109 SER cc_start: 0.8250 (t) cc_final: 0.8004 (m) REVERT: I 169 ARG cc_start: 0.8459 (mmm-85) cc_final: 0.8219 (mtp85) REVERT: E 169 ARG cc_start: 0.8421 (mmm-85) cc_final: 0.8131 (mtp85) REVERT: E 190 GLU cc_start: 0.7754 (tt0) cc_final: 0.7482 (tm-30) REVERT: G 62 ASP cc_start: 0.8340 (m-30) cc_final: 0.7944 (t0) REVERT: G 163 ASP cc_start: 0.7090 (p0) cc_final: 0.6789 (p0) REVERT: G 167 ILE cc_start: 0.8781 (mm) cc_final: 0.8579 (mt) REVERT: G 169 ARG cc_start: 0.8463 (mmm-85) cc_final: 0.7783 (mtt-85) REVERT: F 60 MET cc_start: 0.8230 (ttt) cc_final: 0.7535 (ttt) REVERT: F 62 ASP cc_start: 0.8086 (m-30) cc_final: 0.7823 (t0) REVERT: F 143 ARG cc_start: 0.8467 (ttm-80) cc_final: 0.8210 (ttm-80) REVERT: F 169 ARG cc_start: 0.8394 (mmm-85) cc_final: 0.8141 (mtp85) REVERT: B 73 TYR cc_start: 0.8959 (p90) cc_final: 0.8740 (p90) REVERT: B 164 LYS cc_start: 0.8135 (pttt) cc_final: 0.7933 (ptmt) REVERT: B 169 ARG cc_start: 0.8333 (mmm-85) cc_final: 0.8025 (mmt90) REVERT: C 99 ASN cc_start: 0.8348 (t0) cc_final: 0.8127 (t0) REVERT: D 60 MET cc_start: 0.8263 (ttt) cc_final: 0.6935 (ttt) REVERT: D 62 ASP cc_start: 0.8229 (m-30) cc_final: 0.7705 (t0) REVERT: D 108 ASP cc_start: 0.7915 (m-30) cc_final: 0.6922 (m-30) REVERT: D 169 ARG cc_start: 0.8256 (mmm-85) cc_final: 0.7994 (mtp85) outliers start: 0 outliers final: 0 residues processed: 616 average time/residue: 0.2744 time to fit residues: 235.7417 Evaluate side-chains 420 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 420 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.9990 chunk 128 optimal weight: 20.0000 chunk 71 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13930 Z= 0.205 Angle : 0.623 7.919 18860 Z= 0.337 Chirality : 0.049 0.146 2100 Planarity : 0.005 0.039 2460 Dihedral : 5.349 17.524 1890 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.53 % Allowed : 16.92 % Favored : 80.55 % 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: -3.45 (0.20), residues: 1720 helix: -3.05 (0.16), residues: 490 sheet: -2.53 (0.24), residues: 440 loop : -1.38 (0.25), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 116 HIS 0.003 0.001 HIS B 113 PHE 0.017 0.002 PHE D 77 TYR 0.019 0.002 TYR J 194 ARG 0.006 0.001 ARG H 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 544 time to evaluate : 1.588 Fit side-chains revert: symmetry clash REVERT: J 58 ILE cc_start: 0.8696 (mm) cc_final: 0.8452 (mt) REVERT: J 62 ASP cc_start: 0.8258 (m-30) cc_final: 0.8029 (t0) REVERT: J 84 GLU cc_start: 0.7982 (tp30) cc_final: 0.7773 (tp30) REVERT: J 108 ASP cc_start: 0.8041 (m-30) cc_final: 0.7664 (m-30) REVERT: A 62 ASP cc_start: 0.8246 (m-30) cc_final: 0.7758 (t0) REVERT: A 63 TYR cc_start: 0.8658 (m-80) cc_final: 0.8231 (m-80) REVERT: A 66 LYS cc_start: 0.6740 (mtmm) cc_final: 0.6457 (mtmm) REVERT: A 73 TYR cc_start: 0.8585 (p90) cc_final: 0.8230 (p90) REVERT: A 169 ARG cc_start: 0.8337 (mmm-85) cc_final: 0.8125 (mmt90) REVERT: I 62 ASP cc_start: 0.8164 (m-30) cc_final: 0.7681 (t0) REVERT: I 63 TYR cc_start: 0.8563 (m-80) cc_final: 0.8296 (m-80) REVERT: I 76 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7238 (m-30) REVERT: I 131 ILE cc_start: 0.8869 (mt) cc_final: 0.8656 (tt) REVERT: E 99 ASN cc_start: 0.7981 (t0) cc_final: 0.7699 (t0) REVERT: E 169 ARG cc_start: 0.8176 (mmm-85) cc_final: 0.7798 (mtp85) REVERT: G 62 ASP cc_start: 0.8303 (m-30) cc_final: 0.7890 (t0) REVERT: G 84 GLU cc_start: 0.8005 (tp30) cc_final: 0.7802 (tp30) REVERT: F 44 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7164 (mm-40) REVERT: F 48 GLN cc_start: 0.8873 (mt0) cc_final: 0.8572 (mt0) REVERT: F 60 MET cc_start: 0.8366 (ttt) cc_final: 0.7984 (ttt) REVERT: F 62 ASP cc_start: 0.8220 (m-30) cc_final: 0.7874 (t0) REVERT: F 100 THR cc_start: 0.8921 (m) cc_final: 0.8689 (p) REVERT: F 139 MET cc_start: 0.7986 (mtm) cc_final: 0.7781 (mtm) REVERT: F 169 ARG cc_start: 0.8186 (mmm-85) cc_final: 0.7970 (mmt90) REVERT: B 60 MET cc_start: 0.7541 (ttp) cc_final: 0.6716 (ttp) REVERT: B 145 TYR cc_start: 0.9098 (m-10) cc_final: 0.8806 (m-80) REVERT: C 58 ILE cc_start: 0.8606 (mm) cc_final: 0.8340 (mt) REVERT: C 67 TYR cc_start: 0.8107 (m-10) cc_final: 0.7699 (m-10) REVERT: C 84 GLU cc_start: 0.8068 (tp30) cc_final: 0.7760 (tp30) REVERT: C 99 ASN cc_start: 0.8174 (t0) cc_final: 0.7879 (t0) REVERT: D 62 ASP cc_start: 0.8279 (m-30) cc_final: 0.7978 (t0) REVERT: D 63 TYR cc_start: 0.8584 (m-80) cc_final: 0.8185 (m-80) REVERT: D 67 TYR cc_start: 0.7877 (m-10) cc_final: 0.7300 (m-10) REVERT: D 76 ASP cc_start: 0.7303 (OUTLIER) cc_final: 0.6909 (m-30) REVERT: D 99 ASN cc_start: 0.7990 (t0) cc_final: 0.7788 (t0) REVERT: D 131 ILE cc_start: 0.9064 (mt) cc_final: 0.8790 (tt) REVERT: H 67 TYR cc_start: 0.8073 (m-10) cc_final: 0.7774 (m-10) REVERT: H 100 THR cc_start: 0.9059 (t) cc_final: 0.8839 (p) REVERT: H 169 ARG cc_start: 0.8207 (mmm-85) cc_final: 0.7943 (mmt90) REVERT: H 197 GLU cc_start: 0.7500 (tt0) cc_final: 0.7295 (tt0) outliers start: 37 outliers final: 15 residues processed: 555 average time/residue: 0.2746 time to fit residues: 220.5276 Evaluate side-chains 479 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 462 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 154 optimal weight: 0.0770 chunk 167 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 chunk 153 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 52 ASN J 198 ASN A 193 GLN E 52 ASN E 198 ASN H 198 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 13930 Z= 0.233 Angle : 0.600 9.106 18860 Z= 0.318 Chirality : 0.049 0.143 2100 Planarity : 0.004 0.033 2460 Dihedral : 4.856 19.231 1890 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.26 % Allowed : 18.22 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.21), residues: 1720 helix: -1.95 (0.20), residues: 470 sheet: -2.36 (0.24), residues: 460 loop : -1.05 (0.26), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP I 116 HIS 0.004 0.001 HIS E 113 PHE 0.032 0.002 PHE I 77 TYR 0.028 0.002 TYR G 67 ARG 0.006 0.001 ARG I 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 496 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 58 ILE cc_start: 0.8820 (mm) cc_final: 0.8506 (mt) REVERT: J 62 ASP cc_start: 0.8238 (m-30) cc_final: 0.7947 (t0) REVERT: J 84 GLU cc_start: 0.7762 (tp30) cc_final: 0.7517 (tp30) REVERT: J 108 ASP cc_start: 0.8051 (m-30) cc_final: 0.7759 (m-30) REVERT: J 190 GLU cc_start: 0.7842 (tt0) cc_final: 0.7395 (tm-30) REVERT: J 197 GLU cc_start: 0.7965 (tt0) cc_final: 0.7738 (tt0) REVERT: A 48 GLN cc_start: 0.8727 (mt0) cc_final: 0.8334 (mt0) REVERT: A 62 ASP cc_start: 0.8094 (m-30) cc_final: 0.7784 (t0) REVERT: A 66 LYS cc_start: 0.6781 (mtmm) cc_final: 0.6487 (mtmm) REVERT: A 190 GLU cc_start: 0.8021 (tt0) cc_final: 0.7630 (tm-30) REVERT: I 62 ASP cc_start: 0.8243 (m-30) cc_final: 0.7965 (t0) REVERT: I 76 ASP cc_start: 0.7403 (t0) cc_final: 0.7173 (m-30) REVERT: I 77 PHE cc_start: 0.8645 (m-80) cc_final: 0.8274 (m-10) REVERT: I 99 ASN cc_start: 0.8279 (t0) cc_final: 0.8052 (t0) REVERT: I 190 GLU cc_start: 0.8048 (tt0) cc_final: 0.7476 (tm-30) REVERT: E 58 ILE cc_start: 0.8728 (mm) cc_final: 0.8451 (mt) REVERT: E 77 PHE cc_start: 0.8861 (m-80) cc_final: 0.8642 (m-10) REVERT: E 99 ASN cc_start: 0.8133 (t0) cc_final: 0.7911 (t0) REVERT: G 58 ILE cc_start: 0.8699 (mm) cc_final: 0.8453 (mt) REVERT: G 62 ASP cc_start: 0.8203 (m-30) cc_final: 0.7988 (t0) REVERT: G 84 GLU cc_start: 0.8128 (tp30) cc_final: 0.7868 (tp30) REVERT: G 99 ASN cc_start: 0.8454 (t0) cc_final: 0.8131 (t0) REVERT: F 44 GLN cc_start: 0.7725 (mm-40) cc_final: 0.7293 (mm-40) REVERT: F 60 MET cc_start: 0.8379 (ttt) cc_final: 0.8009 (ttt) REVERT: F 62 ASP cc_start: 0.8182 (m-30) cc_final: 0.7924 (t0) REVERT: F 64 LYS cc_start: 0.7291 (OUTLIER) cc_final: 0.7035 (ttmm) REVERT: F 67 TYR cc_start: 0.7674 (m-10) cc_final: 0.7003 (m-10) REVERT: F 100 THR cc_start: 0.8906 (m) cc_final: 0.8651 (p) REVERT: F 108 ASP cc_start: 0.8142 (m-30) cc_final: 0.7520 (m-30) REVERT: B 63 TYR cc_start: 0.8531 (m-80) cc_final: 0.8173 (m-80) REVERT: B 99 ASN cc_start: 0.8273 (t0) cc_final: 0.7964 (t0) REVERT: B 145 TYR cc_start: 0.9090 (m-10) cc_final: 0.8817 (m-80) REVERT: C 58 ILE cc_start: 0.8732 (mm) cc_final: 0.8487 (mt) REVERT: C 67 TYR cc_start: 0.7908 (m-10) cc_final: 0.7585 (m-10) REVERT: C 84 GLU cc_start: 0.8084 (tp30) cc_final: 0.7786 (tp30) REVERT: D 63 TYR cc_start: 0.8598 (m-80) cc_final: 0.8281 (m-80) REVERT: D 108 ASP cc_start: 0.7714 (t0) cc_final: 0.7513 (t70) REVERT: D 157 ARG cc_start: 0.8593 (mtp85) cc_final: 0.8350 (mtp85) REVERT: D 190 GLU cc_start: 0.7842 (tt0) cc_final: 0.7511 (tm-30) REVERT: H 58 ILE cc_start: 0.8759 (mm) cc_final: 0.8538 (mt) REVERT: H 60 MET cc_start: 0.7892 (ttp) cc_final: 0.7667 (ttp) REVERT: H 67 TYR cc_start: 0.8028 (m-10) cc_final: 0.7815 (m-10) REVERT: H 83 THR cc_start: 0.8811 (m) cc_final: 0.8588 (t) REVERT: H 84 GLU cc_start: 0.8023 (tp30) cc_final: 0.7786 (tp30) REVERT: H 99 ASN cc_start: 0.8203 (t0) cc_final: 0.7908 (t0) REVERT: H 100 THR cc_start: 0.9040 (t) cc_final: 0.8794 (p) REVERT: H 190 GLU cc_start: 0.7973 (tt0) cc_final: 0.7453 (tm-30) outliers start: 33 outliers final: 17 residues processed: 504 average time/residue: 0.2615 time to fit residues: 189.3765 Evaluate side-chains 484 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 466 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain F residue 64 LYS Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 155 optimal weight: 0.9990 chunk 164 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 13930 Z= 0.418 Angle : 0.671 9.546 18860 Z= 0.357 Chirality : 0.052 0.160 2100 Planarity : 0.004 0.034 2460 Dihedral : 4.986 18.252 1890 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.81 % Allowed : 19.38 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.21), residues: 1720 helix: -1.54 (0.20), residues: 470 sheet: -2.34 (0.24), residues: 440 loop : -0.75 (0.26), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP J 116 HIS 0.007 0.002 HIS B 113 PHE 0.017 0.002 PHE I 77 TYR 0.028 0.002 TYR G 67 ARG 0.006 0.001 ARG J 157 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 523 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 58 ILE cc_start: 0.8761 (mm) cc_final: 0.8420 (mt) REVERT: J 62 ASP cc_start: 0.8136 (m-30) cc_final: 0.7871 (t0) REVERT: J 73 TYR cc_start: 0.8589 (p90) cc_final: 0.8143 (p90) REVERT: J 84 GLU cc_start: 0.7864 (tp30) cc_final: 0.7641 (tp30) REVERT: J 190 GLU cc_start: 0.7871 (tt0) cc_final: 0.7485 (tm-30) REVERT: A 48 GLN cc_start: 0.8737 (mt0) cc_final: 0.8444 (mt0) REVERT: A 62 ASP cc_start: 0.8103 (m-30) cc_final: 0.7800 (t0) REVERT: A 66 LYS cc_start: 0.7021 (mtmm) cc_final: 0.6603 (mtmm) REVERT: A 67 TYR cc_start: 0.8285 (m-80) cc_final: 0.7986 (m-80) REVERT: A 186 LEU cc_start: 0.9219 (mt) cc_final: 0.8937 (tp) REVERT: A 190 GLU cc_start: 0.8033 (tt0) cc_final: 0.7713 (tm-30) REVERT: I 62 ASP cc_start: 0.8182 (m-30) cc_final: 0.7799 (t0) REVERT: I 64 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7516 (ttmm) REVERT: I 76 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7392 (m-30) REVERT: I 99 ASN cc_start: 0.8397 (t0) cc_final: 0.7978 (t0) REVERT: I 186 LEU cc_start: 0.9338 (mt) cc_final: 0.7866 (mt) REVERT: I 190 GLU cc_start: 0.8048 (tt0) cc_final: 0.7476 (tm-30) REVERT: E 58 ILE cc_start: 0.8749 (mm) cc_final: 0.8426 (mt) REVERT: E 73 TYR cc_start: 0.8910 (p90) cc_final: 0.8618 (p90) REVERT: E 99 ASN cc_start: 0.8439 (t0) cc_final: 0.8121 (t0) REVERT: E 100 THR cc_start: 0.9140 (t) cc_final: 0.8931 (p) REVERT: E 145 TYR cc_start: 0.9114 (m-80) cc_final: 0.8500 (m-80) REVERT: E 169 ARG cc_start: 0.8012 (mtp85) cc_final: 0.7626 (mtp85) REVERT: E 190 GLU cc_start: 0.7864 (tt0) cc_final: 0.7468 (tm-30) REVERT: E 193 GLN cc_start: 0.7905 (mp10) cc_final: 0.7632 (mp10) REVERT: E 197 GLU cc_start: 0.7913 (tt0) cc_final: 0.7691 (tt0) REVERT: G 58 ILE cc_start: 0.8742 (mm) cc_final: 0.8505 (mt) REVERT: G 64 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.7238 (ttmm) REVERT: G 99 ASN cc_start: 0.8536 (t0) cc_final: 0.8202 (t0) REVERT: G 190 GLU cc_start: 0.8026 (tt0) cc_final: 0.7592 (tm-30) REVERT: F 44 GLN cc_start: 0.7825 (mm-40) cc_final: 0.7400 (mm-40) REVERT: F 60 MET cc_start: 0.8441 (ttt) cc_final: 0.7957 (ttt) REVERT: F 67 TYR cc_start: 0.7924 (m-10) cc_final: 0.7390 (m-10) REVERT: B 63 TYR cc_start: 0.8502 (m-80) cc_final: 0.8180 (m-80) REVERT: B 99 ASN cc_start: 0.8495 (t0) cc_final: 0.8091 (t0) REVERT: B 145 TYR cc_start: 0.9127 (m-10) cc_final: 0.8792 (m-80) REVERT: C 32 MET cc_start: 0.1921 (ptm) cc_final: 0.1707 (ptm) REVERT: C 58 ILE cc_start: 0.8695 (mm) cc_final: 0.8490 (mt) REVERT: C 67 TYR cc_start: 0.8128 (m-10) cc_final: 0.7541 (m-10) REVERT: C 99 ASN cc_start: 0.8396 (t0) cc_final: 0.8132 (t0) REVERT: D 63 TYR cc_start: 0.8585 (m-80) cc_final: 0.8216 (m-80) REVERT: D 67 TYR cc_start: 0.7789 (m-10) cc_final: 0.7387 (m-10) REVERT: D 108 ASP cc_start: 0.8001 (t0) cc_final: 0.7497 (t70) REVERT: D 190 GLU cc_start: 0.7830 (tt0) cc_final: 0.7532 (tm-30) REVERT: H 58 ILE cc_start: 0.8792 (mm) cc_final: 0.8526 (mt) REVERT: H 99 ASN cc_start: 0.8395 (t0) cc_final: 0.8039 (t0) REVERT: H 100 THR cc_start: 0.9172 (t) cc_final: 0.8903 (p) REVERT: H 164 LYS cc_start: 0.7897 (pttt) cc_final: 0.7545 (ptmt) REVERT: H 190 GLU cc_start: 0.7958 (tt0) cc_final: 0.7595 (tm-30) outliers start: 41 outliers final: 30 residues processed: 531 average time/residue: 0.2495 time to fit residues: 191.2588 Evaluate side-chains 528 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 495 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 64 LYS Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain F residue 64 LYS Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 167 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13930 Z= 0.206 Angle : 0.604 9.099 18860 Z= 0.316 Chirality : 0.048 0.142 2100 Planarity : 0.004 0.030 2460 Dihedral : 4.631 20.144 1890 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 2.47 % Allowed : 22.74 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.22), residues: 1720 helix: -1.04 (0.22), residues: 470 sheet: -1.89 (0.25), residues: 460 loop : -0.68 (0.26), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 116 HIS 0.004 0.001 HIS B 170 PHE 0.027 0.002 PHE E 77 TYR 0.020 0.002 TYR G 194 ARG 0.005 0.001 ARG C 169 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 493 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLN cc_start: 0.8692 (mt0) cc_final: 0.8444 (mt0) REVERT: A 64 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7207 (ttmm) REVERT: A 75 MET cc_start: 0.7915 (mtt) cc_final: 0.7704 (mtt) REVERT: A 76 ASP cc_start: 0.7988 (m-30) cc_final: 0.7778 (m-30) REVERT: A 84 GLU cc_start: 0.8200 (tp30) cc_final: 0.7998 (tp30) REVERT: A 190 GLU cc_start: 0.8028 (tt0) cc_final: 0.7694 (tm-30) REVERT: E 73 TYR cc_start: 0.8582 (p90) cc_final: 0.8316 (p90) REVERT: E 76 ASP cc_start: 0.8156 (m-30) cc_final: 0.7652 (m-30) REVERT: E 84 GLU cc_start: 0.8262 (tp30) cc_final: 0.7604 (tp30) REVERT: E 99 ASN cc_start: 0.8312 (t0) cc_final: 0.7793 (t0) REVERT: E 100 THR cc_start: 0.8971 (t) cc_final: 0.8683 (p) REVERT: G 58 ILE cc_start: 0.8734 (mm) cc_final: 0.8468 (mt) REVERT: G 63 TYR cc_start: 0.8582 (m-80) cc_final: 0.7908 (m-80) REVERT: G 122 LYS cc_start: 0.8305 (tptt) cc_final: 0.7818 (pttm) REVERT: G 167 ILE cc_start: 0.8282 (mt) cc_final: 0.8052 (pt) REVERT: G 193 GLN cc_start: 0.8517 (mm-40) cc_final: 0.8292 (mm-40) REVERT: F 44 GLN cc_start: 0.7802 (mm-40) cc_final: 0.7372 (mm-40) REVERT: F 60 MET cc_start: 0.8442 (ttt) cc_final: 0.7923 (ttt) REVERT: F 67 TYR cc_start: 0.7843 (m-10) cc_final: 0.7378 (m-10) REVERT: B 63 TYR cc_start: 0.8424 (m-80) cc_final: 0.8071 (m-80) REVERT: B 84 GLU cc_start: 0.8340 (tp30) cc_final: 0.8068 (tp30) REVERT: B 94 ASP cc_start: 0.8322 (m-30) cc_final: 0.7922 (t0) REVERT: B 102 VAL cc_start: 0.9022 (m) cc_final: 0.8821 (p) REVERT: B 145 TYR cc_start: 0.9025 (m-10) cc_final: 0.8727 (m-80) REVERT: C 58 ILE cc_start: 0.8684 (mm) cc_final: 0.8460 (mt) REVERT: C 67 TYR cc_start: 0.7997 (m-10) cc_final: 0.7324 (m-10) REVERT: C 190 GLU cc_start: 0.8047 (tt0) cc_final: 0.7652 (tm-30) REVERT: D 63 TYR cc_start: 0.8529 (m-80) cc_final: 0.8157 (m-80) REVERT: D 64 LYS cc_start: 0.7268 (OUTLIER) cc_final: 0.6899 (ttmm) REVERT: D 67 TYR cc_start: 0.7847 (m-10) cc_final: 0.7382 (m-10) REVERT: D 190 GLU cc_start: 0.7827 (tt0) cc_final: 0.7552 (tm-30) REVERT: H 58 ILE cc_start: 0.8775 (mm) cc_final: 0.8466 (mt) REVERT: H 99 ASN cc_start: 0.8291 (t0) cc_final: 0.7968 (t0) REVERT: H 190 GLU cc_start: 0.8013 (tt0) cc_final: 0.7547 (tm-30) outliers start: 36 outliers final: 16 residues processed: 502 average time/residue: 0.2527 time to fit residues: 182.4566 Evaluate side-chains 485 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 467 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain H residue 40 GLU Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.9990 chunk 147 optimal weight: 0.0970 chunk 32 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 164 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13930 Z= 0.177 Angle : 0.613 9.260 18860 Z= 0.320 Chirality : 0.047 0.138 2100 Planarity : 0.004 0.038 2460 Dihedral : 4.397 19.087 1890 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 1.92 % Allowed : 23.90 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.21), residues: 1720 helix: -0.79 (0.23), residues: 470 sheet: -1.71 (0.25), residues: 460 loop : -0.70 (0.25), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 116 HIS 0.004 0.001 HIS B 170 PHE 0.043 0.002 PHE E 77 TYR 0.023 0.002 TYR I 67 ARG 0.005 0.000 ARG D 157 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 486 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 58 ILE cc_start: 0.8845 (mm) cc_final: 0.8568 (mt) REVERT: A 58 ILE cc_start: 0.8769 (mm) cc_final: 0.8452 (mt) REVERT: A 60 MET cc_start: 0.6973 (ptp) cc_final: 0.6625 (ptp) REVERT: A 62 ASP cc_start: 0.7952 (m-30) cc_final: 0.7540 (t0) REVERT: A 67 TYR cc_start: 0.7971 (m-80) cc_final: 0.7568 (m-10) REVERT: A 76 ASP cc_start: 0.7923 (m-30) cc_final: 0.7657 (m-30) REVERT: A 84 GLU cc_start: 0.8181 (tp30) cc_final: 0.7923 (tp30) REVERT: A 190 GLU cc_start: 0.7965 (tt0) cc_final: 0.7613 (tm-30) REVERT: I 58 ILE cc_start: 0.8787 (mm) cc_final: 0.8456 (mt) REVERT: I 76 ASP cc_start: 0.7609 (m-30) cc_final: 0.7388 (m-30) REVERT: I 84 GLU cc_start: 0.8269 (tp30) cc_final: 0.7864 (tp30) REVERT: E 58 ILE cc_start: 0.8902 (mm) cc_final: 0.8637 (mt) REVERT: E 84 GLU cc_start: 0.8194 (tp30) cc_final: 0.7557 (tp30) REVERT: E 122 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7058 (tptt) REVERT: G 58 ILE cc_start: 0.8811 (mm) cc_final: 0.8508 (mt) REVERT: G 63 TYR cc_start: 0.8425 (m-80) cc_final: 0.7925 (m-80) REVERT: G 122 LYS cc_start: 0.8278 (tptt) cc_final: 0.7764 (pttm) REVERT: F 44 GLN cc_start: 0.7799 (mm-40) cc_final: 0.7480 (mm-40) REVERT: F 60 MET cc_start: 0.8365 (ttt) cc_final: 0.7796 (ttt) REVERT: F 67 TYR cc_start: 0.7826 (m-10) cc_final: 0.7517 (m-10) REVERT: F 84 GLU cc_start: 0.8142 (tp30) cc_final: 0.7529 (tp30) REVERT: F 139 MET cc_start: 0.8074 (mmm) cc_final: 0.7858 (mmm) REVERT: B 63 TYR cc_start: 0.8362 (m-80) cc_final: 0.8130 (m-80) REVERT: B 84 GLU cc_start: 0.8267 (tp30) cc_final: 0.7799 (tp30) REVERT: B 94 ASP cc_start: 0.8221 (m-30) cc_final: 0.8000 (t0) REVERT: C 58 ILE cc_start: 0.8614 (mm) cc_final: 0.8368 (mt) REVERT: C 67 TYR cc_start: 0.7981 (m-10) cc_final: 0.7231 (m-10) REVERT: D 63 TYR cc_start: 0.8459 (m-80) cc_final: 0.8142 (m-80) REVERT: D 67 TYR cc_start: 0.7963 (m-10) cc_final: 0.7498 (m-10) REVERT: D 190 GLU cc_start: 0.7881 (tt0) cc_final: 0.7541 (tm-30) REVERT: H 58 ILE cc_start: 0.8784 (mm) cc_final: 0.8493 (mt) REVERT: H 84 GLU cc_start: 0.8286 (tp30) cc_final: 0.7959 (tp30) outliers start: 28 outliers final: 12 residues processed: 500 average time/residue: 0.2511 time to fit residues: 181.4175 Evaluate side-chains 459 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 446 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain I residue 200 ASP Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 163 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 99 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 13930 Z= 0.384 Angle : 0.701 9.858 18860 Z= 0.372 Chirality : 0.051 0.189 2100 Planarity : 0.004 0.045 2460 Dihedral : 4.727 21.071 1890 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 2.95 % Allowed : 23.63 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.22), residues: 1720 helix: -0.89 (0.22), residues: 470 sheet: -1.66 (0.25), residues: 460 loop : -0.60 (0.26), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP E 116 HIS 0.007 0.002 HIS E 113 PHE 0.050 0.003 PHE E 77 TYR 0.035 0.002 TYR B 67 ARG 0.004 0.001 ARG C 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 472 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 58 ILE cc_start: 0.8840 (mm) cc_final: 0.8587 (mt) REVERT: J 73 TYR cc_start: 0.8673 (p90) cc_final: 0.8339 (p90) REVERT: J 84 GLU cc_start: 0.8232 (tp30) cc_final: 0.8021 (tp30) REVERT: A 58 ILE cc_start: 0.8808 (mm) cc_final: 0.8519 (mt) REVERT: A 62 ASP cc_start: 0.8045 (m-30) cc_final: 0.7623 (t0) REVERT: A 67 TYR cc_start: 0.8129 (m-80) cc_final: 0.7776 (m-10) REVERT: A 76 ASP cc_start: 0.8052 (m-30) cc_final: 0.7792 (m-30) REVERT: A 84 GLU cc_start: 0.8304 (tp30) cc_final: 0.8056 (tp30) REVERT: A 190 GLU cc_start: 0.7998 (tt0) cc_final: 0.7673 (tm-30) REVERT: I 58 ILE cc_start: 0.8783 (mm) cc_final: 0.8434 (mt) REVERT: I 76 ASP cc_start: 0.8113 (m-30) cc_final: 0.7628 (m-30) REVERT: I 84 GLU cc_start: 0.8207 (tp30) cc_final: 0.7883 (tp30) REVERT: E 58 ILE cc_start: 0.8838 (mm) cc_final: 0.8597 (mt) REVERT: E 84 GLU cc_start: 0.8299 (tp30) cc_final: 0.7747 (tp30) REVERT: E 145 TYR cc_start: 0.9092 (m-80) cc_final: 0.8508 (m-80) REVERT: E 193 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8758 (mm-40) REVERT: G 58 ILE cc_start: 0.8792 (mm) cc_final: 0.8544 (mt) REVERT: G 63 TYR cc_start: 0.8551 (m-80) cc_final: 0.8026 (m-80) REVERT: G 64 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7131 (ttmm) REVERT: G 122 LYS cc_start: 0.8335 (tptt) cc_final: 0.7824 (pttm) REVERT: F 44 GLN cc_start: 0.7904 (mm-40) cc_final: 0.7557 (mm-40) REVERT: F 60 MET cc_start: 0.8485 (ttt) cc_final: 0.8011 (ttt) REVERT: F 67 TYR cc_start: 0.7995 (m-10) cc_final: 0.7679 (m-10) REVERT: F 84 GLU cc_start: 0.8077 (tp30) cc_final: 0.7614 (tp30) REVERT: F 108 ASP cc_start: 0.8020 (m-30) cc_final: 0.7818 (m-30) REVERT: F 139 MET cc_start: 0.8519 (mmm) cc_final: 0.8296 (mmm) REVERT: F 190 GLU cc_start: 0.7874 (tt0) cc_final: 0.7548 (tm-30) REVERT: B 84 GLU cc_start: 0.8290 (tp30) cc_final: 0.7820 (tp30) REVERT: B 145 TYR cc_start: 0.9098 (m-10) cc_final: 0.8756 (m-80) REVERT: C 58 ILE cc_start: 0.8635 (mm) cc_final: 0.8421 (mt) REVERT: C 64 LYS cc_start: 0.7577 (OUTLIER) cc_final: 0.7369 (ttmm) REVERT: D 63 TYR cc_start: 0.8549 (m-80) cc_final: 0.8236 (m-80) REVERT: D 64 LYS cc_start: 0.7436 (OUTLIER) cc_final: 0.7067 (ttmm) REVERT: D 67 TYR cc_start: 0.8098 (m-10) cc_final: 0.7672 (m-10) REVERT: D 84 GLU cc_start: 0.8377 (tp30) cc_final: 0.7848 (tp30) REVERT: D 190 GLU cc_start: 0.7850 (tt0) cc_final: 0.7475 (tm-30) REVERT: H 58 ILE cc_start: 0.8811 (mm) cc_final: 0.8533 (mt) REVERT: H 63 TYR cc_start: 0.8532 (m-80) cc_final: 0.8196 (m-80) REVERT: H 84 GLU cc_start: 0.8345 (tp30) cc_final: 0.8080 (tp30) REVERT: H 190 GLU cc_start: 0.8024 (tt0) cc_final: 0.7561 (tm-30) outliers start: 43 outliers final: 27 residues processed: 488 average time/residue: 0.2533 time to fit residues: 177.6598 Evaluate side-chains 468 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 438 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 64 LYS Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 150 GLU Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain I residue 101 GLN Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 123 LYS Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 167 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 81 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 149 optimal weight: 0.4980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13930 Z= 0.238 Angle : 0.664 9.798 18860 Z= 0.349 Chirality : 0.049 0.150 2100 Planarity : 0.004 0.044 2460 Dihedral : 4.621 19.413 1890 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 2.12 % Allowed : 25.07 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.21), residues: 1720 helix: -0.86 (0.22), residues: 490 sheet: -2.69 (0.28), residues: 340 loop : -0.39 (0.23), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP J 116 HIS 0.006 0.001 HIS E 113 PHE 0.051 0.002 PHE J 77 TYR 0.030 0.002 TYR B 67 ARG 0.005 0.000 ARG G 157 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 439 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 58 ILE cc_start: 0.8864 (mm) cc_final: 0.8579 (mt) REVERT: J 64 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.7056 (tppt) REVERT: J 84 GLU cc_start: 0.8235 (tp30) cc_final: 0.7749 (tp30) REVERT: J 169 ARG cc_start: 0.8286 (mmt90) cc_final: 0.8080 (mmt90) REVERT: A 58 ILE cc_start: 0.8816 (mm) cc_final: 0.8519 (mt) REVERT: A 62 ASP cc_start: 0.7925 (m-30) cc_final: 0.7611 (t0) REVERT: A 67 TYR cc_start: 0.7978 (m-80) cc_final: 0.7681 (m-80) REVERT: A 76 ASP cc_start: 0.8052 (m-30) cc_final: 0.7767 (m-30) REVERT: A 84 GLU cc_start: 0.8233 (tp30) cc_final: 0.7962 (tp30) REVERT: A 190 GLU cc_start: 0.8006 (tt0) cc_final: 0.7613 (tm-30) REVERT: I 58 ILE cc_start: 0.8777 (mm) cc_final: 0.8446 (mt) REVERT: I 76 ASP cc_start: 0.8107 (m-30) cc_final: 0.7770 (m-30) REVERT: I 84 GLU cc_start: 0.8143 (tp30) cc_final: 0.7830 (tp30) REVERT: I 169 ARG cc_start: 0.8493 (mmt90) cc_final: 0.8263 (mmt90) REVERT: E 58 ILE cc_start: 0.8890 (mm) cc_final: 0.8633 (mt) REVERT: E 84 GLU cc_start: 0.8261 (tp30) cc_final: 0.7708 (tp30) REVERT: G 63 TYR cc_start: 0.8467 (m-80) cc_final: 0.7991 (m-80) REVERT: G 122 LYS cc_start: 0.8240 (tptt) cc_final: 0.7809 (pttm) REVERT: F 44 GLN cc_start: 0.7886 (mm-40) cc_final: 0.7484 (mm-40) REVERT: F 60 MET cc_start: 0.8416 (ttt) cc_final: 0.7769 (ttt) REVERT: F 67 TYR cc_start: 0.7865 (m-10) cc_final: 0.7625 (m-10) REVERT: F 84 GLU cc_start: 0.7934 (tp30) cc_final: 0.7563 (tp30) REVERT: F 190 GLU cc_start: 0.7810 (tt0) cc_final: 0.7474 (tm-30) REVERT: B 84 GLU cc_start: 0.8153 (tp30) cc_final: 0.7674 (tp30) REVERT: C 58 ILE cc_start: 0.8683 (mm) cc_final: 0.8431 (mt) REVERT: C 190 GLU cc_start: 0.8001 (tt0) cc_final: 0.7599 (tm-30) REVERT: D 63 TYR cc_start: 0.8521 (m-80) cc_final: 0.8150 (m-80) REVERT: D 67 TYR cc_start: 0.8023 (m-10) cc_final: 0.7556 (m-10) REVERT: D 84 GLU cc_start: 0.8353 (tp30) cc_final: 0.7888 (tp30) REVERT: D 190 GLU cc_start: 0.7835 (tt0) cc_final: 0.7439 (tm-30) REVERT: H 58 ILE cc_start: 0.8804 (mm) cc_final: 0.8514 (mt) REVERT: H 76 ASP cc_start: 0.7848 (m-30) cc_final: 0.7587 (m-30) REVERT: H 84 GLU cc_start: 0.8192 (tp30) cc_final: 0.7875 (tp30) REVERT: H 169 ARG cc_start: 0.8454 (mmt90) cc_final: 0.8098 (mmm-85) outliers start: 31 outliers final: 23 residues processed: 451 average time/residue: 0.2534 time to fit residues: 163.9712 Evaluate side-chains 451 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 427 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 64 LYS Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain I residue 101 GLN Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 123 LYS Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 122 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 144 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 13930 Z= 0.377 Angle : 0.719 10.153 18860 Z= 0.379 Chirality : 0.051 0.154 2100 Planarity : 0.004 0.046 2460 Dihedral : 4.813 20.027 1890 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 2.81 % Allowed : 24.38 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.21), residues: 1720 helix: -0.92 (0.21), residues: 490 sheet: -2.63 (0.29), residues: 340 loop : -0.38 (0.24), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP E 116 HIS 0.006 0.002 HIS J 113 PHE 0.051 0.003 PHE J 77 TYR 0.049 0.003 TYR B 67 ARG 0.006 0.000 ARG D 157 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 464 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 58 ILE cc_start: 0.8863 (mm) cc_final: 0.8549 (mt) REVERT: J 84 GLU cc_start: 0.8262 (tp30) cc_final: 0.7811 (tp30) REVERT: A 58 ILE cc_start: 0.8827 (mm) cc_final: 0.8492 (mt) REVERT: A 64 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7344 (ttmm) REVERT: A 67 TYR cc_start: 0.8118 (m-80) cc_final: 0.7914 (m-80) REVERT: A 76 ASP cc_start: 0.8247 (m-30) cc_final: 0.7989 (m-30) REVERT: A 190 GLU cc_start: 0.8026 (tt0) cc_final: 0.7676 (tm-30) REVERT: I 48 GLN cc_start: 0.8703 (mt0) cc_final: 0.8393 (mt0) REVERT: I 58 ILE cc_start: 0.8909 (mm) cc_final: 0.8583 (mt) REVERT: I 60 MET cc_start: 0.8014 (mpp) cc_final: 0.7403 (mtt) REVERT: I 62 ASP cc_start: 0.7783 (m-30) cc_final: 0.7441 (t0) REVERT: I 76 ASP cc_start: 0.8313 (m-30) cc_final: 0.7970 (m-30) REVERT: I 99 ASN cc_start: 0.8152 (t0) cc_final: 0.7943 (t0) REVERT: E 58 ILE cc_start: 0.8920 (mm) cc_final: 0.8676 (mt) REVERT: E 76 ASP cc_start: 0.8388 (m-30) cc_final: 0.8164 (m-30) REVERT: E 84 GLU cc_start: 0.8326 (tp30) cc_final: 0.7757 (tp30) REVERT: G 58 ILE cc_start: 0.8786 (mm) cc_final: 0.8578 (mt) REVERT: G 63 TYR cc_start: 0.8408 (m-80) cc_final: 0.7998 (m-80) REVERT: G 122 LYS cc_start: 0.8255 (tptt) cc_final: 0.7799 (pttm) REVERT: F 44 GLN cc_start: 0.7858 (mm-40) cc_final: 0.7443 (mm-40) REVERT: F 60 MET cc_start: 0.8516 (ttt) cc_final: 0.8045 (ttt) REVERT: F 67 TYR cc_start: 0.7936 (m-10) cc_final: 0.7716 (m-10) REVERT: F 84 GLU cc_start: 0.8031 (tp30) cc_final: 0.7652 (tp30) REVERT: F 190 GLU cc_start: 0.7846 (tt0) cc_final: 0.7527 (tm-30) REVERT: B 58 ILE cc_start: 0.8857 (mm) cc_final: 0.8582 (mt) REVERT: B 66 LYS cc_start: 0.6566 (mtmm) cc_final: 0.6135 (ptmt) REVERT: B 84 GLU cc_start: 0.8153 (tp30) cc_final: 0.7896 (tp30) REVERT: B 145 TYR cc_start: 0.9046 (m-10) cc_final: 0.8718 (m-80) REVERT: C 58 ILE cc_start: 0.8716 (mm) cc_final: 0.8506 (mt) REVERT: C 64 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.7103 (ttmm) REVERT: C 108 ASP cc_start: 0.8019 (m-30) cc_final: 0.7669 (t70) REVERT: D 64 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.7034 (ttmm) REVERT: D 67 TYR cc_start: 0.8113 (m-10) cc_final: 0.7684 (m-10) REVERT: D 84 GLU cc_start: 0.8348 (tp30) cc_final: 0.7905 (tp30) REVERT: D 190 GLU cc_start: 0.7933 (tt0) cc_final: 0.7447 (tm-30) REVERT: H 58 ILE cc_start: 0.8808 (mm) cc_final: 0.8552 (mt) REVERT: H 76 ASP cc_start: 0.7971 (m-30) cc_final: 0.7602 (m-30) REVERT: H 108 ASP cc_start: 0.8129 (m-30) cc_final: 0.7799 (m-30) REVERT: H 169 ARG cc_start: 0.8413 (mmt90) cc_final: 0.8000 (mmm-85) outliers start: 41 outliers final: 33 residues processed: 472 average time/residue: 0.2621 time to fit residues: 176.5912 Evaluate side-chains 497 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 461 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 40 GLU Chi-restraints excluded: chain J residue 64 LYS Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 150 GLU Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 101 GLN Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 123 LYS Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 169 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 chunk 14 optimal weight: 0.2980 chunk 104 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13930 Z= 0.272 Angle : 0.700 10.140 18860 Z= 0.367 Chirality : 0.049 0.153 2100 Planarity : 0.004 0.043 2460 Dihedral : 4.710 19.036 1890 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 2.33 % Allowed : 25.27 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.21), residues: 1720 helix: -0.69 (0.22), residues: 490 sheet: -2.62 (0.29), residues: 340 loop : -0.39 (0.23), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 116 HIS 0.005 0.001 HIS J 113 PHE 0.046 0.002 PHE J 77 TYR 0.033 0.002 TYR B 67 ARG 0.006 0.000 ARG E 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 443 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 58 ILE cc_start: 0.8833 (mm) cc_final: 0.8550 (mt) REVERT: J 84 GLU cc_start: 0.8287 (tp30) cc_final: 0.7815 (tp30) REVERT: J 169 ARG cc_start: 0.8408 (mmt90) cc_final: 0.8076 (mmt90) REVERT: A 58 ILE cc_start: 0.8845 (mm) cc_final: 0.8528 (mt) REVERT: A 64 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7195 (ttmm) REVERT: A 76 ASP cc_start: 0.8224 (m-30) cc_final: 0.7989 (m-30) REVERT: A 84 GLU cc_start: 0.8156 (tp30) cc_final: 0.7622 (tp30) REVERT: A 190 GLU cc_start: 0.8011 (tt0) cc_final: 0.7636 (tm-30) REVERT: I 48 GLN cc_start: 0.8691 (mt0) cc_final: 0.8398 (mt0) REVERT: I 58 ILE cc_start: 0.8896 (mm) cc_final: 0.8573 (mt) REVERT: I 60 MET cc_start: 0.8029 (mpp) cc_final: 0.7415 (mtt) REVERT: I 62 ASP cc_start: 0.7682 (m-30) cc_final: 0.7374 (t0) REVERT: I 76 ASP cc_start: 0.8290 (m-30) cc_final: 0.8071 (m-30) REVERT: I 84 GLU cc_start: 0.8016 (tp30) cc_final: 0.7513 (tp30) REVERT: I 99 ASN cc_start: 0.8239 (t0) cc_final: 0.8010 (t0) REVERT: E 58 ILE cc_start: 0.8956 (mm) cc_final: 0.8685 (mt) REVERT: E 60 MET cc_start: 0.7849 (mpp) cc_final: 0.7611 (mpp) REVERT: E 84 GLU cc_start: 0.8290 (tp30) cc_final: 0.7736 (tp30) REVERT: G 63 TYR cc_start: 0.8371 (m-80) cc_final: 0.7966 (m-80) REVERT: G 122 LYS cc_start: 0.8213 (tptt) cc_final: 0.7759 (pttm) REVERT: F 44 GLN cc_start: 0.7901 (mm-40) cc_final: 0.7431 (mm-40) REVERT: F 60 MET cc_start: 0.8442 (ttt) cc_final: 0.7843 (ttt) REVERT: F 67 TYR cc_start: 0.7910 (m-10) cc_final: 0.7707 (m-10) REVERT: F 84 GLU cc_start: 0.7947 (tp30) cc_final: 0.7588 (tp30) REVERT: F 190 GLU cc_start: 0.7825 (tt0) cc_final: 0.7493 (tm-30) REVERT: B 58 ILE cc_start: 0.8820 (mm) cc_final: 0.8585 (mt) REVERT: B 84 GLU cc_start: 0.8138 (tp30) cc_final: 0.7669 (tp30) REVERT: B 145 TYR cc_start: 0.9000 (m-10) cc_final: 0.8691 (m-80) REVERT: C 63 TYR cc_start: 0.8606 (m-80) cc_final: 0.7969 (m-80) REVERT: C 64 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.7098 (ttmm) REVERT: C 108 ASP cc_start: 0.7888 (m-30) cc_final: 0.7614 (t70) REVERT: D 64 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.7042 (ttmm) REVERT: D 67 TYR cc_start: 0.8031 (m-10) cc_final: 0.7645 (m-10) REVERT: D 84 GLU cc_start: 0.8327 (tp30) cc_final: 0.7872 (tp30) REVERT: D 190 GLU cc_start: 0.7907 (tt0) cc_final: 0.7529 (tm-30) REVERT: H 58 ILE cc_start: 0.8779 (mm) cc_final: 0.8515 (mt) REVERT: H 76 ASP cc_start: 0.7913 (m-30) cc_final: 0.7537 (m-30) REVERT: H 84 GLU cc_start: 0.8209 (tp30) cc_final: 0.7495 (tp30) REVERT: H 108 ASP cc_start: 0.8116 (m-30) cc_final: 0.7813 (m-30) REVERT: H 169 ARG cc_start: 0.8449 (mmt90) cc_final: 0.8000 (mmm-85) outliers start: 34 outliers final: 25 residues processed: 453 average time/residue: 0.2603 time to fit residues: 168.3720 Evaluate side-chains 463 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 435 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 40 GLU Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain I residue 101 GLN Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 109 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.0770 chunk 124 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 135 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 17 optimal weight: 0.1980 chunk 24 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 7 optimal weight: 0.0270 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.157325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.130848 restraints weight = 18676.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.135121 restraints weight = 11632.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.138151 restraints weight = 8451.863| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.5153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13930 Z= 0.200 Angle : 0.665 10.083 18860 Z= 0.348 Chirality : 0.048 0.148 2100 Planarity : 0.004 0.042 2460 Dihedral : 4.547 17.912 1890 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 1.64 % Allowed : 26.37 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.21), residues: 1720 helix: -0.47 (0.22), residues: 490 sheet: -2.30 (0.30), residues: 320 loop : -0.55 (0.23), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 116 HIS 0.005 0.001 HIS J 113 PHE 0.040 0.002 PHE J 77 TYR 0.028 0.002 TYR B 67 ARG 0.007 0.000 ARG B 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3438.89 seconds wall clock time: 62 minutes 43.72 seconds (3763.72 seconds total)