Starting phenix.real_space_refine on Sat Jul 27 03:07:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmk_19362/07_2024/8rmk_19362.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmk_19362/07_2024/8rmk_19362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmk_19362/07_2024/8rmk_19362.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmk_19362/07_2024/8rmk_19362.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmk_19362/07_2024/8rmk_19362.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmk_19362/07_2024/8rmk_19362.cif" } resolution = 3.07 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= 0.008 sd= 0.057 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 P 11 5.49 5 S 132 5.16 5 C 23122 2.51 5 N 6259 2.21 5 O 6589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 85": "OE1" <-> "OE2" Residue "A GLU 236": "OE1" <-> "OE2" Residue "B GLU 85": "OE1" <-> "OE2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "D GLU 85": "OE1" <-> "OE2" Residue "D GLU 236": "OE1" <-> "OE2" Residue "E GLU 85": "OE1" <-> "OE2" Residue "E GLU 236": "OE1" <-> "OE2" Residue "F GLU 85": "OE1" <-> "OE2" Residue "F GLU 236": "OE1" <-> "OE2" Residue "G GLU 85": "OE1" <-> "OE2" Residue "G GLU 236": "OE1" <-> "OE2" Residue "H GLU 85": "OE1" <-> "OE2" Residue "H GLU 236": "OE1" <-> "OE2" Residue "I GLU 85": "OE1" <-> "OE2" Residue "I GLU 236": "OE1" <-> "OE2" Residue "J GLU 85": "OE1" <-> "OE2" Residue "J GLU 236": "OE1" <-> "OE2" Residue "K GLU 85": "OE1" <-> "OE2" Residue "K GLU 236": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 36113 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2281 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "L" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "B" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2281 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "C" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2281 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "D" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2281 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "E" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2281 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "F" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2281 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "G" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2281 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "H" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2281 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "I" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2281 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "J" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2281 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "K" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2281 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "M" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "O" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "P" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "Q" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "R" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "S" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "T" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "U" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "V" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 19.48, per 1000 atoms: 0.54 Number of scatterers: 36113 At special positions: 0 Unit cell: (200.43, 200.43, 134.93, 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) S 132 16.00 P 11 15.00 O 6589 8.00 N 6259 7.00 C 23122 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.04 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 130 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 130 " distance=2.03 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS D 46 " - pdb=" SG CYS D 130 " distance=2.03 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 162 " distance=2.03 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 130 " distance=2.03 Simple disulfide: pdb=" SG CYS E 48 " - pdb=" SG CYS E 162 " distance=2.03 Simple disulfide: pdb=" SG CYS F 46 " - pdb=" SG CYS F 130 " distance=2.03 Simple disulfide: pdb=" SG CYS F 48 " - pdb=" SG CYS F 162 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 130 " distance=2.03 Simple disulfide: pdb=" SG CYS G 48 " - pdb=" SG CYS G 162 " distance=2.03 Simple disulfide: pdb=" SG CYS H 46 " - pdb=" SG CYS H 130 " distance=2.03 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 162 " distance=2.03 Simple disulfide: pdb=" SG CYS I 46 " - pdb=" SG CYS I 130 " distance=2.03 Simple disulfide: pdb=" SG CYS I 48 " - pdb=" SG CYS I 162 " distance=2.03 Simple disulfide: pdb=" SG CYS J 46 " - pdb=" SG CYS J 130 " distance=2.03 Simple disulfide: pdb=" SG CYS J 48 " - pdb=" SG CYS J 162 " distance=2.03 Simple disulfide: pdb=" SG CYS K 46 " - pdb=" SG CYS K 130 " distance=2.03 Simple disulfide: pdb=" SG CYS K 48 " - pdb=" SG CYS K 162 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS T 96 " distance=2.04 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 96 " distance=2.04 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.89 Conformation dependent library (CDL) restraints added in 6.5 seconds 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8426 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 44 sheets defined 53.0% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.11 Creating SS restraints... Processing helix chain 'A' and resid 52 through 76 Proline residue: A 64 - end of helix Processing helix chain 'A' and resid 77 through 90 Processing helix chain 'A' and resid 95 through 111 removed outlier: 3.650A pdb=" N THR A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 125 Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 152 through 160 Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 169 through 210 removed outlier: 3.596A pdb=" N GLU A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 252 Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 274 through 280 Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.726A pdb=" N PHE A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 91 removed outlier: 3.511A pdb=" N THR L 91 " --> pdb=" O PRO L 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 76 Proline residue: B 64 - end of helix Processing helix chain 'B' and resid 77 through 90 Processing helix chain 'B' and resid 95 through 111 removed outlier: 3.650A pdb=" N THR B 99 " --> pdb=" O SER B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 125 Processing helix chain 'B' and resid 125 through 133 Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 152 through 160 Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 169 through 210 removed outlier: 3.595A pdb=" N GLU B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 252 Processing helix chain 'B' and resid 257 through 267 Processing helix chain 'B' and resid 274 through 280 Processing helix chain 'B' and resid 297 through 304 Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.725A pdb=" N PHE B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 76 Proline residue: C 64 - end of helix Processing helix chain 'C' and resid 77 through 90 Processing helix chain 'C' and resid 95 through 111 removed outlier: 3.651A pdb=" N THR C 99 " --> pdb=" O SER C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 Processing helix chain 'C' and resid 125 through 133 Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' Processing helix chain 'C' and resid 152 through 160 Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'C' and resid 169 through 210 removed outlier: 3.596A pdb=" N GLU C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR C 182 " --> pdb=" O ARG C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 252 Processing helix chain 'C' and resid 257 through 267 Processing helix chain 'C' and resid 274 through 280 Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 323 through 329 removed outlier: 3.726A pdb=" N PHE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 76 Proline residue: D 64 - end of helix Processing helix chain 'D' and resid 77 through 90 Processing helix chain 'D' and resid 95 through 111 removed outlier: 3.650A pdb=" N THR D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 125 Processing helix chain 'D' and resid 125 through 133 Processing helix chain 'D' and resid 134 through 136 No H-bonds generated for 'chain 'D' and resid 134 through 136' Processing helix chain 'D' and resid 152 through 160 Processing helix chain 'D' and resid 161 through 163 No H-bonds generated for 'chain 'D' and resid 161 through 163' Processing helix chain 'D' and resid 166 through 168 No H-bonds generated for 'chain 'D' and resid 166 through 168' Processing helix chain 'D' and resid 169 through 210 removed outlier: 3.596A pdb=" N GLU D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 252 Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 274 through 280 Processing helix chain 'D' and resid 297 through 304 Processing helix chain 'D' and resid 323 through 329 removed outlier: 3.726A pdb=" N PHE D 329 " --> pdb=" O LEU D 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 76 Proline residue: E 64 - end of helix Processing helix chain 'E' and resid 77 through 90 Processing helix chain 'E' and resid 95 through 111 removed outlier: 3.651A pdb=" N THR E 99 " --> pdb=" O SER E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 125 Processing helix chain 'E' and resid 125 through 133 Processing helix chain 'E' and resid 134 through 136 No H-bonds generated for 'chain 'E' and resid 134 through 136' Processing helix chain 'E' and resid 152 through 160 Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 166 through 168 No H-bonds generated for 'chain 'E' and resid 166 through 168' Processing helix chain 'E' and resid 169 through 210 removed outlier: 3.596A pdb=" N GLU E 174 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR E 182 " --> pdb=" O ARG E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 252 Processing helix chain 'E' and resid 257 through 267 Processing helix chain 'E' and resid 274 through 280 Processing helix chain 'E' and resid 297 through 304 Processing helix chain 'E' and resid 323 through 329 removed outlier: 3.726A pdb=" N PHE E 329 " --> pdb=" O LEU E 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 76 Proline residue: F 64 - end of helix Processing helix chain 'F' and resid 77 through 90 Processing helix chain 'F' and resid 95 through 111 removed outlier: 3.650A pdb=" N THR F 99 " --> pdb=" O SER F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 125 Processing helix chain 'F' and resid 125 through 133 Processing helix chain 'F' and resid 134 through 136 No H-bonds generated for 'chain 'F' and resid 134 through 136' Processing helix chain 'F' and resid 152 through 160 Processing helix chain 'F' and resid 161 through 163 No H-bonds generated for 'chain 'F' and resid 161 through 163' Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 169 through 210 removed outlier: 3.595A pdb=" N GLU F 174 " --> pdb=" O SER F 170 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR F 182 " --> pdb=" O ARG F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 252 Processing helix chain 'F' and resid 257 through 267 Processing helix chain 'F' and resid 274 through 280 Processing helix chain 'F' and resid 297 through 304 Processing helix chain 'F' and resid 323 through 329 removed outlier: 3.726A pdb=" N PHE F 329 " --> pdb=" O LEU F 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 76 Proline residue: G 64 - end of helix Processing helix chain 'G' and resid 77 through 90 Processing helix chain 'G' and resid 95 through 111 removed outlier: 3.650A pdb=" N THR G 99 " --> pdb=" O SER G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 125 Processing helix chain 'G' and resid 125 through 133 Processing helix chain 'G' and resid 134 through 136 No H-bonds generated for 'chain 'G' and resid 134 through 136' Processing helix chain 'G' and resid 152 through 160 Processing helix chain 'G' and resid 161 through 163 No H-bonds generated for 'chain 'G' and resid 161 through 163' Processing helix chain 'G' and resid 166 through 168 No H-bonds generated for 'chain 'G' and resid 166 through 168' Processing helix chain 'G' and resid 169 through 210 removed outlier: 3.596A pdb=" N GLU G 174 " --> pdb=" O SER G 170 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR G 182 " --> pdb=" O ARG G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 252 Processing helix chain 'G' and resid 257 through 267 Processing helix chain 'G' and resid 274 through 280 Processing helix chain 'G' and resid 297 through 304 Processing helix chain 'G' and resid 323 through 329 removed outlier: 3.725A pdb=" N PHE G 329 " --> pdb=" O LEU G 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 76 Proline residue: H 64 - end of helix Processing helix chain 'H' and resid 77 through 90 Processing helix chain 'H' and resid 95 through 111 removed outlier: 3.651A pdb=" N THR H 99 " --> pdb=" O SER H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 125 Processing helix chain 'H' and resid 125 through 133 Processing helix chain 'H' and resid 134 through 136 No H-bonds generated for 'chain 'H' and resid 134 through 136' Processing helix chain 'H' and resid 152 through 160 Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'H' and resid 169 through 210 removed outlier: 3.596A pdb=" N GLU H 174 " --> pdb=" O SER H 170 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR H 182 " --> pdb=" O ARG H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 252 Processing helix chain 'H' and resid 257 through 267 Processing helix chain 'H' and resid 274 through 280 Processing helix chain 'H' and resid 297 through 304 Processing helix chain 'H' and resid 323 through 329 removed outlier: 3.725A pdb=" N PHE H 329 " --> pdb=" O LEU H 325 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 76 Proline residue: I 64 - end of helix Processing helix chain 'I' and resid 77 through 90 Processing helix chain 'I' and resid 95 through 111 removed outlier: 3.651A pdb=" N THR I 99 " --> pdb=" O SER I 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 125 Processing helix chain 'I' and resid 125 through 133 Processing helix chain 'I' and resid 134 through 136 No H-bonds generated for 'chain 'I' and resid 134 through 136' Processing helix chain 'I' and resid 152 through 160 Processing helix chain 'I' and resid 161 through 163 No H-bonds generated for 'chain 'I' and resid 161 through 163' Processing helix chain 'I' and resid 166 through 168 No H-bonds generated for 'chain 'I' and resid 166 through 168' Processing helix chain 'I' and resid 169 through 210 removed outlier: 3.595A pdb=" N GLU I 174 " --> pdb=" O SER I 170 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR I 182 " --> pdb=" O ARG I 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 213 through 252 Processing helix chain 'I' and resid 257 through 267 Processing helix chain 'I' and resid 274 through 280 Processing helix chain 'I' and resid 297 through 304 Processing helix chain 'I' and resid 323 through 329 removed outlier: 3.726A pdb=" N PHE I 329 " --> pdb=" O LEU I 325 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 76 Proline residue: J 64 - end of helix Processing helix chain 'J' and resid 77 through 90 Processing helix chain 'J' and resid 95 through 111 removed outlier: 3.651A pdb=" N THR J 99 " --> pdb=" O SER J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 125 Processing helix chain 'J' and resid 125 through 133 Processing helix chain 'J' and resid 134 through 136 No H-bonds generated for 'chain 'J' and resid 134 through 136' Processing helix chain 'J' and resid 152 through 160 Processing helix chain 'J' and resid 161 through 163 No H-bonds generated for 'chain 'J' and resid 161 through 163' Processing helix chain 'J' and resid 166 through 168 No H-bonds generated for 'chain 'J' and resid 166 through 168' Processing helix chain 'J' and resid 169 through 210 removed outlier: 3.595A pdb=" N GLU J 174 " --> pdb=" O SER J 170 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR J 182 " --> pdb=" O ARG J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 213 through 252 Processing helix chain 'J' and resid 257 through 267 Processing helix chain 'J' and resid 274 through 280 Processing helix chain 'J' and resid 297 through 304 Processing helix chain 'J' and resid 323 through 329 removed outlier: 3.726A pdb=" N PHE J 329 " --> pdb=" O LEU J 325 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 76 Proline residue: K 64 - end of helix Processing helix chain 'K' and resid 77 through 90 Processing helix chain 'K' and resid 95 through 111 removed outlier: 3.650A pdb=" N THR K 99 " --> pdb=" O SER K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 125 Processing helix chain 'K' and resid 125 through 133 Processing helix chain 'K' and resid 134 through 136 No H-bonds generated for 'chain 'K' and resid 134 through 136' Processing helix chain 'K' and resid 152 through 160 Processing helix chain 'K' and resid 161 through 163 No H-bonds generated for 'chain 'K' and resid 161 through 163' Processing helix chain 'K' and resid 166 through 168 No H-bonds generated for 'chain 'K' and resid 166 through 168' Processing helix chain 'K' and resid 169 through 210 removed outlier: 3.595A pdb=" N GLU K 174 " --> pdb=" O SER K 170 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR K 182 " --> pdb=" O ARG K 178 " (cutoff:3.500A) Processing helix chain 'K' and resid 213 through 252 Processing helix chain 'K' and resid 257 through 267 Processing helix chain 'K' and resid 274 through 280 Processing helix chain 'K' and resid 297 through 304 Processing helix chain 'K' and resid 323 through 329 removed outlier: 3.726A pdb=" N PHE K 329 " --> pdb=" O LEU K 325 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 91 removed outlier: 3.511A pdb=" N THR M 91 " --> pdb=" O PRO M 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.511A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 91 removed outlier: 3.511A pdb=" N THR O 91 " --> pdb=" O PRO O 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 91 removed outlier: 3.511A pdb=" N THR P 91 " --> pdb=" O PRO P 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 91 removed outlier: 3.511A pdb=" N THR Q 91 " --> pdb=" O PRO Q 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 91 removed outlier: 3.511A pdb=" N THR R 91 " --> pdb=" O PRO R 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.511A pdb=" N THR S 91 " --> pdb=" O PRO S 88 " (cutoff:3.500A) Processing helix chain 'T' and resid 87 through 91 removed outlier: 3.512A pdb=" N THR T 91 " --> pdb=" O PRO T 88 " (cutoff:3.500A) Processing helix chain 'U' and resid 87 through 91 removed outlier: 3.512A pdb=" N THR U 91 " --> pdb=" O PRO U 88 " (cutoff:3.500A) Processing helix chain 'V' and resid 87 through 91 removed outlier: 3.511A pdb=" N THR V 91 " --> pdb=" O PRO V 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 289 through 290 Processing sheet with id=AA2, first strand: chain 'A' and resid 315 through 319 removed outlier: 5.117A pdb=" N ASN A 315 " --> pdb=" O GLU V 114 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLU V 114 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N GLU A 317 " --> pdb=" O TYR V 112 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N TYR V 112 " --> pdb=" O GLU A 317 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'V' and resid 58 through 60 removed outlier: 6.947A pdb=" N TRP V 36 " --> pdb=" O VAL V 48 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA V 50 " --> pdb=" O LEU V 34 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU V 34 " --> pdb=" O ALA V 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 58 through 60 removed outlier: 6.948A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU L 34 " --> pdb=" O ALA L 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 103 through 105 Processing sheet with id=AA7, first strand: chain 'B' and resid 289 through 290 Processing sheet with id=AA8, first strand: chain 'C' and resid 289 through 290 Processing sheet with id=AA9, first strand: chain 'C' and resid 315 through 319 removed outlier: 5.344A pdb=" N ASN C 315 " --> pdb=" O GLU M 114 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLU M 114 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N GLU C 317 " --> pdb=" O TYR M 112 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N TYR M 112 " --> pdb=" O GLU C 317 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR M 110 " --> pdb=" O ALA C 319 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 58 through 60 removed outlier: 6.947A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA M 50 " --> pdb=" O LEU M 34 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU M 34 " --> pdb=" O ALA M 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 289 through 290 Processing sheet with id=AB3, first strand: chain 'D' and resid 315 through 319 removed outlier: 5.109A pdb=" N ASN D 315 " --> pdb=" O GLU N 114 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLU N 114 " --> pdb=" O ASN D 315 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLU D 317 " --> pdb=" O TYR N 112 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N TYR N 112 " --> pdb=" O GLU D 317 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.948A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA N 50 " --> pdb=" O LEU N 34 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU N 34 " --> pdb=" O ALA N 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 289 through 290 Processing sheet with id=AB6, first strand: chain 'E' and resid 315 through 319 removed outlier: 5.671A pdb=" N TYR O 110 " --> pdb=" O MET E 318 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'O' and resid 58 through 60 removed outlier: 6.948A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA O 50 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU O 34 " --> pdb=" O ALA O 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 289 through 290 Processing sheet with id=AB9, first strand: chain 'F' and resid 315 through 319 removed outlier: 5.675A pdb=" N TYR P 110 " --> pdb=" O MET F 318 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 58 through 60 removed outlier: 6.948A pdb=" N TRP P 36 " --> pdb=" O VAL P 48 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA P 50 " --> pdb=" O LEU P 34 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU P 34 " --> pdb=" O ALA P 50 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 289 through 290 Processing sheet with id=AC3, first strand: chain 'G' and resid 315 through 319 removed outlier: 5.718A pdb=" N TYR Q 110 " --> pdb=" O MET G 318 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Q' and resid 58 through 60 removed outlier: 6.948A pdb=" N TRP Q 36 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA Q 50 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU Q 34 " --> pdb=" O ALA Q 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 289 through 290 Processing sheet with id=AC6, first strand: chain 'H' and resid 315 through 319 removed outlier: 5.760A pdb=" N TYR R 110 " --> pdb=" O MET H 318 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'R' and resid 58 through 60 removed outlier: 6.948A pdb=" N TRP R 36 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA R 50 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU R 34 " --> pdb=" O ALA R 50 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 289 through 290 Processing sheet with id=AC9, first strand: chain 'I' and resid 315 through 319 removed outlier: 5.780A pdb=" N TYR S 110 " --> pdb=" O MET I 318 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.947A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA S 50 " --> pdb=" O LEU S 34 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU S 34 " --> pdb=" O ALA S 50 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 289 through 290 Processing sheet with id=AD3, first strand: chain 'J' and resid 315 through 319 removed outlier: 4.938A pdb=" N ASN J 315 " --> pdb=" O GLU T 114 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLU T 114 " --> pdb=" O ASN J 315 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLU J 317 " --> pdb=" O TYR T 112 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N TYR T 112 " --> pdb=" O GLU J 317 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR T 110 " --> pdb=" O ALA J 319 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'T' and resid 58 through 60 removed outlier: 6.947A pdb=" N TRP T 36 " --> pdb=" O VAL T 48 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA T 50 " --> pdb=" O LEU T 34 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU T 34 " --> pdb=" O ALA T 50 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 289 through 290 Processing sheet with id=AD6, first strand: chain 'K' and resid 315 through 319 removed outlier: 4.865A pdb=" N ASN K 315 " --> pdb=" O GLU U 114 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLU U 114 " --> pdb=" O ASN K 315 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N GLU K 317 " --> pdb=" O TYR U 112 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N TYR U 112 " --> pdb=" O GLU K 317 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR U 110 " --> pdb=" O ALA K 319 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'U' and resid 58 through 60 removed outlier: 6.948A pdb=" N TRP U 36 " --> pdb=" O VAL U 48 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA U 50 " --> pdb=" O LEU U 34 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU U 34 " --> pdb=" O ALA U 50 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AD9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AE1, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AE2, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'Q' and resid 3 through 7 Processing sheet with id=AE4, first strand: chain 'R' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'T' and resid 3 through 7 Processing sheet with id=AE7, first strand: chain 'U' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'V' and resid 3 through 7 2083 hydrogen bonds defined for protein. 6078 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: 12.83 Time building geometry restraints manager: 15.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6463 1.33 - 1.45: 10139 1.45 - 1.57: 20215 1.57 - 1.69: 22 1.69 - 1.81: 154 Bond restraints: 36993 Sorted by residual: bond pdb=" CB TYR R 33 " pdb=" CG TYR R 33 " ideal model delta sigma weight residual 1.512 1.474 0.038 2.20e-02 2.07e+03 3.01e+00 bond pdb=" CB TYR M 33 " pdb=" CG TYR M 33 " ideal model delta sigma weight residual 1.512 1.474 0.038 2.20e-02 2.07e+03 2.98e+00 bond pdb=" CB TYR N 33 " pdb=" CG TYR N 33 " ideal model delta sigma weight residual 1.512 1.474 0.038 2.20e-02 2.07e+03 2.92e+00 bond pdb=" CB TYR O 33 " pdb=" CG TYR O 33 " ideal model delta sigma weight residual 1.512 1.474 0.038 2.20e-02 2.07e+03 2.91e+00 bond pdb=" CB TYR Q 33 " pdb=" CG TYR Q 33 " ideal model delta sigma weight residual 1.512 1.475 0.037 2.20e-02 2.07e+03 2.90e+00 ... (remaining 36988 not shown) Histogram of bond angle deviations from ideal: 93.73 - 101.88: 33 101.88 - 110.04: 5368 110.04 - 118.20: 22402 118.20 - 126.35: 21796 126.35 - 134.51: 671 Bond angle restraints: 50270 Sorted by residual: angle pdb=" C SER N 101 " pdb=" CA SER N 101 " pdb=" CB SER N 101 " ideal model delta sigma weight residual 117.23 109.10 8.13 1.36e+00 5.41e-01 3.57e+01 angle pdb=" C SER M 101 " pdb=" CA SER M 101 " pdb=" CB SER M 101 " ideal model delta sigma weight residual 117.23 109.12 8.11 1.36e+00 5.41e-01 3.56e+01 angle pdb=" C SER U 101 " pdb=" CA SER U 101 " pdb=" CB SER U 101 " ideal model delta sigma weight residual 117.23 109.12 8.11 1.36e+00 5.41e-01 3.56e+01 angle pdb=" C SER T 101 " pdb=" CA SER T 101 " pdb=" CB SER T 101 " ideal model delta sigma weight residual 117.23 109.13 8.10 1.36e+00 5.41e-01 3.55e+01 angle pdb=" C SER V 101 " pdb=" CA SER V 101 " pdb=" CB SER V 101 " ideal model delta sigma weight residual 117.23 109.14 8.09 1.36e+00 5.41e-01 3.54e+01 ... (remaining 50265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.20: 21406 34.20 - 68.40: 462 68.40 - 102.59: 11 102.59 - 136.79: 0 136.79 - 170.99: 44 Dihedral angle restraints: 21923 sinusoidal: 8778 harmonic: 13145 Sorted by residual: dihedral pdb=" C2' PLC I 401 " pdb=" C' PLC I 401 " pdb=" C1' PLC I 401 " pdb=" O' PLC I 401 " ideal model delta sinusoidal sigma weight residual -11.03 159.96 -170.99 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C2' PLC H 401 " pdb=" C' PLC H 401 " pdb=" C1' PLC H 401 " pdb=" O' PLC H 401 " ideal model delta sinusoidal sigma weight residual -11.03 159.95 -170.98 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C2' PLC J 401 " pdb=" C' PLC J 401 " pdb=" C1' PLC J 401 " pdb=" O' PLC J 401 " ideal model delta sinusoidal sigma weight residual -11.03 159.94 -170.97 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 21920 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3550 0.034 - 0.068: 1379 0.068 - 0.102: 348 0.102 - 0.136: 146 0.136 - 0.170: 22 Chirality restraints: 5445 Sorted by residual: chirality pdb=" CA TYR H 287 " pdb=" N TYR H 287 " pdb=" C TYR H 287 " pdb=" CB TYR H 287 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA TYR G 287 " pdb=" N TYR G 287 " pdb=" C TYR G 287 " pdb=" CB TYR G 287 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA TYR B 287 " pdb=" N TYR B 287 " pdb=" C TYR B 287 " pdb=" CB TYR B 287 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.17e-01 ... (remaining 5442 not shown) Planarity restraints: 6457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP S 52 " -0.024 2.00e-02 2.50e+03 1.99e-02 9.86e+00 pdb=" CG TRP S 52 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP S 52 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP S 52 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP S 52 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP S 52 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP S 52 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP S 52 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP S 52 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP S 52 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP V 52 " 0.024 2.00e-02 2.50e+03 1.99e-02 9.86e+00 pdb=" CG TRP V 52 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP V 52 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP V 52 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP V 52 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP V 52 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP V 52 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP V 52 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP V 52 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP V 52 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP N 52 " 0.024 2.00e-02 2.50e+03 1.98e-02 9.81e+00 pdb=" CG TRP N 52 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP N 52 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP N 52 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP N 52 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP N 52 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP N 52 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP N 52 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP N 52 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP N 52 " -0.002 2.00e-02 2.50e+03 ... (remaining 6454 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7903 2.79 - 3.31: 34684 3.31 - 3.84: 58911 3.84 - 4.37: 69654 4.37 - 4.90: 119145 Nonbonded interactions: 290297 Sorted by model distance: nonbonded pdb=" O LEU C 122 " pdb=" OG SER C 184 " model vdw 2.257 2.440 nonbonded pdb=" O LEU B 122 " pdb=" OG SER B 184 " model vdw 2.257 2.440 nonbonded pdb=" O LEU D 122 " pdb=" OG SER D 184 " model vdw 2.257 2.440 nonbonded pdb=" O LEU G 122 " pdb=" OG SER G 184 " model vdw 2.257 2.440 nonbonded pdb=" O LEU E 122 " pdb=" OG SER E 184 " model vdw 2.257 2.440 ... (remaining 290292 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' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 1.400 Check model and map are aligned: 0.280 Set scattering table: 0.350 Process input model: 92.270 Find NCS groups from input model: 4.160 Set up NCS constraints: 0.220 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: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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 : 0.003 0.043 36993 Z= 0.199 Angle : 0.611 10.416 50270 Z= 0.337 Chirality : 0.041 0.170 5445 Planarity : 0.004 0.025 6457 Dihedral : 15.808 170.988 13398 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.45 % Allowed : 9.55 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.13), residues: 4455 helix: 2.23 (0.11), residues: 2123 sheet: 1.03 (0.18), residues: 814 loop : -0.32 (0.17), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP S 52 HIS 0.005 0.001 HIS B 88 PHE 0.022 0.002 PHE F 329 TYR 0.031 0.002 TYR Q 33 ARG 0.003 0.000 ARG M 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 384 time to evaluate : 3.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 HIS cc_start: 0.7685 (m-70) cc_final: 0.7355 (m-70) REVERT: A 172 PHE cc_start: 0.7842 (m-80) cc_final: 0.7585 (m-80) REVERT: B 155 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7078 (mp0) REVERT: B 173 ARG cc_start: 0.6833 (ttt90) cc_final: 0.6449 (ttp80) REVERT: C 172 PHE cc_start: 0.7299 (m-80) cc_final: 0.7089 (m-80) REVERT: C 203 LYS cc_start: 0.8133 (tttp) cc_final: 0.7888 (tttp) REVERT: C 317 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7823 (mm-30) REVERT: D 102 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7671 (mm) REVERT: D 137 ASP cc_start: 0.8007 (t0) cc_final: 0.7236 (t0) REVERT: E 152 HIS cc_start: 0.7144 (m-70) cc_final: 0.6882 (m-70) REVERT: F 100 PHE cc_start: 0.7081 (t80) cc_final: 0.6716 (t80) REVERT: H 171 ASP cc_start: 0.8359 (m-30) cc_final: 0.7890 (m-30) REVERT: H 203 LYS cc_start: 0.8249 (tttp) cc_final: 0.7937 (tttt) REVERT: H 206 LYS cc_start: 0.8413 (ttpp) cc_final: 0.8207 (tttp) REVERT: H 291 GLN cc_start: 0.8119 (mt0) cc_final: 0.7905 (mm-40) REVERT: H 318 MET cc_start: 0.8681 (ptm) cc_final: 0.8457 (mtm) REVERT: I 206 LYS cc_start: 0.8389 (ttpp) cc_final: 0.8154 (tttm) REVERT: I 260 ASP cc_start: 0.8243 (m-30) cc_final: 0.7939 (m-30) REVERT: I 317 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7819 (mt-10) REVERT: J 100 PHE cc_start: 0.6897 (t80) cc_final: 0.6392 (t80) REVERT: J 102 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7792 (mm) REVERT: J 321 LEU cc_start: 0.8597 (pp) cc_final: 0.8376 (pp) REVERT: K 102 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7463 (mm) REVERT: K 318 MET cc_start: 0.8710 (ptm) cc_final: 0.8395 (mtm) REVERT: M 95 TYR cc_start: 0.7404 (m-80) cc_final: 0.7042 (m-80) REVERT: N 32 SER cc_start: 0.6436 (m) cc_final: 0.6004 (p) REVERT: N 34 LEU cc_start: 0.7692 (mt) cc_final: 0.7490 (mm) REVERT: O 32 SER cc_start: 0.6481 (m) cc_final: 0.6162 (p) REVERT: P 32 SER cc_start: 0.6574 (m) cc_final: 0.6353 (p) REVERT: P 83 MET cc_start: 0.4448 (mmm) cc_final: 0.3010 (tmm) REVERT: Q 95 TYR cc_start: 0.7043 (m-80) cc_final: 0.6579 (m-80) REVERT: R 34 LEU cc_start: 0.8408 (mt) cc_final: 0.8143 (mm) REVERT: R 95 TYR cc_start: 0.6499 (m-80) cc_final: 0.6228 (m-80) REVERT: S 34 LEU cc_start: 0.7763 (mt) cc_final: 0.7511 (mm) REVERT: S 95 TYR cc_start: 0.7013 (m-80) cc_final: 0.6661 (m-80) REVERT: T 34 LEU cc_start: 0.8162 (mt) cc_final: 0.7945 (mm) REVERT: T 83 MET cc_start: 0.4270 (mmm) cc_final: 0.3687 (ppp) REVERT: T 95 TYR cc_start: 0.7072 (m-80) cc_final: 0.6849 (m-80) REVERT: U 34 LEU cc_start: 0.8215 (mt) cc_final: 0.7930 (mm) REVERT: U 83 MET cc_start: 0.4627 (mmm) cc_final: 0.3982 (ppp) REVERT: V 95 TYR cc_start: 0.6730 (m-80) cc_final: 0.6462 (m-80) REVERT: V 103 GLN cc_start: 0.6346 (mp10) cc_final: 0.6122 (mp10) outliers start: 17 outliers final: 2 residues processed: 394 average time/residue: 0.4910 time to fit residues: 310.0626 Evaluate side-chains 269 residues out of total 3740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 264 time to evaluate : 3.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain K residue 102 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 371 optimal weight: 9.9990 chunk 333 optimal weight: 20.0000 chunk 185 optimal weight: 30.0000 chunk 113 optimal weight: 3.9990 chunk 224 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 344 optimal weight: 20.0000 chunk 133 optimal weight: 6.9990 chunk 209 optimal weight: 0.0980 chunk 256 optimal weight: 4.9990 chunk 399 optimal weight: 30.0000 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN A 246 ASN ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN C 152 HIS C 246 ASN D 229 GLN D 246 ASN E 246 ASN F 229 GLN F 246 ASN G 246 ASN H 229 GLN H 246 ASN I 246 ASN I 315 ASN J 246 ASN K 246 ASN M 103 GLN M 113 ASN N 103 GLN O 39 GLN ** O 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 GLN Q 103 GLN R 103 GLN S 103 GLN ** T 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 113 ASN V 103 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 36993 Z= 0.508 Angle : 0.721 19.389 50270 Z= 0.360 Chirality : 0.048 0.214 5445 Planarity : 0.006 0.058 6457 Dihedral : 16.344 175.145 5424 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.38 % Allowed : 10.80 % Favored : 86.82 % 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: 1.38 (0.13), residues: 4455 helix: 1.69 (0.11), residues: 2178 sheet: 1.21 (0.18), residues: 792 loop : -0.38 (0.18), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP M 52 HIS 0.011 0.002 HIS K 88 PHE 0.022 0.002 PHE H 69 TYR 0.036 0.003 TYR F 54 ARG 0.010 0.001 ARG D 288 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 258 time to evaluate : 3.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 HIS cc_start: 0.7497 (m-70) cc_final: 0.7210 (m-70) REVERT: A 172 PHE cc_start: 0.7688 (m-80) cc_final: 0.7369 (m-80) REVERT: A 201 LEU cc_start: 0.8602 (mt) cc_final: 0.8373 (mt) REVERT: B 155 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6926 (mp0) REVERT: B 228 ASP cc_start: 0.8247 (m-30) cc_final: 0.8023 (m-30) REVERT: B 263 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8445 (tp) REVERT: C 286 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8001 (mt) REVERT: D 100 PHE cc_start: 0.7287 (t80) cc_final: 0.6895 (t80) REVERT: D 102 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7587 (mm) REVERT: E 49 SER cc_start: 0.9019 (m) cc_final: 0.8785 (t) REVERT: E 102 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7283 (mm) REVERT: E 155 GLU cc_start: 0.7000 (mm-30) cc_final: 0.6716 (mp0) REVERT: E 286 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8363 (mp) REVERT: F 100 PHE cc_start: 0.7174 (t80) cc_final: 0.6852 (t80) REVERT: G 102 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7713 (mm) REVERT: H 49 SER cc_start: 0.9107 (m) cc_final: 0.8907 (t) REVERT: H 228 ASP cc_start: 0.8333 (m-30) cc_final: 0.8118 (m-30) REVERT: I 206 LYS cc_start: 0.8528 (ttpp) cc_final: 0.8169 (tttm) REVERT: I 321 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8169 (pp) REVERT: J 100 PHE cc_start: 0.7032 (t80) cc_final: 0.6517 (t80) REVERT: J 102 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7541 (mm) REVERT: J 129 VAL cc_start: 0.8782 (m) cc_final: 0.8553 (t) REVERT: J 163 LYS cc_start: 0.7560 (mttp) cc_final: 0.7353 (mmmt) REVERT: J 321 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8389 (pp) REVERT: K 102 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7506 (mm) REVERT: K 321 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8522 (pp) REVERT: M 95 TYR cc_start: 0.7260 (m-80) cc_final: 0.6711 (m-80) REVERT: Q 95 TYR cc_start: 0.7467 (m-80) cc_final: 0.7011 (m-80) REVERT: R 32 SER cc_start: 0.6730 (m) cc_final: 0.6463 (p) REVERT: R 34 LEU cc_start: 0.8173 (mt) cc_final: 0.7944 (mm) REVERT: R 46 GLU cc_start: 0.8337 (tp30) cc_final: 0.7124 (pm20) REVERT: R 83 MET cc_start: 0.5162 (mpp) cc_final: 0.4189 (tmm) REVERT: S 95 TYR cc_start: 0.7181 (m-80) cc_final: 0.6941 (m-80) REVERT: T 83 MET cc_start: 0.4393 (mmm) cc_final: 0.3723 (ppp) REVERT: T 95 TYR cc_start: 0.6987 (m-80) cc_final: 0.6651 (m-80) REVERT: U 83 MET cc_start: 0.4783 (mmm) cc_final: 0.4229 (ppp) REVERT: V 46 GLU cc_start: 0.8390 (tp30) cc_final: 0.7199 (pm20) outliers start: 89 outliers final: 54 residues processed: 334 average time/residue: 0.4433 time to fit residues: 246.3465 Evaluate side-chains 288 residues out of total 3740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 223 time to evaluate : 3.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 261 GLU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 261 GLU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 257 ASN Chi-restraints excluded: chain I residue 261 GLU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 261 GLU Chi-restraints excluded: chain J residue 301 LYS Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 257 ASN Chi-restraints excluded: chain K residue 261 GLU Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain O residue 71 SER Chi-restraints excluded: chain V residue 32 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 222 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 332 optimal weight: 30.0000 chunk 272 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 400 optimal weight: 9.9990 chunk 432 optimal weight: 5.9990 chunk 356 optimal weight: 20.0000 chunk 396 optimal weight: 10.0000 chunk 136 optimal weight: 0.8980 chunk 321 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 ASN ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN H 229 GLN H 257 ASN M 113 ASN N 103 GLN O 27 ASN ** O 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 ASN ** Q 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 103 GLN S 27 ASN ** S 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 ASN ** T 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 103 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 36993 Z= 0.295 Angle : 0.602 15.984 50270 Z= 0.298 Chirality : 0.041 0.176 5445 Planarity : 0.004 0.054 6457 Dihedral : 15.994 178.898 5421 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.49 % Allowed : 11.90 % Favored : 85.61 % 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: 1.57 (0.13), residues: 4455 helix: 1.99 (0.11), residues: 2178 sheet: 1.04 (0.18), residues: 814 loop : -0.37 (0.18), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP V 52 HIS 0.006 0.001 HIS C 88 PHE 0.023 0.001 PHE F 172 TYR 0.023 0.002 TYR J 287 ARG 0.006 0.001 ARG J 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 223 time to evaluate : 4.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 PHE cc_start: 0.7731 (m-80) cc_final: 0.7475 (m-80) REVERT: A 175 GLU cc_start: 0.7374 (tp30) cc_final: 0.7170 (tm-30) REVERT: L 81 LEU cc_start: 0.5447 (OUTLIER) cc_final: 0.4844 (tp) REVERT: B 142 THR cc_start: 0.6517 (OUTLIER) cc_final: 0.5761 (m) REVERT: B 155 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6865 (mp0) REVERT: B 175 GLU cc_start: 0.7744 (tp30) cc_final: 0.7304 (tt0) REVERT: B 228 ASP cc_start: 0.8260 (m-30) cc_final: 0.8044 (m-30) REVERT: C 172 PHE cc_start: 0.7591 (m-80) cc_final: 0.7373 (m-80) REVERT: D 100 PHE cc_start: 0.7232 (t80) cc_final: 0.6696 (t80) REVERT: D 104 SER cc_start: 0.9022 (p) cc_final: 0.8650 (p) REVERT: D 206 LYS cc_start: 0.8410 (ttpp) cc_final: 0.8161 (tttm) REVERT: D 263 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8414 (mt) REVERT: E 49 SER cc_start: 0.9013 (m) cc_final: 0.8786 (t) REVERT: E 102 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7139 (mm) REVERT: F 100 PHE cc_start: 0.7122 (t80) cc_final: 0.6817 (t80) REVERT: F 286 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7958 (mt) REVERT: G 49 SER cc_start: 0.9188 (m) cc_final: 0.8917 (t) REVERT: G 102 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7770 (mm) REVERT: G 160 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.7699 (m-80) REVERT: I 206 LYS cc_start: 0.8651 (ttpp) cc_final: 0.8307 (tttm) REVERT: I 321 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.7881 (pp) REVERT: J 100 PHE cc_start: 0.6945 (t80) cc_final: 0.6417 (t80) REVERT: J 129 VAL cc_start: 0.8737 (m) cc_final: 0.8534 (t) REVERT: J 259 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7662 (p0) REVERT: J 321 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8417 (pp) REVERT: K 321 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8422 (pp) REVERT: M 34 LEU cc_start: 0.7962 (mt) cc_final: 0.7747 (mm) REVERT: M 95 TYR cc_start: 0.7427 (m-80) cc_final: 0.6881 (m-80) REVERT: N 83 MET cc_start: 0.4374 (mmm) cc_final: 0.3056 (tmm) REVERT: P 68 PHE cc_start: 0.3305 (OUTLIER) cc_final: 0.2926 (m-10) REVERT: P 105 ASN cc_start: 0.8219 (p0) cc_final: 0.7907 (p0) REVERT: Q 95 TYR cc_start: 0.7511 (m-80) cc_final: 0.7093 (m-80) REVERT: R 32 SER cc_start: 0.6914 (m) cc_final: 0.6612 (p) REVERT: R 34 LEU cc_start: 0.8197 (mt) cc_final: 0.7968 (mm) REVERT: R 83 MET cc_start: 0.4726 (mpp) cc_final: 0.3745 (tmm) REVERT: S 68 PHE cc_start: 0.2702 (OUTLIER) cc_final: 0.2179 (m-80) REVERT: S 95 TYR cc_start: 0.7216 (m-80) cc_final: 0.6971 (m-80) REVERT: T 83 MET cc_start: 0.4130 (mmm) cc_final: 0.3525 (ppp) REVERT: T 95 TYR cc_start: 0.7053 (m-80) cc_final: 0.6612 (m-80) REVERT: T 103 GLN cc_start: 0.7111 (mp10) cc_final: 0.6754 (mp10) REVERT: U 83 MET cc_start: 0.5328 (mmm) cc_final: 0.4016 (ppp) REVERT: V 46 GLU cc_start: 0.8304 (tp30) cc_final: 0.7164 (pm20) outliers start: 93 outliers final: 54 residues processed: 302 average time/residue: 0.4843 time to fit residues: 238.4219 Evaluate side-chains 280 residues out of total 3740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 213 time to evaluate : 3.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 257 ASN Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 160 PHE Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 261 GLU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 298 ARG Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 257 ASN Chi-restraints excluded: chain I residue 261 GLU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 257 ASN Chi-restraints excluded: chain J residue 259 ASP Chi-restraints excluded: chain J residue 261 GLU Chi-restraints excluded: chain J residue 298 ARG Chi-restraints excluded: chain J residue 301 LYS Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 257 ASN Chi-restraints excluded: chain K residue 259 ASP Chi-restraints excluded: chain K residue 261 GLU Chi-restraints excluded: chain K residue 298 ARG Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain O residue 68 PHE Chi-restraints excluded: chain O residue 71 SER Chi-restraints excluded: chain P residue 68 PHE Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain S residue 68 PHE Chi-restraints excluded: chain V residue 32 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 395 optimal weight: 9.9990 chunk 300 optimal weight: 5.9990 chunk 207 optimal weight: 0.0870 chunk 44 optimal weight: 3.9990 chunk 191 optimal weight: 0.9990 chunk 268 optimal weight: 0.4980 chunk 401 optimal weight: 20.0000 chunk 425 optimal weight: 7.9990 chunk 209 optimal weight: 4.9990 chunk 380 optimal weight: 30.0000 chunk 114 optimal weight: 0.6980 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN A 246 ASN L 27 ASN ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN C 246 ASN E 229 GLN F 246 ASN G 246 ASN M 113 ASN O 27 ASN ** O 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 27 ASN Q 27 ASN ** Q 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 27 ASN T 27 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 36993 Z= 0.190 Angle : 0.550 14.013 50270 Z= 0.273 Chirality : 0.039 0.162 5445 Planarity : 0.004 0.049 6457 Dihedral : 15.454 167.003 5415 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.89 % Allowed : 11.90 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.13), residues: 4455 helix: 2.35 (0.11), residues: 2178 sheet: 0.99 (0.18), residues: 836 loop : -0.42 (0.17), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP U 52 HIS 0.006 0.001 HIS C 88 PHE 0.020 0.001 PHE F 172 TYR 0.019 0.002 TYR K 287 ARG 0.004 0.000 ARG E 298 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 216 time to evaluate : 3.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 LEU cc_start: 0.8601 (mt) cc_final: 0.8392 (mt) REVERT: L 81 LEU cc_start: 0.5455 (OUTLIER) cc_final: 0.4852 (tp) REVERT: B 142 THR cc_start: 0.6287 (OUTLIER) cc_final: 0.5701 (m) REVERT: B 175 GLU cc_start: 0.7640 (tp30) cc_final: 0.7286 (tt0) REVERT: B 228 ASP cc_start: 0.8243 (m-30) cc_final: 0.8000 (m-30) REVERT: B 259 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7820 (p0) REVERT: C 286 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7770 (mt) REVERT: D 100 PHE cc_start: 0.7267 (t80) cc_final: 0.6892 (t80) REVERT: D 259 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7531 (p0) REVERT: E 49 SER cc_start: 0.9019 (m) cc_final: 0.8797 (t) REVERT: E 102 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7122 (mm) REVERT: E 160 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7800 (m-10) REVERT: F 100 PHE cc_start: 0.7092 (t80) cc_final: 0.6793 (t80) REVERT: F 286 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7968 (mt) REVERT: G 102 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7803 (mm) REVERT: G 160 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.7659 (m-80) REVERT: I 175 GLU cc_start: 0.7315 (tp30) cc_final: 0.6957 (tt0) REVERT: I 206 LYS cc_start: 0.8557 (ttpp) cc_final: 0.8203 (tttm) REVERT: I 321 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.7831 (pp) REVERT: J 100 PHE cc_start: 0.7018 (t80) cc_final: 0.6510 (t80) REVERT: J 321 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8315 (pp) REVERT: K 321 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8396 (pp) REVERT: M 46 GLU cc_start: 0.6697 (pm20) cc_final: 0.6437 (pm20) REVERT: M 95 TYR cc_start: 0.7447 (m-80) cc_final: 0.6939 (m-80) REVERT: N 83 MET cc_start: 0.4464 (mmm) cc_final: 0.2932 (tmm) REVERT: N 105 ASN cc_start: 0.7927 (p0) cc_final: 0.7484 (p0) REVERT: P 83 MET cc_start: 0.4863 (mmm) cc_final: 0.3197 (tmm) REVERT: P 105 ASN cc_start: 0.8120 (p0) cc_final: 0.7852 (p0) REVERT: Q 81 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6337 (tp) REVERT: Q 95 TYR cc_start: 0.7442 (m-80) cc_final: 0.7053 (m-80) REVERT: R 32 SER cc_start: 0.6958 (m) cc_final: 0.6613 (p) REVERT: R 34 LEU cc_start: 0.8179 (mt) cc_final: 0.7949 (mm) REVERT: R 46 GLU cc_start: 0.8271 (tp30) cc_final: 0.7132 (pm20) REVERT: S 68 PHE cc_start: 0.2837 (OUTLIER) cc_final: 0.2271 (m-80) REVERT: S 95 TYR cc_start: 0.7227 (m-80) cc_final: 0.7008 (m-80) REVERT: T 83 MET cc_start: 0.4178 (mmm) cc_final: 0.3641 (ppp) REVERT: T 95 TYR cc_start: 0.7057 (m-80) cc_final: 0.6639 (m-80) REVERT: V 46 GLU cc_start: 0.8313 (tp30) cc_final: 0.7148 (pm20) REVERT: V 81 LEU cc_start: 0.6328 (OUTLIER) cc_final: 0.5807 (tp) outliers start: 108 outliers final: 61 residues processed: 311 average time/residue: 0.5014 time to fit residues: 256.7939 Evaluate side-chains 285 residues out of total 3740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 208 time to evaluate : 4.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 298 ARG Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 257 ASN Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 160 PHE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 160 PHE Chi-restraints excluded: chain H residue 257 ASN Chi-restraints excluded: chain H residue 261 GLU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 298 ARG Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 257 ASN Chi-restraints excluded: chain I residue 261 GLU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 160 PHE Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 257 ASN Chi-restraints excluded: chain J residue 261 GLU Chi-restraints excluded: chain J residue 298 ARG Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 257 ASN Chi-restraints excluded: chain K residue 259 ASP Chi-restraints excluded: chain K residue 261 GLU Chi-restraints excluded: chain K residue 298 ARG Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain S residue 68 PHE Chi-restraints excluded: chain V residue 81 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 354 optimal weight: 0.0010 chunk 241 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 316 optimal weight: 0.9990 chunk 175 optimal weight: 0.1980 chunk 362 optimal weight: 4.9990 chunk 293 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 217 optimal weight: 6.9990 chunk 381 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 overall best weight: 2.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN L 27 ASN C 246 ASN E 229 GLN F 246 ASN G 246 ASN H 229 GLN M 113 ASN N 27 ASN O 27 ASN P 27 ASN Q 27 ASN R 27 ASN S 27 ASN T 27 ASN T 103 GLN T 111 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 36993 Z= 0.286 Angle : 0.592 16.117 50270 Z= 0.293 Chirality : 0.041 0.182 5445 Planarity : 0.004 0.052 6457 Dihedral : 15.072 169.753 5412 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.56 % Allowed : 11.76 % Favored : 84.68 % 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: 1.83 (0.13), residues: 4455 helix: 2.25 (0.11), residues: 2178 sheet: 1.16 (0.19), residues: 814 loop : -0.33 (0.18), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP V 52 HIS 0.007 0.001 HIS J 88 PHE 0.019 0.001 PHE F 172 TYR 0.025 0.002 TYR F 54 ARG 0.005 0.000 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 214 time to evaluate : 3.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 LEU cc_start: 0.8629 (mt) cc_final: 0.8379 (mt) REVERT: L 81 LEU cc_start: 0.5509 (OUTLIER) cc_final: 0.4882 (tp) REVERT: B 142 THR cc_start: 0.6726 (OUTLIER) cc_final: 0.6115 (m) REVERT: B 175 GLU cc_start: 0.7621 (tp30) cc_final: 0.7223 (tt0) REVERT: B 228 ASP cc_start: 0.8262 (m-30) cc_final: 0.8029 (m-30) REVERT: B 259 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7851 (p0) REVERT: C 286 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7806 (mt) REVERT: D 100 PHE cc_start: 0.7384 (t80) cc_final: 0.6822 (t80) REVERT: D 104 SER cc_start: 0.9016 (p) cc_final: 0.8660 (p) REVERT: D 168 ASN cc_start: 0.7155 (OUTLIER) cc_final: 0.6693 (t0) REVERT: D 259 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7372 (p0) REVERT: D 263 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8400 (mp) REVERT: E 49 SER cc_start: 0.8999 (m) cc_final: 0.8767 (t) REVERT: E 102 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7157 (mm) REVERT: E 160 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7645 (m-10) REVERT: E 286 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7965 (mp) REVERT: F 100 PHE cc_start: 0.7118 (t80) cc_final: 0.6824 (t80) REVERT: F 286 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7968 (mt) REVERT: G 102 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7756 (mm) REVERT: G 160 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7645 (m-80) REVERT: I 206 LYS cc_start: 0.8588 (ttpp) cc_final: 0.8219 (ttpt) REVERT: I 321 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8026 (pp) REVERT: J 100 PHE cc_start: 0.7039 (t80) cc_final: 0.6504 (t80) REVERT: J 259 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7581 (p0) REVERT: J 321 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8366 (pp) REVERT: K 321 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8427 (pp) REVERT: M 46 GLU cc_start: 0.6716 (pm20) cc_final: 0.6435 (pm20) REVERT: M 95 TYR cc_start: 0.7451 (m-80) cc_final: 0.6880 (m-80) REVERT: N 83 MET cc_start: 0.4643 (mmm) cc_final: 0.3023 (tmm) REVERT: O 83 MET cc_start: 0.5049 (mmm) cc_final: 0.3682 (tpp) REVERT: P 105 ASN cc_start: 0.8200 (p0) cc_final: 0.7954 (p0) REVERT: Q 81 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6365 (tp) REVERT: Q 95 TYR cc_start: 0.7453 (m-80) cc_final: 0.7098 (m-80) REVERT: R 34 LEU cc_start: 0.8195 (mt) cc_final: 0.7984 (mm) REVERT: S 68 PHE cc_start: 0.2968 (OUTLIER) cc_final: 0.2450 (m-80) REVERT: T 83 MET cc_start: 0.4087 (mmm) cc_final: 0.3583 (ppp) REVERT: T 95 TYR cc_start: 0.6787 (m-80) cc_final: 0.6414 (m-80) REVERT: T 103 GLN cc_start: 0.7206 (mp-120) cc_final: 0.6876 (mp10) REVERT: V 46 GLU cc_start: 0.8287 (tp30) cc_final: 0.7157 (pm20) REVERT: V 81 LEU cc_start: 0.6327 (OUTLIER) cc_final: 0.5789 (tp) REVERT: V 95 TYR cc_start: 0.6514 (m-80) cc_final: 0.6289 (m-80) outliers start: 133 outliers final: 88 residues processed: 327 average time/residue: 0.4586 time to fit residues: 247.7207 Evaluate side-chains 317 residues out of total 3740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 209 time to evaluate : 3.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 298 ARG Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 257 ASN Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 160 PHE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 160 PHE Chi-restraints excluded: chain H residue 229 GLN Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 261 GLU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 298 ARG Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 257 ASN Chi-restraints excluded: chain I residue 261 GLU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 257 ASN Chi-restraints excluded: chain J residue 259 ASP Chi-restraints excluded: chain J residue 261 GLU Chi-restraints excluded: chain J residue 298 ARG Chi-restraints excluded: chain J residue 301 LYS Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 257 ASN Chi-restraints excluded: chain K residue 259 ASP Chi-restraints excluded: chain K residue 261 GLU Chi-restraints excluded: chain K residue 298 ARG Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain S residue 68 PHE Chi-restraints excluded: chain T residue 71 SER Chi-restraints excluded: chain T residue 81 LEU Chi-restraints excluded: chain U residue 81 LEU Chi-restraints excluded: chain V residue 32 SER Chi-restraints excluded: chain V residue 81 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 143 optimal weight: 0.7980 chunk 383 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 249 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 425 optimal weight: 20.0000 chunk 353 optimal weight: 30.0000 chunk 197 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 223 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 ASN L 39 GLN C 229 GLN D 229 GLN E 229 GLN O 27 ASN P 27 ASN S 27 ASN V 27 ASN V 111 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 36993 Z= 0.254 Angle : 0.572 15.440 50270 Z= 0.283 Chirality : 0.040 0.178 5445 Planarity : 0.004 0.049 6457 Dihedral : 14.726 176.536 5412 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.61 % Allowed : 11.87 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.13), residues: 4455 helix: 2.31 (0.11), residues: 2178 sheet: 1.41 (0.19), residues: 770 loop : -0.41 (0.17), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP P 52 HIS 0.006 0.001 HIS J 88 PHE 0.025 0.001 PHE F 329 TYR 0.023 0.002 TYR F 54 ARG 0.003 0.000 ARG I 240 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 206 time to evaluate : 3.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 LEU cc_start: 0.8624 (mt) cc_final: 0.8374 (mt) REVERT: L 81 LEU cc_start: 0.5450 (OUTLIER) cc_final: 0.4786 (tp) REVERT: B 142 THR cc_start: 0.6770 (OUTLIER) cc_final: 0.6150 (m) REVERT: B 175 GLU cc_start: 0.7611 (tp30) cc_final: 0.7224 (tt0) REVERT: B 228 ASP cc_start: 0.8262 (m-30) cc_final: 0.8026 (m-30) REVERT: B 259 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7839 (p0) REVERT: C 329 PHE cc_start: 0.5583 (m-80) cc_final: 0.5255 (m-80) REVERT: D 100 PHE cc_start: 0.7404 (t80) cc_final: 0.6848 (t80) REVERT: D 104 SER cc_start: 0.9000 (p) cc_final: 0.8644 (p) REVERT: D 168 ASN cc_start: 0.7159 (OUTLIER) cc_final: 0.6696 (t0) REVERT: D 259 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7457 (p0) REVERT: E 49 SER cc_start: 0.9013 (m) cc_final: 0.8786 (t) REVERT: E 102 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7157 (mm) REVERT: E 160 PHE cc_start: 0.7868 (OUTLIER) cc_final: 0.7652 (m-10) REVERT: E 286 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7989 (mp) REVERT: F 100 PHE cc_start: 0.7103 (t80) cc_final: 0.6816 (t80) REVERT: F 286 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7965 (mt) REVERT: G 102 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7818 (mm) REVERT: G 160 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7638 (m-80) REVERT: G 298 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8392 (ptp-170) REVERT: I 206 LYS cc_start: 0.8617 (ttpp) cc_final: 0.8267 (ttpt) REVERT: I 321 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8000 (pp) REVERT: J 100 PHE cc_start: 0.7030 (t80) cc_final: 0.6500 (t80) REVERT: J 259 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7611 (p0) REVERT: J 321 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8411 (pp) REVERT: K 321 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8415 (pp) REVERT: K 329 PHE cc_start: 0.5816 (m-80) cc_final: 0.5420 (m-80) REVERT: M 46 GLU cc_start: 0.6705 (pm20) cc_final: 0.6414 (pm20) REVERT: O 83 MET cc_start: 0.5109 (mmm) cc_final: 0.3754 (tpp) REVERT: P 83 MET cc_start: 0.4905 (mmp) cc_final: 0.3670 (tmm) REVERT: P 105 ASN cc_start: 0.8167 (p0) cc_final: 0.7948 (p0) REVERT: Q 81 LEU cc_start: 0.6675 (OUTLIER) cc_final: 0.6339 (tp) REVERT: Q 95 TYR cc_start: 0.7539 (m-80) cc_final: 0.7203 (m-80) REVERT: R 34 LEU cc_start: 0.8174 (mt) cc_final: 0.7946 (mm) REVERT: T 46 GLU cc_start: 0.8459 (tp30) cc_final: 0.8206 (tp30) REVERT: T 83 MET cc_start: 0.4076 (mmm) cc_final: 0.3571 (ppp) REVERT: T 95 TYR cc_start: 0.6782 (m-80) cc_final: 0.6422 (m-80) REVERT: T 103 GLN cc_start: 0.7185 (mp-120) cc_final: 0.6845 (mp10) REVERT: V 46 GLU cc_start: 0.8353 (tp30) cc_final: 0.7242 (pm20) REVERT: V 81 LEU cc_start: 0.6321 (OUTLIER) cc_final: 0.5776 (tp) REVERT: V 95 TYR cc_start: 0.6539 (m-80) cc_final: 0.6289 (m-80) outliers start: 135 outliers final: 92 residues processed: 324 average time/residue: 0.4678 time to fit residues: 248.9309 Evaluate side-chains 314 residues out of total 3740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 204 time to evaluate : 4.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 298 ARG Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 257 ASN Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 160 PHE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 261 GLU Chi-restraints excluded: chain G residue 298 ARG Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 160 PHE Chi-restraints excluded: chain H residue 257 ASN Chi-restraints excluded: chain H residue 261 GLU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 298 ARG Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 160 PHE Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 257 ASN Chi-restraints excluded: chain I residue 261 GLU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 257 ASN Chi-restraints excluded: chain J residue 259 ASP Chi-restraints excluded: chain J residue 261 GLU Chi-restraints excluded: chain J residue 298 ARG Chi-restraints excluded: chain J residue 301 LYS Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 257 ASN Chi-restraints excluded: chain K residue 259 ASP Chi-restraints excluded: chain K residue 261 GLU Chi-restraints excluded: chain K residue 298 ARG Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 81 LEU Chi-restraints excluded: chain T residue 100 THR Chi-restraints excluded: chain U residue 81 LEU Chi-restraints excluded: chain V residue 32 SER Chi-restraints excluded: chain V residue 81 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 410 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 242 optimal weight: 4.9990 chunk 310 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 chunk 358 optimal weight: 40.0000 chunk 237 optimal weight: 2.9990 chunk 424 optimal weight: 3.9990 chunk 265 optimal weight: 2.9990 chunk 258 optimal weight: 6.9990 chunk 195 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 ASN L 39 GLN O 27 ASN O 39 GLN P 27 ASN R 27 ASN S 27 ASN T 27 ASN U 27 ASN V 27 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 36993 Z= 0.278 Angle : 0.587 16.102 50270 Z= 0.289 Chirality : 0.041 0.182 5445 Planarity : 0.004 0.051 6457 Dihedral : 13.957 167.346 5412 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.06 % Allowed : 11.55 % Favored : 84.39 % 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: 1.92 (0.13), residues: 4455 helix: 2.31 (0.11), residues: 2178 sheet: 1.65 (0.18), residues: 748 loop : -0.48 (0.17), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP L 52 HIS 0.006 0.001 HIS J 88 PHE 0.017 0.001 PHE F 172 TYR 0.024 0.002 TYR K 287 ARG 0.006 0.000 ARG I 240 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 222 time to evaluate : 4.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ASN cc_start: 0.7141 (OUTLIER) cc_final: 0.6174 (t0) REVERT: A 201 LEU cc_start: 0.8633 (mt) cc_final: 0.8373 (mt) REVERT: L 81 LEU cc_start: 0.5478 (OUTLIER) cc_final: 0.4755 (tp) REVERT: B 142 THR cc_start: 0.6778 (OUTLIER) cc_final: 0.6275 (m) REVERT: B 168 ASN cc_start: 0.6998 (OUTLIER) cc_final: 0.6468 (t0) REVERT: B 175 GLU cc_start: 0.7623 (tp30) cc_final: 0.7220 (tt0) REVERT: B 228 ASP cc_start: 0.8265 (m-30) cc_final: 0.8012 (m-30) REVERT: B 259 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7852 (p0) REVERT: C 229 GLN cc_start: 0.8662 (tt0) cc_final: 0.8448 (tt0) REVERT: C 286 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7792 (mt) REVERT: C 329 PHE cc_start: 0.5850 (m-80) cc_final: 0.5561 (m-80) REVERT: D 100 PHE cc_start: 0.7382 (t80) cc_final: 0.6827 (t80) REVERT: D 102 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7479 (mm) REVERT: D 104 SER cc_start: 0.8979 (p) cc_final: 0.8620 (p) REVERT: D 168 ASN cc_start: 0.7178 (OUTLIER) cc_final: 0.6705 (t0) REVERT: D 259 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7344 (p0) REVERT: D 263 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8386 (mp) REVERT: E 49 SER cc_start: 0.9000 (m) cc_final: 0.8768 (t) REVERT: E 102 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7158 (mm) REVERT: E 286 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7980 (mp) REVERT: F 100 PHE cc_start: 0.7098 (t80) cc_final: 0.6865 (t80) REVERT: F 286 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7965 (mt) REVERT: G 102 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7810 (mm) REVERT: G 160 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7670 (m-80) REVERT: I 206 LYS cc_start: 0.8652 (ttpp) cc_final: 0.8312 (ttpt) REVERT: I 321 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8001 (pp) REVERT: J 100 PHE cc_start: 0.7045 (t80) cc_final: 0.6498 (t80) REVERT: J 168 ASN cc_start: 0.6685 (OUTLIER) cc_final: 0.6021 (t0) REVERT: J 259 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7626 (p0) REVERT: J 321 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8431 (pp) REVERT: K 321 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8475 (pp) REVERT: K 329 PHE cc_start: 0.5943 (m-80) cc_final: 0.5592 (m-80) REVERT: M 46 GLU cc_start: 0.6798 (pm20) cc_final: 0.6504 (pm20) REVERT: M 95 TYR cc_start: 0.7300 (m-80) cc_final: 0.6905 (m-80) REVERT: N 83 MET cc_start: 0.4696 (mmm) cc_final: 0.3102 (tmm) REVERT: O 83 MET cc_start: 0.5188 (mmm) cc_final: 0.3836 (tpp) REVERT: P 83 MET cc_start: 0.4945 (mmp) cc_final: 0.3770 (tmm) REVERT: P 105 ASN cc_start: 0.8213 (p0) cc_final: 0.7958 (p0) REVERT: Q 95 TYR cc_start: 0.7553 (m-80) cc_final: 0.7208 (m-80) REVERT: Q 103 GLN cc_start: 0.7204 (mp10) cc_final: 0.6941 (mp10) REVERT: R 46 GLU cc_start: 0.8335 (tp30) cc_final: 0.7233 (pm20) REVERT: T 83 MET cc_start: 0.4099 (mmm) cc_final: 0.3592 (ppp) REVERT: T 95 TYR cc_start: 0.6840 (m-80) cc_final: 0.6424 (m-80) REVERT: T 103 GLN cc_start: 0.7320 (mp-120) cc_final: 0.7002 (mp10) REVERT: V 46 GLU cc_start: 0.8253 (tp30) cc_final: 0.7191 (pm20) REVERT: V 81 LEU cc_start: 0.6388 (OUTLIER) cc_final: 0.5841 (tp) REVERT: V 95 TYR cc_start: 0.6693 (m-80) cc_final: 0.6404 (m-80) REVERT: V 103 GLN cc_start: 0.7302 (mp10) cc_final: 0.6952 (mp10) outliers start: 152 outliers final: 109 residues processed: 353 average time/residue: 0.4643 time to fit residues: 270.6861 Evaluate side-chains 350 residues out of total 3740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 220 time to evaluate : 3.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 298 ARG Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 257 ASN Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 160 PHE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 261 GLU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 160 PHE Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 261 GLU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 298 ARG Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 160 PHE Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 257 ASN Chi-restraints excluded: chain I residue 261 GLU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 168 ASN Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 257 ASN Chi-restraints excluded: chain J residue 259 ASP Chi-restraints excluded: chain J residue 261 GLU Chi-restraints excluded: chain J residue 298 ARG Chi-restraints excluded: chain J residue 301 LYS Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 257 ASN Chi-restraints excluded: chain K residue 259 ASP Chi-restraints excluded: chain K residue 261 GLU Chi-restraints excluded: chain K residue 298 ARG Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain Q residue 32 SER Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 71 SER Chi-restraints excluded: chain T residue 100 THR Chi-restraints excluded: chain V residue 32 SER Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 100 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 262 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 253 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 269 optimal weight: 30.0000 chunk 288 optimal weight: 0.9980 chunk 209 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 333 optimal weight: 5.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN L 27 ASN C 246 ASN F 246 ASN G 246 ASN M 27 ASN M 103 GLN M 111 HIS O 27 ASN P 27 ASN R 27 ASN T 27 ASN V 27 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 36993 Z= 0.188 Angle : 0.541 14.014 50270 Z= 0.267 Chirality : 0.039 0.158 5445 Planarity : 0.004 0.045 6457 Dihedral : 13.089 144.416 5412 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.18 % Allowed : 12.62 % Favored : 84.20 % 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: 2.17 (0.13), residues: 4455 helix: 2.60 (0.11), residues: 2178 sheet: 1.49 (0.18), residues: 792 loop : -0.39 (0.17), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 52 HIS 0.004 0.001 HIS I 238 PHE 0.015 0.001 PHE G 329 TYR 0.021 0.002 TYR A 287 ARG 0.006 0.000 ARG J 173 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 219 time to evaluate : 3.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7336 (mm) REVERT: A 168 ASN cc_start: 0.7246 (OUTLIER) cc_final: 0.6300 (t0) REVERT: A 201 LEU cc_start: 0.8616 (mt) cc_final: 0.8372 (mt) REVERT: L 81 LEU cc_start: 0.5455 (OUTLIER) cc_final: 0.4764 (tp) REVERT: B 142 THR cc_start: 0.6765 (OUTLIER) cc_final: 0.6288 (m) REVERT: B 175 GLU cc_start: 0.7560 (tp30) cc_final: 0.7200 (tt0) REVERT: B 228 ASP cc_start: 0.8251 (m-30) cc_final: 0.8002 (m-30) REVERT: B 259 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7842 (p0) REVERT: C 286 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7644 (mp) REVERT: C 329 PHE cc_start: 0.5864 (m-80) cc_final: 0.5616 (m-80) REVERT: D 100 PHE cc_start: 0.7346 (t80) cc_final: 0.6788 (t80) REVERT: D 104 SER cc_start: 0.8999 (p) cc_final: 0.8660 (p) REVERT: E 49 SER cc_start: 0.9031 (m) cc_final: 0.8796 (t) REVERT: E 102 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7116 (mm) REVERT: F 100 PHE cc_start: 0.7056 (t80) cc_final: 0.6814 (t80) REVERT: F 168 ASN cc_start: 0.6576 (OUTLIER) cc_final: 0.6159 (t0) REVERT: F 286 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7882 (mt) REVERT: G 102 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7803 (mm) REVERT: G 160 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7678 (m-80) REVERT: G 298 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8382 (ptp-170) REVERT: I 175 GLU cc_start: 0.7383 (tp30) cc_final: 0.7174 (tt0) REVERT: I 206 LYS cc_start: 0.8646 (ttpp) cc_final: 0.8290 (ttpt) REVERT: I 321 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.7958 (pp) REVERT: J 100 PHE cc_start: 0.7014 (t80) cc_final: 0.6476 (t80) REVERT: K 321 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8465 (pp) REVERT: K 329 PHE cc_start: 0.6111 (m-80) cc_final: 0.5771 (m-80) REVERT: N 100 THR cc_start: 0.7417 (OUTLIER) cc_final: 0.6922 (t) REVERT: O 83 MET cc_start: 0.5233 (mmm) cc_final: 0.3932 (tpp) REVERT: P 83 MET cc_start: 0.5032 (mmp) cc_final: 0.3945 (tmm) REVERT: P 105 ASN cc_start: 0.8132 (p0) cc_final: 0.7858 (p0) REVERT: Q 81 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6586 (tt) REVERT: Q 83 MET cc_start: 0.4693 (mmm) cc_final: 0.3941 (tmm) REVERT: Q 95 TYR cc_start: 0.7557 (m-80) cc_final: 0.7222 (m-80) REVERT: Q 103 GLN cc_start: 0.7342 (mp10) cc_final: 0.7103 (mp10) REVERT: R 100 THR cc_start: 0.7656 (OUTLIER) cc_final: 0.7236 (t) REVERT: T 46 GLU cc_start: 0.8495 (tp30) cc_final: 0.8278 (tp30) REVERT: T 83 MET cc_start: 0.4067 (mmm) cc_final: 0.3565 (ppp) REVERT: T 95 TYR cc_start: 0.6850 (m-80) cc_final: 0.6436 (m-80) REVERT: T 103 GLN cc_start: 0.7256 (mp-120) cc_final: 0.6931 (mp10) REVERT: V 34 LEU cc_start: 0.7907 (mp) cc_final: 0.7648 (mp) REVERT: V 46 GLU cc_start: 0.8364 (tp30) cc_final: 0.7286 (pm20) REVERT: V 81 LEU cc_start: 0.6366 (OUTLIER) cc_final: 0.5701 (tp) REVERT: V 95 TYR cc_start: 0.6583 (m-80) cc_final: 0.6290 (m-80) REVERT: V 103 GLN cc_start: 0.7263 (mp10) cc_final: 0.6892 (mp10) outliers start: 119 outliers final: 92 residues processed: 316 average time/residue: 0.4761 time to fit residues: 243.8537 Evaluate side-chains 326 residues out of total 3740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 216 time to evaluate : 3.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 298 ARG Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 257 ASN Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 168 ASN Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 160 PHE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 261 GLU Chi-restraints excluded: chain G residue 298 ARG Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 160 PHE Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 257 ASN Chi-restraints excluded: chain H residue 261 GLU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 298 ARG Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 160 PHE Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 257 ASN Chi-restraints excluded: chain I residue 261 GLU Chi-restraints excluded: chain I residue 298 ARG Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 257 ASN Chi-restraints excluded: chain J residue 261 GLU Chi-restraints excluded: chain J residue 298 ARG Chi-restraints excluded: chain J residue 301 LYS Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 257 ASN Chi-restraints excluded: chain K residue 259 ASP Chi-restraints excluded: chain K residue 261 GLU Chi-restraints excluded: chain K residue 298 ARG Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 71 SER Chi-restraints excluded: chain T residue 100 THR Chi-restraints excluded: chain U residue 100 THR Chi-restraints excluded: chain V residue 32 SER Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 100 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 385 optimal weight: 6.9990 chunk 406 optimal weight: 20.0000 chunk 370 optimal weight: 8.9990 chunk 395 optimal weight: 10.0000 chunk 237 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 chunk 310 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 357 optimal weight: 10.0000 chunk 373 optimal weight: 10.0000 chunk 393 optimal weight: 7.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN L 27 ASN C 229 GLN C 246 ASN F 246 ASN G 246 ASN J 315 ASN M 27 ASN O 27 ASN T 113 ASN U 103 GLN U 111 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 36993 Z= 0.369 Angle : 0.634 17.694 50270 Z= 0.311 Chirality : 0.043 0.206 5445 Planarity : 0.005 0.055 6457 Dihedral : 12.839 143.116 5412 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.42 % Allowed : 12.62 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.13), residues: 4455 helix: 2.18 (0.11), residues: 2178 sheet: 1.66 (0.18), residues: 748 loop : -0.52 (0.17), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP L 52 HIS 0.006 0.001 HIS A 238 PHE 0.017 0.002 PHE F 172 TYR 0.028 0.002 TYR K 287 ARG 0.007 0.001 ARG D 240 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 228 time to evaluate : 3.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7314 (mm) REVERT: A 168 ASN cc_start: 0.7494 (OUTLIER) cc_final: 0.6723 (t0) REVERT: A 201 LEU cc_start: 0.8654 (mt) cc_final: 0.8374 (mt) REVERT: L 81 LEU cc_start: 0.5500 (OUTLIER) cc_final: 0.4815 (tp) REVERT: B 142 THR cc_start: 0.6933 (OUTLIER) cc_final: 0.6427 (m) REVERT: B 168 ASN cc_start: 0.6920 (OUTLIER) cc_final: 0.6388 (t0) REVERT: B 175 GLU cc_start: 0.7639 (tp30) cc_final: 0.7229 (tt0) REVERT: B 228 ASP cc_start: 0.8282 (m-30) cc_final: 0.8044 (m-30) REVERT: B 259 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7876 (p0) REVERT: B 263 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8441 (tp) REVERT: C 286 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7878 (mt) REVERT: C 329 PHE cc_start: 0.5887 (m-80) cc_final: 0.5679 (m-80) REVERT: D 100 PHE cc_start: 0.7389 (t80) cc_final: 0.6828 (t80) REVERT: D 104 SER cc_start: 0.8974 (p) cc_final: 0.8625 (p) REVERT: D 168 ASN cc_start: 0.7258 (OUTLIER) cc_final: 0.6814 (t0) REVERT: D 259 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7412 (p0) REVERT: D 263 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8427 (mt) REVERT: E 49 SER cc_start: 0.9004 (m) cc_final: 0.8773 (t) REVERT: E 102 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7190 (mm) REVERT: E 155 GLU cc_start: 0.6818 (mm-30) cc_final: 0.6558 (mp0) REVERT: E 286 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8121 (mp) REVERT: F 100 PHE cc_start: 0.7117 (t80) cc_final: 0.6873 (t80) REVERT: F 168 ASN cc_start: 0.6574 (OUTLIER) cc_final: 0.6185 (t0) REVERT: F 286 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8002 (mt) REVERT: G 102 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7774 (mm) REVERT: G 160 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7789 (m-80) REVERT: I 206 LYS cc_start: 0.8670 (ttpp) cc_final: 0.8333 (ttpt) REVERT: I 321 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8031 (pp) REVERT: J 100 PHE cc_start: 0.7125 (t80) cc_final: 0.6569 (t80) REVERT: J 168 ASN cc_start: 0.6688 (OUTLIER) cc_final: 0.6035 (t0) REVERT: J 259 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7621 (p0) REVERT: K 321 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8555 (pp) REVERT: K 329 PHE cc_start: 0.6253 (m-80) cc_final: 0.5954 (m-80) REVERT: N 83 MET cc_start: 0.4897 (mmm) cc_final: 0.3419 (tmm) REVERT: N 103 GLN cc_start: 0.7261 (mp-120) cc_final: 0.6942 (mp10) REVERT: O 83 MET cc_start: 0.5477 (mmm) cc_final: 0.4294 (tpp) REVERT: P 83 MET cc_start: 0.5261 (mmp) cc_final: 0.3783 (tmm) REVERT: Q 83 MET cc_start: 0.4835 (mmm) cc_final: 0.3969 (tmm) REVERT: Q 95 TYR cc_start: 0.7558 (m-80) cc_final: 0.7266 (m-80) REVERT: Q 103 GLN cc_start: 0.7474 (mp10) cc_final: 0.7249 (mp10) REVERT: R 46 GLU cc_start: 0.8319 (tp30) cc_final: 0.7255 (pm20) REVERT: T 83 MET cc_start: 0.4134 (mmm) cc_final: 0.3589 (ppp) REVERT: T 103 GLN cc_start: 0.7459 (mp-120) cc_final: 0.7146 (mp10) REVERT: V 34 LEU cc_start: 0.7996 (mp) cc_final: 0.7759 (mp) REVERT: V 46 GLU cc_start: 0.8249 (tp30) cc_final: 0.7210 (pm20) REVERT: V 81 LEU cc_start: 0.6407 (OUTLIER) cc_final: 0.5749 (tp) REVERT: V 95 TYR cc_start: 0.6741 (m-80) cc_final: 0.6428 (m-80) REVERT: V 103 GLN cc_start: 0.7413 (mp10) cc_final: 0.7036 (mp10) outliers start: 128 outliers final: 99 residues processed: 330 average time/residue: 0.4620 time to fit residues: 250.6084 Evaluate side-chains 345 residues out of total 3740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 224 time to evaluate : 3.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 298 ARG Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 257 ASN Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 168 ASN Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 160 PHE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 261 GLU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 160 PHE Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 261 GLU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 257 ASN Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 168 ASN Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 257 ASN Chi-restraints excluded: chain J residue 259 ASP Chi-restraints excluded: chain J residue 261 GLU Chi-restraints excluded: chain J residue 298 ARG Chi-restraints excluded: chain J residue 301 LYS Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 257 ASN Chi-restraints excluded: chain K residue 259 ASP Chi-restraints excluded: chain K residue 261 GLU Chi-restraints excluded: chain K residue 298 ARG Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 71 SER Chi-restraints excluded: chain T residue 100 THR Chi-restraints excluded: chain U residue 100 THR Chi-restraints excluded: chain V residue 32 SER Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 259 optimal weight: 0.9980 chunk 417 optimal weight: 0.1980 chunk 255 optimal weight: 0.6980 chunk 198 optimal weight: 0.6980 chunk 290 optimal weight: 0.5980 chunk 438 optimal weight: 4.9990 chunk 403 optimal weight: 7.9990 chunk 349 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 269 optimal weight: 30.0000 chunk 214 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN L 27 ASN C 246 ASN F 246 ASN G 246 ASN H 246 ASN N 27 ASN O 27 ASN P 27 ASN R 27 ASN S 27 ASN U 27 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 36993 Z= 0.142 Angle : 0.522 12.713 50270 Z= 0.259 Chirality : 0.038 0.137 5445 Planarity : 0.003 0.043 6457 Dihedral : 12.056 143.172 5412 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.27 % Allowed : 13.93 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.13), residues: 4455 helix: 2.68 (0.11), residues: 2189 sheet: 1.51 (0.18), residues: 792 loop : -0.35 (0.18), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP U 52 HIS 0.004 0.001 HIS D 238 PHE 0.017 0.001 PHE G 329 TYR 0.017 0.001 TYR G 287 ARG 0.006 0.000 ARG J 173 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 224 time to evaluate : 3.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7525 (mm) REVERT: A 201 LEU cc_start: 0.8619 (mt) cc_final: 0.8383 (mt) REVERT: B 142 THR cc_start: 0.6609 (OUTLIER) cc_final: 0.6186 (m) REVERT: B 168 ASN cc_start: 0.6960 (OUTLIER) cc_final: 0.6354 (t0) REVERT: B 175 GLU cc_start: 0.7550 (tp30) cc_final: 0.7207 (tt0) REVERT: B 228 ASP cc_start: 0.8248 (m-30) cc_final: 0.7998 (m-30) REVERT: C 286 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7581 (mp) REVERT: D 81 ASN cc_start: 0.8218 (p0) cc_final: 0.7889 (p0) REVERT: D 100 PHE cc_start: 0.7324 (t80) cc_final: 0.6765 (t80) REVERT: D 104 SER cc_start: 0.8987 (p) cc_final: 0.8641 (p) REVERT: D 168 ASN cc_start: 0.7236 (OUTLIER) cc_final: 0.6787 (t0) REVERT: E 49 SER cc_start: 0.9009 (m) cc_final: 0.8768 (t) REVERT: E 102 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7115 (mm) REVERT: E 286 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7876 (mp) REVERT: F 100 PHE cc_start: 0.6981 (t80) cc_final: 0.6744 (t80) REVERT: F 286 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7737 (mt) REVERT: G 102 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7729 (mm) REVERT: G 160 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7641 (m-80) REVERT: G 298 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8376 (ptp-170) REVERT: I 206 LYS cc_start: 0.8641 (ttpp) cc_final: 0.8289 (ttpt) REVERT: I 321 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.7934 (pp) REVERT: J 100 PHE cc_start: 0.6991 (t80) cc_final: 0.6458 (t80) REVERT: J 168 ASN cc_start: 0.6699 (OUTLIER) cc_final: 0.6028 (t0) REVERT: K 321 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8448 (pp) REVERT: K 329 PHE cc_start: 0.6228 (m-80) cc_final: 0.5952 (m-80) REVERT: M 46 GLU cc_start: 0.6415 (pm20) cc_final: 0.6196 (pm20) REVERT: N 100 THR cc_start: 0.7305 (OUTLIER) cc_final: 0.6824 (t) REVERT: O 83 MET cc_start: 0.5340 (mmm) cc_final: 0.4969 (tpp) REVERT: P 83 MET cc_start: 0.5087 (mmp) cc_final: 0.3530 (tmm) REVERT: P 105 ASN cc_start: 0.8063 (p0) cc_final: 0.7817 (p0) REVERT: Q 81 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6530 (tt) REVERT: Q 83 MET cc_start: 0.4731 (mmm) cc_final: 0.3898 (tmm) REVERT: Q 95 TYR cc_start: 0.7577 (m-80) cc_final: 0.7246 (m-80) REVERT: Q 103 GLN cc_start: 0.7260 (mp10) cc_final: 0.6985 (mp10) REVERT: R 46 GLU cc_start: 0.8314 (tp30) cc_final: 0.7219 (pm20) REVERT: R 100 THR cc_start: 0.7467 (OUTLIER) cc_final: 0.7007 (t) REVERT: T 83 MET cc_start: 0.4063 (mmm) cc_final: 0.3519 (ppp) REVERT: T 95 TYR cc_start: 0.7189 (m-80) cc_final: 0.6706 (m-80) REVERT: T 103 GLN cc_start: 0.7294 (mp-120) cc_final: 0.6966 (mp10) REVERT: V 34 LEU cc_start: 0.8008 (mp) cc_final: 0.7723 (mp) REVERT: V 46 GLU cc_start: 0.8288 (tp30) cc_final: 0.7229 (pm20) REVERT: V 81 LEU cc_start: 0.6270 (OUTLIER) cc_final: 0.5531 (tp) REVERT: V 95 TYR cc_start: 0.6679 (m-80) cc_final: 0.6363 (m-80) REVERT: V 103 GLN cc_start: 0.7278 (mp10) cc_final: 0.6882 (mp10) outliers start: 85 outliers final: 62 residues processed: 290 average time/residue: 0.4777 time to fit residues: 224.6858 Evaluate side-chains 295 residues out of total 3740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 215 time to evaluate : 3.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 298 ARG Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 257 ASN Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 160 PHE Chi-restraints excluded: chain G residue 261 GLU Chi-restraints excluded: chain G residue 298 ARG Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 160 PHE Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 261 GLU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 257 ASN Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 168 ASN Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 257 ASN Chi-restraints excluded: chain J residue 261 GLU Chi-restraints excluded: chain J residue 298 ARG Chi-restraints excluded: chain J residue 301 LYS Chi-restraints excluded: chain K residue 257 ASN Chi-restraints excluded: chain K residue 261 GLU Chi-restraints excluded: chain K residue 298 ARG Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 100 THR Chi-restraints excluded: chain U residue 100 THR Chi-restraints excluded: chain V residue 32 SER Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 277 optimal weight: 0.5980 chunk 371 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 chunk 321 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 349 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 chunk 359 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 ASN B 246 ASN F 246 ASN G 246 ASN H 246 ASN J 246 ASN M 27 ASN N 27 ASN O 27 ASN P 27 ASN R 27 ASN R 111 HIS S 27 ASN T 113 ASN U 27 ASN V 27 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.192746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.123041 restraints weight = 46013.923| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.42 r_work: 0.3226 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 36993 Z= 0.159 Angle : 0.526 13.510 50270 Z= 0.259 Chirality : 0.038 0.150 5445 Planarity : 0.004 0.042 6457 Dihedral : 11.430 141.911 5412 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.25 % Allowed : 14.04 % Favored : 83.72 % 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: 2.35 (0.13), residues: 4455 helix: 2.81 (0.11), residues: 2200 sheet: 1.54 (0.18), residues: 803 loop : -0.47 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP U 52 HIS 0.003 0.001 HIS H 300 PHE 0.018 0.001 PHE G 329 TYR 0.018 0.001 TYR A 287 ARG 0.006 0.000 ARG J 173 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6765.28 seconds wall clock time: 122 minutes 30.97 seconds (7350.97 seconds total)