Starting phenix.real_space_refine on Wed Feb 21 00:21:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bok_30131/02_2024/7bok_30131_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bok_30131/02_2024/7bok_30131.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/7bok_30131/02_2024/7bok_30131.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bok_30131/02_2024/7bok_30131.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bok_30131/02_2024/7bok_30131_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bok_30131/02_2024/7bok_30131_updated.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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 12 7.16 5 S 108 5.16 5 C 18480 2.51 5 N 4848 2.21 5 O 5664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 119": "OE1" <-> "OE2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 267": "NH1" <-> "NH2" Residue "A PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 267": "NH1" <-> "NH2" Residue "B PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 267": "NH1" <-> "NH2" Residue "C PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 267": "NH1" <-> "NH2" Residue "D PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 119": "OE1" <-> "OE2" Residue "E TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 267": "NH1" <-> "NH2" Residue "E PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 119": "OE1" <-> "OE2" Residue "F TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 267": "NH1" <-> "NH2" Residue "F PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 119": "OE1" <-> "OE2" Residue "G TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 267": "NH1" <-> "NH2" Residue "G PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 119": "OE1" <-> "OE2" Residue "H TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 267": "NH1" <-> "NH2" Residue "H PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 119": "OE1" <-> "OE2" Residue "I TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 267": "NH1" <-> "NH2" Residue "I PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 119": "OE1" <-> "OE2" Residue "J TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 267": "NH1" <-> "NH2" Residue "J PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 119": "OE1" <-> "OE2" Residue "K TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 267": "NH1" <-> "NH2" Residue "K PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 119": "OE1" <-> "OE2" Residue "L TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 267": "NH1" <-> "NH2" Residue "L PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29112 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "B" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "C" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "D" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "E" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "F" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "H" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "I" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "J" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "K" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "L" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.56, per 1000 atoms: 0.53 Number of scatterers: 29112 At special positions: 0 Unit cell: (184.08, 115.44, 108.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 12 26.01 S 108 16.00 O 5664 8.00 N 4848 7.00 C 18480 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.53 Conformation dependent library (CDL) restraints added in 5.7 seconds 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6768 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 24 sheets defined 28.1% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.98 Creating SS restraints... Processing helix chain 'A' and resid 29 through 46 Proline residue: A 37 - end of helix removed outlier: 5.309A pdb=" N SER A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY A 41 " --> pdb=" O PRO A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 53 No H-bonds generated for 'chain 'A' and resid 51 through 53' Processing helix chain 'A' and resid 63 through 69 Processing helix chain 'A' and resid 107 through 120 removed outlier: 3.625A pdb=" N GLU A 119 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 161 removed outlier: 5.001A pdb=" N VAL A 159 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 186 through 190 removed outlier: 3.591A pdb=" N SER A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 186 through 190' Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 220 through 223 No H-bonds generated for 'chain 'A' and resid 220 through 223' Processing helix chain 'A' and resid 262 through 272 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'B' and resid 29 through 46 Proline residue: B 37 - end of helix removed outlier: 5.309A pdb=" N SER B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY B 41 " --> pdb=" O PRO B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 53 No H-bonds generated for 'chain 'B' and resid 51 through 53' Processing helix chain 'B' and resid 63 through 69 Processing helix chain 'B' and resid 107 through 120 removed outlier: 3.625A pdb=" N GLU B 119 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 161 removed outlier: 5.000A pdb=" N VAL B 159 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 170 No H-bonds generated for 'chain 'B' and resid 168 through 170' Processing helix chain 'B' and resid 186 through 190 removed outlier: 3.591A pdb=" N SER B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 186 through 190' Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 220 through 224 Processing helix chain 'B' and resid 262 through 272 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'C' and resid 29 through 46 Proline residue: C 37 - end of helix removed outlier: 5.309A pdb=" N SER C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLY C 41 " --> pdb=" O PRO C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 53 No H-bonds generated for 'chain 'C' and resid 51 through 53' Processing helix chain 'C' and resid 63 through 69 Processing helix chain 'C' and resid 107 through 120 removed outlier: 3.626A pdb=" N GLU C 119 " --> pdb=" O THR C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 161 removed outlier: 5.000A pdb=" N VAL C 159 " --> pdb=" O LEU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 186 through 190 removed outlier: 3.591A pdb=" N SER C 190 " --> pdb=" O ALA C 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 186 through 190' Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 220 through 224 Processing helix chain 'C' and resid 262 through 272 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'D' and resid 29 through 46 Proline residue: D 37 - end of helix removed outlier: 5.309A pdb=" N SER D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY D 41 " --> pdb=" O PRO D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 53 No H-bonds generated for 'chain 'D' and resid 51 through 53' Processing helix chain 'D' and resid 63 through 69 Processing helix chain 'D' and resid 107 through 120 removed outlier: 3.626A pdb=" N GLU D 119 " --> pdb=" O THR D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 161 removed outlier: 5.001A pdb=" N VAL D 159 " --> pdb=" O LEU D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 170 No H-bonds generated for 'chain 'D' and resid 168 through 170' Processing helix chain 'D' and resid 186 through 190 removed outlier: 3.590A pdb=" N SER D 190 " --> pdb=" O ALA D 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 186 through 190' Processing helix chain 'D' and resid 193 through 200 Processing helix chain 'D' and resid 220 through 224 Processing helix chain 'D' and resid 262 through 272 Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'E' and resid 29 through 46 Proline residue: E 37 - end of helix removed outlier: 5.310A pdb=" N SER E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY E 41 " --> pdb=" O PRO E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 53 No H-bonds generated for 'chain 'E' and resid 51 through 53' Processing helix chain 'E' and resid 63 through 69 Processing helix chain 'E' and resid 107 through 120 removed outlier: 3.625A pdb=" N GLU E 119 " --> pdb=" O THR E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 161 removed outlier: 5.000A pdb=" N VAL E 159 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 170 No H-bonds generated for 'chain 'E' and resid 168 through 170' Processing helix chain 'E' and resid 186 through 190 removed outlier: 3.591A pdb=" N SER E 190 " --> pdb=" O ALA E 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 186 through 190' Processing helix chain 'E' and resid 193 through 200 Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'E' and resid 262 through 272 Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'F' and resid 29 through 46 Proline residue: F 37 - end of helix removed outlier: 5.310A pdb=" N SER F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY F 41 " --> pdb=" O PRO F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 53 No H-bonds generated for 'chain 'F' and resid 51 through 53' Processing helix chain 'F' and resid 63 through 69 Processing helix chain 'F' and resid 107 through 120 removed outlier: 3.625A pdb=" N GLU F 119 " --> pdb=" O THR F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 161 removed outlier: 5.000A pdb=" N VAL F 159 " --> pdb=" O LEU F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 170 No H-bonds generated for 'chain 'F' and resid 168 through 170' Processing helix chain 'F' and resid 186 through 190 removed outlier: 3.591A pdb=" N SER F 190 " --> pdb=" O ALA F 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 186 through 190' Processing helix chain 'F' and resid 193 through 200 Processing helix chain 'F' and resid 220 through 224 Processing helix chain 'F' and resid 262 through 272 Processing helix chain 'F' and resid 301 through 305 Processing helix chain 'G' and resid 29 through 46 Proline residue: G 37 - end of helix removed outlier: 5.309A pdb=" N SER G 40 " --> pdb=" O LEU G 36 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY G 41 " --> pdb=" O PRO G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 53 No H-bonds generated for 'chain 'G' and resid 51 through 53' Processing helix chain 'G' and resid 63 through 69 Processing helix chain 'G' and resid 107 through 120 removed outlier: 3.625A pdb=" N GLU G 119 " --> pdb=" O THR G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 161 removed outlier: 5.001A pdb=" N VAL G 159 " --> pdb=" O LEU G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 170 No H-bonds generated for 'chain 'G' and resid 168 through 170' Processing helix chain 'G' and resid 186 through 190 removed outlier: 3.591A pdb=" N SER G 190 " --> pdb=" O ALA G 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 186 through 190' Processing helix chain 'G' and resid 193 through 200 Processing helix chain 'G' and resid 220 through 223 No H-bonds generated for 'chain 'G' and resid 220 through 223' Processing helix chain 'G' and resid 262 through 272 Processing helix chain 'G' and resid 301 through 305 Processing helix chain 'H' and resid 29 through 46 Proline residue: H 37 - end of helix removed outlier: 5.309A pdb=" N SER H 40 " --> pdb=" O LEU H 36 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY H 41 " --> pdb=" O PRO H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 53 No H-bonds generated for 'chain 'H' and resid 51 through 53' Processing helix chain 'H' and resid 63 through 69 Processing helix chain 'H' and resid 107 through 120 removed outlier: 3.625A pdb=" N GLU H 119 " --> pdb=" O THR H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 161 removed outlier: 5.000A pdb=" N VAL H 159 " --> pdb=" O LEU H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 170 No H-bonds generated for 'chain 'H' and resid 168 through 170' Processing helix chain 'H' and resid 186 through 190 removed outlier: 3.591A pdb=" N SER H 190 " --> pdb=" O ALA H 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 186 through 190' Processing helix chain 'H' and resid 193 through 200 Processing helix chain 'H' and resid 220 through 224 Processing helix chain 'H' and resid 262 through 272 Processing helix chain 'H' and resid 301 through 305 Processing helix chain 'I' and resid 29 through 46 Proline residue: I 37 - end of helix removed outlier: 5.309A pdb=" N SER I 40 " --> pdb=" O LEU I 36 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLY I 41 " --> pdb=" O PRO I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 53 No H-bonds generated for 'chain 'I' and resid 51 through 53' Processing helix chain 'I' and resid 63 through 69 Processing helix chain 'I' and resid 107 through 120 removed outlier: 3.626A pdb=" N GLU I 119 " --> pdb=" O THR I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 161 removed outlier: 5.000A pdb=" N VAL I 159 " --> pdb=" O LEU I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 170 No H-bonds generated for 'chain 'I' and resid 168 through 170' Processing helix chain 'I' and resid 186 through 190 removed outlier: 3.591A pdb=" N SER I 190 " --> pdb=" O ALA I 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 186 through 190' Processing helix chain 'I' and resid 193 through 200 Processing helix chain 'I' and resid 220 through 224 Processing helix chain 'I' and resid 262 through 272 Processing helix chain 'I' and resid 301 through 305 Processing helix chain 'J' and resid 29 through 46 Proline residue: J 37 - end of helix removed outlier: 5.309A pdb=" N SER J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY J 41 " --> pdb=" O PRO J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 53 No H-bonds generated for 'chain 'J' and resid 51 through 53' Processing helix chain 'J' and resid 63 through 69 Processing helix chain 'J' and resid 107 through 120 removed outlier: 3.626A pdb=" N GLU J 119 " --> pdb=" O THR J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 154 through 161 removed outlier: 5.001A pdb=" N VAL J 159 " --> pdb=" O LEU J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 170 No H-bonds generated for 'chain 'J' and resid 168 through 170' Processing helix chain 'J' and resid 186 through 190 removed outlier: 3.590A pdb=" N SER J 190 " --> pdb=" O ALA J 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 186 through 190' Processing helix chain 'J' and resid 193 through 200 Processing helix chain 'J' and resid 220 through 224 Processing helix chain 'J' and resid 262 through 272 Processing helix chain 'J' and resid 301 through 305 Processing helix chain 'K' and resid 29 through 46 Proline residue: K 37 - end of helix removed outlier: 5.310A pdb=" N SER K 40 " --> pdb=" O LEU K 36 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY K 41 " --> pdb=" O PRO K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 53 No H-bonds generated for 'chain 'K' and resid 51 through 53' Processing helix chain 'K' and resid 63 through 69 Processing helix chain 'K' and resid 107 through 120 removed outlier: 3.625A pdb=" N GLU K 119 " --> pdb=" O THR K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 154 through 161 removed outlier: 5.000A pdb=" N VAL K 159 " --> pdb=" O LEU K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 170 No H-bonds generated for 'chain 'K' and resid 168 through 170' Processing helix chain 'K' and resid 186 through 190 removed outlier: 3.591A pdb=" N SER K 190 " --> pdb=" O ALA K 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 186 through 190' Processing helix chain 'K' and resid 193 through 200 Processing helix chain 'K' and resid 220 through 224 Processing helix chain 'K' and resid 262 through 272 Processing helix chain 'K' and resid 301 through 305 Processing helix chain 'L' and resid 29 through 46 Proline residue: L 37 - end of helix removed outlier: 5.310A pdb=" N SER L 40 " --> pdb=" O LEU L 36 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY L 41 " --> pdb=" O PRO L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 53 No H-bonds generated for 'chain 'L' and resid 51 through 53' Processing helix chain 'L' and resid 63 through 69 Processing helix chain 'L' and resid 107 through 120 removed outlier: 3.625A pdb=" N GLU L 119 " --> pdb=" O THR L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 154 through 161 removed outlier: 5.000A pdb=" N VAL L 159 " --> pdb=" O LEU L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 170 No H-bonds generated for 'chain 'L' and resid 168 through 170' Processing helix chain 'L' and resid 186 through 190 removed outlier: 3.591A pdb=" N SER L 190 " --> pdb=" O ALA L 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 186 through 190' Processing helix chain 'L' and resid 193 through 200 Processing helix chain 'L' and resid 220 through 224 Processing helix chain 'L' and resid 262 through 272 Processing helix chain 'L' and resid 301 through 305 Processing sheet with id= A, first strand: chain 'A' and resid 56 through 61 removed outlier: 3.523A pdb=" N THR A 131 " --> pdb=" O PHE A 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR A 23 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE A 127 " --> pdb=" O THR A 23 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 294 through 298 Processing sheet with id= C, first strand: chain 'B' and resid 56 through 61 removed outlier: 3.522A pdb=" N THR B 131 " --> pdb=" O PHE B 19 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR B 23 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE B 127 " --> pdb=" O THR B 23 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 294 through 298 Processing sheet with id= E, first strand: chain 'C' and resid 56 through 61 removed outlier: 3.522A pdb=" N THR C 131 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR C 23 " --> pdb=" O ILE C 127 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE C 127 " --> pdb=" O THR C 23 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 294 through 298 Processing sheet with id= G, first strand: chain 'D' and resid 56 through 61 removed outlier: 3.523A pdb=" N THR D 131 " --> pdb=" O PHE D 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR D 23 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE D 127 " --> pdb=" O THR D 23 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 294 through 298 Processing sheet with id= I, first strand: chain 'E' and resid 56 through 61 removed outlier: 3.522A pdb=" N THR E 131 " --> pdb=" O PHE E 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR E 23 " --> pdb=" O ILE E 127 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE E 127 " --> pdb=" O THR E 23 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 294 through 298 Processing sheet with id= K, first strand: chain 'F' and resid 56 through 61 removed outlier: 3.523A pdb=" N THR F 131 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR F 23 " --> pdb=" O ILE F 127 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ILE F 127 " --> pdb=" O THR F 23 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 294 through 298 Processing sheet with id= M, first strand: chain 'G' and resid 56 through 61 removed outlier: 3.523A pdb=" N THR G 131 " --> pdb=" O PHE G 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR G 23 " --> pdb=" O ILE G 127 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE G 127 " --> pdb=" O THR G 23 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 294 through 298 Processing sheet with id= O, first strand: chain 'H' and resid 56 through 61 removed outlier: 3.522A pdb=" N THR H 131 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR H 23 " --> pdb=" O ILE H 127 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE H 127 " --> pdb=" O THR H 23 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 294 through 298 Processing sheet with id= Q, first strand: chain 'I' and resid 56 through 61 removed outlier: 3.522A pdb=" N THR I 131 " --> pdb=" O PHE I 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR I 23 " --> pdb=" O ILE I 127 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE I 127 " --> pdb=" O THR I 23 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 294 through 298 Processing sheet with id= S, first strand: chain 'J' and resid 56 through 61 removed outlier: 3.523A pdb=" N THR J 131 " --> pdb=" O PHE J 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR J 23 " --> pdb=" O ILE J 127 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE J 127 " --> pdb=" O THR J 23 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 294 through 298 Processing sheet with id= U, first strand: chain 'K' and resid 56 through 61 removed outlier: 3.522A pdb=" N THR K 131 " --> pdb=" O PHE K 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR K 23 " --> pdb=" O ILE K 127 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE K 127 " --> pdb=" O THR K 23 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 294 through 298 Processing sheet with id= W, first strand: chain 'L' and resid 56 through 61 removed outlier: 3.523A pdb=" N THR L 131 " --> pdb=" O PHE L 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR L 23 " --> pdb=" O ILE L 127 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ILE L 127 " --> pdb=" O THR L 23 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'L' and resid 294 through 298 898 hydrogen bonds defined for protein. 2298 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: 11.03 Time building geometry restraints manager: 13.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.40: 12468 1.40 - 1.57: 17208 1.57 - 1.75: 0 1.75 - 1.93: 204 1.93 - 2.10: 36 Bond restraints: 29916 Sorted by residual: bond pdb=" C3B HEM J 401 " pdb=" CAB HEM J 401 " ideal model delta sigma weight residual 1.544 1.468 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C3B HEM D 401 " pdb=" CAB HEM D 401 " ideal model delta sigma weight residual 1.544 1.468 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C3B HEM A 401 " pdb=" CAB HEM A 401 " ideal model delta sigma weight residual 1.544 1.468 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C3B HEM G 401 " pdb=" CAB HEM G 401 " ideal model delta sigma weight residual 1.544 1.468 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C3B HEM E 401 " pdb=" CAB HEM E 401 " ideal model delta sigma weight residual 1.544 1.469 0.075 2.00e-02 2.50e+03 1.42e+01 ... (remaining 29911 not shown) Histogram of bond angle deviations from ideal: 86.22 - 104.40: 862 104.40 - 122.58: 35632 122.58 - 140.76: 4426 140.76 - 158.94: 0 158.94 - 177.12: 24 Bond angle restraints: 40944 Sorted by residual: angle pdb=" N VAL C 193 " pdb=" CA VAL C 193 " pdb=" C VAL C 193 " ideal model delta sigma weight residual 110.42 116.95 -6.53 9.60e-01 1.09e+00 4.63e+01 angle pdb=" N VAL I 193 " pdb=" CA VAL I 193 " pdb=" C VAL I 193 " ideal model delta sigma weight residual 110.42 116.95 -6.53 9.60e-01 1.09e+00 4.63e+01 angle pdb=" N VAL D 193 " pdb=" CA VAL D 193 " pdb=" C VAL D 193 " ideal model delta sigma weight residual 110.42 116.95 -6.53 9.60e-01 1.09e+00 4.62e+01 angle pdb=" N VAL J 193 " pdb=" CA VAL J 193 " pdb=" C VAL J 193 " ideal model delta sigma weight residual 110.42 116.95 -6.53 9.60e-01 1.09e+00 4.62e+01 angle pdb=" N VAL E 193 " pdb=" CA VAL E 193 " pdb=" C VAL E 193 " ideal model delta sigma weight residual 110.62 117.07 -6.45 1.02e+00 9.61e-01 4.00e+01 ... (remaining 40939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 15906 17.22 - 34.43: 1254 34.43 - 51.65: 314 51.65 - 68.86: 22 68.86 - 86.08: 72 Dihedral angle restraints: 17568 sinusoidal: 7032 harmonic: 10536 Sorted by residual: dihedral pdb=" C2B HEM A 401 " pdb=" C3B HEM A 401 " pdb=" CAB HEM A 401 " pdb=" CBB HEM A 401 " ideal model delta sinusoidal sigma weight residual 180.00 -111.02 -68.98 2 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" C2B HEM G 401 " pdb=" C3B HEM G 401 " pdb=" CAB HEM G 401 " pdb=" CBB HEM G 401 " ideal model delta sinusoidal sigma weight residual -180.00 -111.02 -68.98 2 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" C2B HEM E 401 " pdb=" C3B HEM E 401 " pdb=" CAB HEM E 401 " pdb=" CBB HEM E 401 " ideal model delta sinusoidal sigma weight residual -180.00 -111.02 -68.98 2 1.00e+01 1.00e-02 4.18e+01 ... (remaining 17565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3242 0.055 - 0.110: 1018 0.110 - 0.165: 118 0.165 - 0.220: 0 0.220 - 0.275: 14 Chirality restraints: 4392 Sorted by residual: chirality pdb=" CA VAL G 225 " pdb=" N VAL G 225 " pdb=" C VAL G 225 " pdb=" CB VAL G 225 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA VAL A 225 " pdb=" N VAL A 225 " pdb=" C VAL A 225 " pdb=" CB VAL A 225 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB ILE B 256 " pdb=" CA ILE B 256 " pdb=" CG1 ILE B 256 " pdb=" CG2 ILE B 256 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 4389 not shown) Planarity restraints: 5484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CBD HEM G 401 " -0.034 2.00e-02 2.50e+03 6.61e-02 4.37e+01 pdb=" CGD HEM G 401 " 0.114 2.00e-02 2.50e+03 pdb=" O1D HEM G 401 " -0.041 2.00e-02 2.50e+03 pdb=" O2D HEM G 401 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CBD HEM A 401 " 0.034 2.00e-02 2.50e+03 6.61e-02 4.37e+01 pdb=" CGD HEM A 401 " -0.114 2.00e-02 2.50e+03 pdb=" O1D HEM A 401 " 0.041 2.00e-02 2.50e+03 pdb=" O2D HEM A 401 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CBD HEM J 401 " -0.033 2.00e-02 2.50e+03 6.61e-02 4.36e+01 pdb=" CGD HEM J 401 " 0.114 2.00e-02 2.50e+03 pdb=" O1D HEM J 401 " -0.041 2.00e-02 2.50e+03 pdb=" O2D HEM J 401 " -0.040 2.00e-02 2.50e+03 ... (remaining 5481 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 353 2.61 - 3.18: 24499 3.18 - 3.75: 48114 3.75 - 4.33: 67871 4.33 - 4.90: 108629 Nonbonded interactions: 249466 Sorted by model distance: nonbonded pdb=" NH1 ARG F 198 " pdb=" CA SER I 187 " model vdw 2.036 3.550 nonbonded pdb=" CA SER C 187 " pdb=" NH1 ARG L 198 " model vdw 2.036 3.550 nonbonded pdb=" OG1 THR C 149 " pdb=" O ARG E 44 " model vdw 2.233 2.440 nonbonded pdb=" OG1 THR I 149 " pdb=" O ARG K 44 " model vdw 2.233 2.440 nonbonded pdb=" OG1 THR G 149 " pdb=" O ARG I 44 " model vdw 2.257 2.440 ... (remaining 249461 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.040 Check model and map are aligned: 0.440 Set scattering table: 0.250 Process input model: 78.610 Find NCS groups from input model: 2.190 Set up NCS constraints: 0.250 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:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.223 29916 Z= 0.581 Angle : 0.923 7.121 40944 Z= 0.496 Chirality : 0.051 0.275 4392 Planarity : 0.009 0.066 5484 Dihedral : 14.399 86.079 10800 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % 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: -3.42 (0.13), residues: 3684 helix: -3.40 (0.12), residues: 996 sheet: -2.20 (0.19), residues: 876 loop : -1.46 (0.13), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 66 HIS 0.004 0.001 HIS G 79 PHE 0.010 0.002 PHE C 303 TYR 0.009 0.002 TYR E 255 ARG 0.002 0.000 ARG I 238 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 655 time to evaluate : 3.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LEU cc_start: 0.8628 (mt) cc_final: 0.7041 (mt) REVERT: A 281 THR cc_start: 0.7158 (m) cc_final: 0.6713 (m) REVERT: B 240 ASN cc_start: 0.8572 (m-40) cc_final: 0.8344 (m-40) REVERT: C 13 LEU cc_start: 0.8536 (mt) cc_final: 0.8333 (tt) REVERT: C 139 ASN cc_start: 0.8480 (m-40) cc_final: 0.8157 (m-40) REVERT: C 240 ASN cc_start: 0.8422 (m-40) cc_final: 0.7940 (m110) REVERT: D 53 LYS cc_start: 0.8370 (mttt) cc_final: 0.7986 (mttt) REVERT: D 155 ASN cc_start: 0.7069 (t0) cc_final: 0.6865 (p0) REVERT: D 175 TYR cc_start: 0.8197 (m-80) cc_final: 0.7992 (m-80) REVERT: D 226 ILE cc_start: 0.8832 (mt) cc_final: 0.8569 (pt) REVERT: E 181 TYR cc_start: 0.8163 (m-80) cc_final: 0.7933 (m-80) REVERT: G 182 LEU cc_start: 0.8624 (mt) cc_final: 0.7037 (mt) REVERT: G 281 THR cc_start: 0.7152 (m) cc_final: 0.6705 (m) REVERT: H 240 ASN cc_start: 0.8573 (m-40) cc_final: 0.8346 (m-40) REVERT: I 139 ASN cc_start: 0.8481 (m-40) cc_final: 0.8157 (m-40) REVERT: I 240 ASN cc_start: 0.8410 (m-40) cc_final: 0.7934 (m110) REVERT: J 53 LYS cc_start: 0.8364 (mttt) cc_final: 0.7991 (mttt) REVERT: J 155 ASN cc_start: 0.7070 (t0) cc_final: 0.6866 (p0) REVERT: J 175 TYR cc_start: 0.8192 (m-80) cc_final: 0.7987 (m-80) REVERT: J 226 ILE cc_start: 0.8830 (mt) cc_final: 0.8564 (pt) REVERT: K 181 TYR cc_start: 0.8168 (m-80) cc_final: 0.7937 (m-80) outliers start: 0 outliers final: 0 residues processed: 655 average time/residue: 0.4518 time to fit residues: 449.4757 Evaluate side-chains 269 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 3.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 10.0000 chunk 272 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 184 optimal weight: 0.0770 chunk 145 optimal weight: 1.9990 chunk 282 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 171 optimal weight: 6.9990 chunk 210 optimal weight: 10.0000 chunk 326 optimal weight: 9.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 HIS A 177 HIS ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 HIS B 183 HIS B 239 HIS B 271 ASN ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 HIS ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 HIS G 177 HIS ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 HIS H 183 HIS H 239 HIS H 271 ASN ** I 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 239 HIS ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 29916 Z= 0.361 Angle : 0.659 6.109 40944 Z= 0.323 Chirality : 0.042 0.198 4392 Planarity : 0.006 0.046 5484 Dihedral : 10.003 89.960 4056 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.14 % Allowed : 15.05 % Favored : 82.81 % 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: -2.36 (0.13), residues: 3684 helix: -2.08 (0.14), residues: 1068 sheet: -1.88 (0.19), residues: 828 loop : -0.87 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 188 HIS 0.008 0.001 HIS A 177 PHE 0.011 0.001 PHE D 303 TYR 0.013 0.002 TYR F 181 ARG 0.008 0.001 ARG F 198 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 314 time to evaluate : 3.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6832 (tt0) REVERT: B 46 ILE cc_start: 0.9381 (OUTLIER) cc_final: 0.8467 (tp) REVERT: B 241 MET cc_start: 0.8692 (mmm) cc_final: 0.8460 (mmm) REVERT: C 139 ASN cc_start: 0.8658 (m-40) cc_final: 0.8360 (m-40) REVERT: C 143 MET cc_start: 0.8773 (mmt) cc_final: 0.8571 (mmm) REVERT: C 240 ASN cc_start: 0.8234 (m-40) cc_final: 0.7978 (m-40) REVERT: D 155 ASN cc_start: 0.7485 (t0) cc_final: 0.7120 (p0) REVERT: D 213 ASP cc_start: 0.7064 (p0) cc_final: 0.6861 (p0) REVERT: D 226 ILE cc_start: 0.8828 (mt) cc_final: 0.8596 (pt) REVERT: G 112 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6834 (tt0) REVERT: H 46 ILE cc_start: 0.9385 (OUTLIER) cc_final: 0.8475 (tp) REVERT: H 241 MET cc_start: 0.8683 (mmm) cc_final: 0.8460 (mmm) REVERT: I 139 ASN cc_start: 0.8624 (m-40) cc_final: 0.8347 (m-40) REVERT: I 143 MET cc_start: 0.8769 (mmt) cc_final: 0.8565 (mmm) REVERT: I 240 ASN cc_start: 0.8252 (m-40) cc_final: 0.7968 (m-40) REVERT: J 155 ASN cc_start: 0.7481 (t0) cc_final: 0.7122 (p0) REVERT: J 213 ASP cc_start: 0.7070 (p0) cc_final: 0.6863 (p0) REVERT: J 226 ILE cc_start: 0.8822 (mt) cc_final: 0.8591 (pt) REVERT: L 59 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8611 (p) outliers start: 66 outliers final: 39 residues processed: 360 average time/residue: 0.3925 time to fit residues: 228.1890 Evaluate side-chains 292 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 248 time to evaluate : 3.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 90 HIS Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 204 LYS Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 174 CYS Chi-restraints excluded: chain H residue 180 LYS Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain I residue 158 VAL Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain J residue 174 CYS Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 90 HIS Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain L residue 302 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 272 optimal weight: 20.0000 chunk 222 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 327 optimal weight: 10.0000 chunk 353 optimal weight: 0.9990 chunk 291 optimal weight: 5.9990 chunk 324 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 262 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN D 132 HIS ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN G 177 HIS ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 271 ASN J 132 HIS ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 239 HIS ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 280 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.125 29916 Z= 0.537 Angle : 0.775 12.410 40944 Z= 0.380 Chirality : 0.045 0.217 4392 Planarity : 0.006 0.054 5484 Dihedral : 9.544 89.156 4056 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.28 % Allowed : 15.27 % Favored : 80.45 % 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: -1.72 (0.14), residues: 3684 helix: -1.13 (0.15), residues: 1080 sheet: -1.45 (0.19), residues: 852 loop : -0.80 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 66 HIS 0.009 0.002 HIS G 239 PHE 0.018 0.002 PHE A 296 TYR 0.018 0.002 TYR J 175 ARG 0.005 0.001 ARG F 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 264 time to evaluate : 3.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.9049 (tpt) cc_final: 0.8843 (tpp) REVERT: C 136 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.8011 (t80) REVERT: C 143 MET cc_start: 0.8977 (mmt) cc_final: 0.8408 (mmm) REVERT: D 213 ASP cc_start: 0.7484 (p0) cc_final: 0.7161 (p0) REVERT: F 138 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7506 (p0) REVERT: G 107 MET cc_start: 0.9053 (tpt) cc_final: 0.8847 (tpp) REVERT: I 136 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.8024 (t80) REVERT: I 143 MET cc_start: 0.8972 (mmt) cc_final: 0.8407 (mmm) REVERT: J 213 ASP cc_start: 0.7486 (p0) cc_final: 0.7162 (p0) REVERT: L 138 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7511 (p0) outliers start: 132 outliers final: 74 residues processed: 376 average time/residue: 0.4034 time to fit residues: 250.0391 Evaluate side-chains 290 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 212 time to evaluate : 3.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 183 HIS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain F residue 90 HIS Chi-restraints excluded: chain F residue 136 PHE Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 197 GLU Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 301 VAL Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 136 PHE Chi-restraints excluded: chain I residue 138 ASP Chi-restraints excluded: chain I residue 183 HIS Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 136 PHE Chi-restraints excluded: chain J residue 174 CYS Chi-restraints excluded: chain J residue 240 ASN Chi-restraints excluded: chain J residue 246 ILE Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain L residue 90 HIS Chi-restraints excluded: chain L residue 136 PHE Chi-restraints excluded: chain L residue 138 ASP Chi-restraints excluded: chain L residue 206 ASP Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain L residue 302 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 1.9990 chunk 246 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 156 optimal weight: 9.9990 chunk 219 optimal weight: 3.9990 chunk 328 optimal weight: 3.9990 chunk 347 optimal weight: 5.9990 chunk 171 optimal weight: 0.8980 chunk 311 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS B 132 HIS B 177 HIS C 239 HIS ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 HIS ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 239 HIS H 132 HIS H 177 HIS I 239 HIS ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 224 ASN ** L 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 29916 Z= 0.337 Angle : 0.632 8.294 40944 Z= 0.307 Chirality : 0.042 0.158 4392 Planarity : 0.005 0.046 5484 Dihedral : 9.213 86.917 4056 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.60 % Allowed : 16.76 % Favored : 79.64 % 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: -1.25 (0.14), residues: 3684 helix: -0.56 (0.15), residues: 1080 sheet: -1.24 (0.19), residues: 828 loop : -0.62 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 188 HIS 0.005 0.001 HIS J 177 PHE 0.013 0.001 PHE J 303 TYR 0.019 0.002 TYR A 254 ARG 0.006 0.000 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 244 time to evaluate : 3.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.8996 (tpt) cc_final: 0.8783 (tpp) REVERT: A 143 MET cc_start: 0.8930 (tpp) cc_final: 0.8698 (tpp) REVERT: B 143 MET cc_start: 0.8347 (mmt) cc_final: 0.7766 (mmm) REVERT: C 136 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.7952 (t80) REVERT: C 143 MET cc_start: 0.8919 (mmt) cc_final: 0.8256 (mmm) REVERT: C 240 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.8408 (m-40) REVERT: G 107 MET cc_start: 0.9001 (tpt) cc_final: 0.8785 (tpp) REVERT: G 143 MET cc_start: 0.8928 (tpp) cc_final: 0.8694 (tpp) REVERT: H 143 MET cc_start: 0.8351 (mmt) cc_final: 0.7769 (mmm) REVERT: I 143 MET cc_start: 0.8916 (mmt) cc_final: 0.8262 (mmm) REVERT: I 240 ASN cc_start: 0.8640 (OUTLIER) cc_final: 0.8401 (m-40) outliers start: 111 outliers final: 76 residues processed: 333 average time/residue: 0.3784 time to fit residues: 206.8185 Evaluate side-chains 294 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 215 time to evaluate : 3.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 183 HIS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 136 PHE Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 177 HIS Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 174 CYS Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 158 VAL Chi-restraints excluded: chain I residue 183 HIS Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 240 ASN Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 136 PHE Chi-restraints excluded: chain J residue 174 CYS Chi-restraints excluded: chain J residue 240 ASN Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 136 PHE Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain L residue 302 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 0.0980 chunk 197 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 259 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 296 optimal weight: 0.7980 chunk 240 optimal weight: 0.0980 chunk 0 optimal weight: 9.9990 chunk 177 optimal weight: 7.9990 chunk 312 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 29916 Z= 0.342 Angle : 0.632 7.595 40944 Z= 0.305 Chirality : 0.042 0.164 4392 Planarity : 0.005 0.043 5484 Dihedral : 9.032 85.872 4056 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.25 % Allowed : 16.89 % Favored : 78.86 % 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: -1.00 (0.14), residues: 3684 helix: -0.29 (0.16), residues: 1080 sheet: -1.08 (0.19), residues: 828 loop : -0.53 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 66 HIS 0.019 0.001 HIS G 177 PHE 0.014 0.001 PHE J 303 TYR 0.014 0.002 TYR B 255 ARG 0.006 0.000 ARG G 88 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 237 time to evaluate : 3.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7791 (m-30) REVERT: A 107 MET cc_start: 0.9000 (tpt) cc_final: 0.8772 (tpp) REVERT: A 143 MET cc_start: 0.8873 (tpp) cc_final: 0.8634 (tpp) REVERT: B 99 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8934 (tp) REVERT: C 143 MET cc_start: 0.8908 (mmt) cc_final: 0.8254 (mmm) REVERT: C 240 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.8414 (m-40) REVERT: C 248 LYS cc_start: 0.8193 (mttt) cc_final: 0.7981 (mttp) REVERT: D 105 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7730 (mm-30) REVERT: E 143 MET cc_start: 0.7874 (mmm) cc_final: 0.7417 (mmt) REVERT: E 306 ASP cc_start: 0.8087 (t0) cc_final: 0.7334 (p0) REVERT: F 138 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7344 (p0) REVERT: F 143 MET cc_start: 0.8137 (mmm) cc_final: 0.7856 (mmp) REVERT: G 64 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7791 (m-30) REVERT: G 107 MET cc_start: 0.9004 (tpt) cc_final: 0.8775 (tpp) REVERT: G 143 MET cc_start: 0.8874 (tpp) cc_final: 0.8632 (tpp) REVERT: H 99 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8932 (tp) REVERT: I 136 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.8012 (t80) REVERT: I 143 MET cc_start: 0.8901 (mmt) cc_final: 0.8246 (mmm) REVERT: I 240 ASN cc_start: 0.8624 (OUTLIER) cc_final: 0.8400 (m-40) REVERT: I 248 LYS cc_start: 0.8190 (mttt) cc_final: 0.7982 (mttp) REVERT: J 105 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7730 (mm-30) REVERT: K 143 MET cc_start: 0.7869 (mmm) cc_final: 0.7409 (mmt) REVERT: K 306 ASP cc_start: 0.8089 (t0) cc_final: 0.7337 (p0) REVERT: L 138 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7352 (p0) REVERT: L 143 MET cc_start: 0.8131 (mmm) cc_final: 0.7854 (mmp) outliers start: 131 outliers final: 90 residues processed: 348 average time/residue: 0.3643 time to fit residues: 210.3218 Evaluate side-chains 322 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 223 time to evaluate : 3.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 183 HIS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 90 HIS Chi-restraints excluded: chain F residue 136 PHE Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 174 CYS Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 288 SER Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 136 PHE Chi-restraints excluded: chain I residue 138 ASP Chi-restraints excluded: chain I residue 158 VAL Chi-restraints excluded: chain I residue 183 HIS Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 240 ASN Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 136 PHE Chi-restraints excluded: chain J residue 138 ASP Chi-restraints excluded: chain J residue 174 CYS Chi-restraints excluded: chain J residue 240 ASN Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 90 HIS Chi-restraints excluded: chain L residue 136 PHE Chi-restraints excluded: chain L residue 138 ASP Chi-restraints excluded: chain L residue 206 ASP Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain L residue 302 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 10.0000 chunk 313 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 204 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 348 optimal weight: 9.9990 chunk 289 optimal weight: 0.1980 chunk 161 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 182 optimal weight: 20.0000 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS A 224 ASN ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS G 224 ASN ** I 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 29916 Z= 0.316 Angle : 0.615 7.335 40944 Z= 0.296 Chirality : 0.041 0.140 4392 Planarity : 0.005 0.041 5484 Dihedral : 8.869 84.419 4056 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.47 % Allowed : 16.93 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.14), residues: 3684 helix: 0.08 (0.16), residues: 1056 sheet: -0.97 (0.19), residues: 828 loop : -0.50 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 66 HIS 0.004 0.001 HIS D 177 PHE 0.014 0.001 PHE D 303 TYR 0.009 0.001 TYR E 258 ARG 0.004 0.000 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 242 time to evaluate : 3.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7864 (m-30) REVERT: A 107 MET cc_start: 0.8982 (tpt) cc_final: 0.8772 (tpp) REVERT: B 99 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8949 (tp) REVERT: C 130 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7279 (tt0) REVERT: C 136 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.7937 (t80) REVERT: C 143 MET cc_start: 0.8915 (mmt) cc_final: 0.8051 (mmm) REVERT: C 240 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.8362 (m-40) REVERT: C 248 LYS cc_start: 0.8201 (mttt) cc_final: 0.7985 (mttp) REVERT: D 105 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7663 (mm-30) REVERT: E 143 MET cc_start: 0.7950 (mmm) cc_final: 0.7582 (mmt) REVERT: E 306 ASP cc_start: 0.8106 (t0) cc_final: 0.7303 (p0) REVERT: F 138 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7342 (p0) REVERT: F 143 MET cc_start: 0.8160 (mmm) cc_final: 0.7861 (mmp) REVERT: G 64 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7860 (m-30) REVERT: G 107 MET cc_start: 0.8984 (tpt) cc_final: 0.8776 (tpp) REVERT: H 99 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8947 (tp) REVERT: I 130 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7272 (tt0) REVERT: I 136 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7967 (t80) REVERT: I 143 MET cc_start: 0.8910 (mmt) cc_final: 0.8050 (mmm) REVERT: I 240 ASN cc_start: 0.8555 (OUTLIER) cc_final: 0.8350 (m-40) REVERT: I 248 LYS cc_start: 0.8199 (mttt) cc_final: 0.7981 (mttp) REVERT: J 105 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7662 (mm-30) REVERT: K 143 MET cc_start: 0.7945 (mmm) cc_final: 0.7577 (mmt) REVERT: K 306 ASP cc_start: 0.8108 (t0) cc_final: 0.7305 (p0) REVERT: L 60 SER cc_start: 0.8882 (m) cc_final: 0.8622 (p) REVERT: L 138 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7348 (p0) REVERT: L 143 MET cc_start: 0.8166 (mmm) cc_final: 0.7874 (mmp) outliers start: 138 outliers final: 96 residues processed: 360 average time/residue: 0.3817 time to fit residues: 224.2374 Evaluate side-chains 330 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 222 time to evaluate : 3.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 183 HIS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 90 HIS Chi-restraints excluded: chain F residue 136 PHE Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 306 ASP Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 177 HIS Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 174 CYS Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 288 SER Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain I residue 136 PHE Chi-restraints excluded: chain I residue 138 ASP Chi-restraints excluded: chain I residue 158 VAL Chi-restraints excluded: chain I residue 183 HIS Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 240 ASN Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 136 PHE Chi-restraints excluded: chain J residue 138 ASP Chi-restraints excluded: chain J residue 174 CYS Chi-restraints excluded: chain J residue 240 ASN Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 90 HIS Chi-restraints excluded: chain L residue 136 PHE Chi-restraints excluded: chain L residue 138 ASP Chi-restraints excluded: chain L residue 206 ASP Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain L residue 302 ASP Chi-restraints excluded: chain L residue 306 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 198 optimal weight: 10.0000 chunk 254 optimal weight: 8.9990 chunk 197 optimal weight: 2.9990 chunk 293 optimal weight: 4.9990 chunk 194 optimal weight: 10.0000 chunk 346 optimal weight: 9.9990 chunk 217 optimal weight: 0.6980 chunk 211 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 29916 Z= 0.417 Angle : 0.671 8.512 40944 Z= 0.324 Chirality : 0.043 0.157 4392 Planarity : 0.005 0.046 5484 Dihedral : 8.860 84.662 4056 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 4.73 % Allowed : 17.51 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3684 helix: 0.02 (0.16), residues: 1056 sheet: -0.92 (0.19), residues: 828 loop : -0.55 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 66 HIS 0.022 0.001 HIS A 177 PHE 0.015 0.001 PHE D 303 TYR 0.018 0.002 TYR F 33 ARG 0.003 0.000 ARG F 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 229 time to evaluate : 3.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7893 (m-30) REVERT: A 107 MET cc_start: 0.9003 (tpt) cc_final: 0.8757 (tpp) REVERT: A 143 MET cc_start: 0.8652 (tpp) cc_final: 0.8424 (tpp) REVERT: B 250 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7318 (mt-10) REVERT: C 130 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7339 (tt0) REVERT: C 136 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.8084 (t80) REVERT: C 143 MET cc_start: 0.8961 (mmt) cc_final: 0.8030 (mmm) REVERT: D 105 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7645 (mm-30) REVERT: E 182 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7617 (tt) REVERT: E 306 ASP cc_start: 0.8100 (t0) cc_final: 0.7331 (p0) REVERT: F 143 MET cc_start: 0.8192 (mmm) cc_final: 0.7858 (mmp) REVERT: G 64 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7890 (m-30) REVERT: G 107 MET cc_start: 0.9005 (tpt) cc_final: 0.8760 (tpp) REVERT: G 143 MET cc_start: 0.8653 (tpp) cc_final: 0.8428 (tpp) REVERT: H 250 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7323 (mt-10) REVERT: I 130 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7340 (tt0) REVERT: I 136 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.8090 (t80) REVERT: I 143 MET cc_start: 0.8962 (mmt) cc_final: 0.8033 (mmm) REVERT: J 105 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7646 (mm-30) REVERT: K 182 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7617 (tt) REVERT: K 306 ASP cc_start: 0.8103 (t0) cc_final: 0.7331 (p0) REVERT: L 143 MET cc_start: 0.8194 (mmm) cc_final: 0.7869 (mmp) outliers start: 146 outliers final: 104 residues processed: 354 average time/residue: 0.3827 time to fit residues: 222.5296 Evaluate side-chains 314 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 202 time to evaluate : 3.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 183 HIS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 90 HIS Chi-restraints excluded: chain F residue 136 PHE Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 306 ASP Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain G residue 298 THR Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 174 CYS Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 288 SER Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain I residue 136 PHE Chi-restraints excluded: chain I residue 138 ASP Chi-restraints excluded: chain I residue 158 VAL Chi-restraints excluded: chain I residue 183 HIS Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 136 PHE Chi-restraints excluded: chain J residue 138 ASP Chi-restraints excluded: chain J residue 174 CYS Chi-restraints excluded: chain J residue 240 ASN Chi-restraints excluded: chain J residue 246 ILE Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 121 MET Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 90 HIS Chi-restraints excluded: chain L residue 136 PHE Chi-restraints excluded: chain L residue 138 ASP Chi-restraints excluded: chain L residue 206 ASP Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain L residue 302 ASP Chi-restraints excluded: chain L residue 306 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 67 optimal weight: 0.0270 chunk 220 optimal weight: 0.9980 chunk 236 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 272 optimal weight: 8.9990 overall best weight: 0.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS B 177 HIS ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN F 218 ASN ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS H 177 HIS ** H 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 224 ASN L 177 HIS L 218 ASN ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29916 Z= 0.223 Angle : 0.603 8.110 40944 Z= 0.287 Chirality : 0.041 0.204 4392 Planarity : 0.004 0.042 5484 Dihedral : 8.726 82.741 4056 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.95 % Allowed : 19.10 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 3684 helix: 0.40 (0.17), residues: 1056 sheet: -1.01 (0.19), residues: 840 loop : -0.36 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 66 HIS 0.004 0.001 HIS D 177 PHE 0.013 0.001 PHE D 303 TYR 0.014 0.001 TYR B 255 ARG 0.004 0.000 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 282 time to evaluate : 3.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7871 (m-30) REVERT: C 5 GLN cc_start: 0.8308 (tp40) cc_final: 0.7887 (tp40) REVERT: C 130 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7383 (tt0) REVERT: C 143 MET cc_start: 0.8873 (mmt) cc_final: 0.7887 (mmm) REVERT: D 105 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7651 (mm-30) REVERT: E 29 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8595 (mm-30) REVERT: E 182 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7535 (tt) REVERT: E 250 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6693 (tt0) REVERT: E 306 ASP cc_start: 0.8016 (t0) cc_final: 0.7328 (p0) REVERT: F 138 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.7239 (p0) REVERT: F 218 ASN cc_start: 0.8447 (OUTLIER) cc_final: 0.8071 (p0) REVERT: G 64 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7867 (m-30) REVERT: I 5 GLN cc_start: 0.8308 (tp40) cc_final: 0.7887 (tp40) REVERT: I 130 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7379 (tt0) REVERT: I 136 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7837 (t80) REVERT: I 143 MET cc_start: 0.8871 (mmt) cc_final: 0.7873 (mmm) REVERT: J 105 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7650 (mm-30) REVERT: K 29 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8595 (mm-30) REVERT: K 182 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7540 (tt) REVERT: K 250 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6697 (tt0) REVERT: K 306 ASP cc_start: 0.8017 (t0) cc_final: 0.7326 (p0) REVERT: L 60 SER cc_start: 0.8859 (m) cc_final: 0.8636 (p) REVERT: L 138 ASP cc_start: 0.7489 (OUTLIER) cc_final: 0.7248 (p0) REVERT: L 218 ASN cc_start: 0.8445 (OUTLIER) cc_final: 0.8070 (p0) outliers start: 91 outliers final: 58 residues processed: 349 average time/residue: 0.3953 time to fit residues: 223.9023 Evaluate side-chains 322 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 251 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 183 HIS Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 136 PHE Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 218 ASN Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 174 CYS Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 288 SER Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain I residue 136 PHE Chi-restraints excluded: chain I residue 138 ASP Chi-restraints excluded: chain I residue 158 VAL Chi-restraints excluded: chain I residue 183 HIS Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 138 ASP Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 250 GLU Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 136 PHE Chi-restraints excluded: chain L residue 138 ASP Chi-restraints excluded: chain L residue 206 ASP Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 218 ASN Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain L residue 302 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 7.9990 chunk 332 optimal weight: 9.9990 chunk 303 optimal weight: 8.9990 chunk 323 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 253 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 292 optimal weight: 6.9990 chunk 305 optimal weight: 9.9990 chunk 322 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS ** H 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.121 29916 Z= 0.542 Angle : 0.766 10.672 40944 Z= 0.369 Chirality : 0.046 0.192 4392 Planarity : 0.006 0.059 5484 Dihedral : 8.895 87.918 4056 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.63 % Allowed : 19.13 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.14), residues: 3684 helix: -0.04 (0.16), residues: 1056 sheet: -0.87 (0.19), residues: 828 loop : -0.64 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 66 HIS 0.019 0.002 HIS B 177 PHE 0.019 0.002 PHE H 251 TYR 0.039 0.003 TYR E 255 ARG 0.004 0.001 ARG L 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 232 time to evaluate : 3.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7966 (m-30) REVERT: B 179 GLN cc_start: 0.8921 (tt0) cc_final: 0.8608 (tt0) REVERT: C 130 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7254 (tt0) REVERT: C 136 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.8087 (t80) REVERT: C 143 MET cc_start: 0.8947 (mmt) cc_final: 0.8057 (mmm) REVERT: D 105 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7657 (mm-30) REVERT: E 29 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8593 (mm-30) REVERT: E 143 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.8082 (mmm) REVERT: E 182 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7722 (tt) REVERT: E 306 ASP cc_start: 0.8083 (t0) cc_final: 0.7341 (p0) REVERT: F 38 ASP cc_start: 0.8328 (t0) cc_final: 0.8118 (t0) REVERT: F 183 HIS cc_start: 0.9028 (OUTLIER) cc_final: 0.7620 (p90) REVERT: G 64 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7965 (m-30) REVERT: H 179 GLN cc_start: 0.8922 (tt0) cc_final: 0.8614 (tt0) REVERT: I 130 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7253 (tt0) REVERT: I 136 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.8188 (t80) REVERT: I 143 MET cc_start: 0.8948 (mmt) cc_final: 0.8060 (mmm) REVERT: J 105 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7661 (mm-30) REVERT: K 29 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8606 (mm-30) REVERT: K 143 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8075 (mmm) REVERT: K 182 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7718 (tt) REVERT: K 306 ASP cc_start: 0.8082 (t0) cc_final: 0.7341 (p0) outliers start: 112 outliers final: 88 residues processed: 328 average time/residue: 0.3736 time to fit residues: 201.9333 Evaluate side-chains 305 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 206 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 183 HIS Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 136 PHE Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 183 HIS Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 306 ASP Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 177 HIS Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain G residue 298 THR Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 174 CYS Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain I residue 136 PHE Chi-restraints excluded: chain I residue 138 ASP Chi-restraints excluded: chain I residue 158 VAL Chi-restraints excluded: chain I residue 183 HIS Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 136 PHE Chi-restraints excluded: chain J residue 138 ASP Chi-restraints excluded: chain J residue 143 MET Chi-restraints excluded: chain J residue 240 ASN Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 143 MET Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 211 ASP Chi-restraints excluded: chain K residue 250 GLU Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain L residue 136 PHE Chi-restraints excluded: chain L residue 138 ASP Chi-restraints excluded: chain L residue 206 ASP Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain L residue 302 ASP Chi-restraints excluded: chain L residue 306 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 3.9990 chunk 341 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 chunk 162 optimal weight: 10.0000 chunk 237 optimal weight: 0.0980 chunk 358 optimal weight: 6.9990 chunk 330 optimal weight: 1.9990 chunk 285 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS ** H 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 177 HIS ** L 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 29916 Z= 0.262 Angle : 0.635 8.794 40944 Z= 0.305 Chirality : 0.042 0.156 4392 Planarity : 0.005 0.042 5484 Dihedral : 8.790 86.428 4056 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.56 % Allowed : 20.10 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.14), residues: 3684 helix: 0.34 (0.17), residues: 1056 sheet: -0.64 (0.19), residues: 792 loop : -0.56 (0.15), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 66 HIS 0.011 0.001 HIS B 183 PHE 0.022 0.001 PHE F 136 TYR 0.031 0.002 TYR B 255 ARG 0.003 0.000 ARG D 202 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 246 time to evaluate : 3.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7860 (m-30) REVERT: B 179 GLN cc_start: 0.8803 (tt0) cc_final: 0.8497 (tt0) REVERT: C 5 GLN cc_start: 0.8322 (tp40) cc_final: 0.7918 (tp40) REVERT: C 130 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7382 (tt0) REVERT: C 143 MET cc_start: 0.8893 (mmt) cc_final: 0.7973 (mmm) REVERT: D 105 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7609 (mm-30) REVERT: E 29 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8501 (mm-30) REVERT: E 143 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7985 (mmm) REVERT: E 182 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7255 (tt) REVERT: E 250 GLU cc_start: 0.7660 (tp30) cc_final: 0.6866 (tt0) REVERT: E 306 ASP cc_start: 0.7984 (t0) cc_final: 0.7320 (p0) REVERT: F 38 ASP cc_start: 0.8278 (t0) cc_final: 0.8055 (t0) REVERT: F 138 ASP cc_start: 0.7361 (OUTLIER) cc_final: 0.7082 (p0) REVERT: G 64 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7853 (m-30) REVERT: H 179 GLN cc_start: 0.8809 (tt0) cc_final: 0.8504 (tt0) REVERT: I 5 GLN cc_start: 0.8319 (tp40) cc_final: 0.7914 (tp40) REVERT: I 130 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7378 (tt0) REVERT: I 136 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7952 (t80) REVERT: I 143 MET cc_start: 0.8887 (mmt) cc_final: 0.7955 (mmm) REVERT: J 105 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7613 (mm-30) REVERT: K 29 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8499 (mm-30) REVERT: K 143 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7984 (mmm) REVERT: K 182 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7255 (tt) REVERT: K 250 GLU cc_start: 0.7655 (tp30) cc_final: 0.6867 (tt0) REVERT: K 306 ASP cc_start: 0.7985 (t0) cc_final: 0.7319 (p0) REVERT: L 38 ASP cc_start: 0.8293 (t0) cc_final: 0.8075 (t0) REVERT: L 138 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.7214 (p0) outliers start: 79 outliers final: 64 residues processed: 310 average time/residue: 0.3796 time to fit residues: 193.0663 Evaluate side-chains 308 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 233 time to evaluate : 3.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 183 HIS Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 136 PHE Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 306 ASP Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 174 CYS Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain I residue 136 PHE Chi-restraints excluded: chain I residue 138 ASP Chi-restraints excluded: chain I residue 158 VAL Chi-restraints excluded: chain I residue 183 HIS Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 138 ASP Chi-restraints excluded: chain J residue 246 ILE Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 143 MET Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 211 ASP Chi-restraints excluded: chain K residue 300 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain L residue 136 PHE Chi-restraints excluded: chain L residue 138 ASP Chi-restraints excluded: chain L residue 206 ASP Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain L residue 302 ASP Chi-restraints excluded: chain L residue 306 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 10.0000 chunk 304 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 263 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 chunk 286 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 293 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS B 177 HIS B 224 ASN ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS H 177 HIS H 224 ASN ** I 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 177 HIS ** L 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.072055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.063912 restraints weight = 96551.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.065740 restraints weight = 48337.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.066996 restraints weight = 29705.921| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 29916 Z= 0.316 Angle : 0.638 8.602 40944 Z= 0.305 Chirality : 0.042 0.167 4392 Planarity : 0.005 0.042 5484 Dihedral : 8.720 88.004 4056 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.79 % Allowed : 20.10 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.14), residues: 3684 helix: 0.34 (0.17), residues: 1056 sheet: -0.52 (0.19), residues: 792 loop : -0.54 (0.15), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 66 HIS 0.016 0.001 HIS B 177 PHE 0.018 0.001 PHE F 136 TYR 0.055 0.002 TYR B 255 ARG 0.003 0.000 ARG B 267 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5271.91 seconds wall clock time: 97 minutes 24.03 seconds (5844.03 seconds total)