Starting phenix.real_space_refine on Wed Feb 21 00:02:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g1u_29677/02_2024/8g1u_29677_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g1u_29677/02_2024/8g1u_29677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g1u_29677/02_2024/8g1u_29677.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g1u_29677/02_2024/8g1u_29677.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g1u_29677/02_2024/8g1u_29677_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g1u_29677/02_2024/8g1u_29677_trim_updated.pdb" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.233 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 140 5.16 5 C 18457 2.51 5 N 5013 2.21 5 O 5438 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 19": "OD1" <-> "OD2" Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A ARG 52": "NH1" <-> "NH2" Residue "A PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 68": "NH1" <-> "NH2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A ASP 166": "OD1" <-> "OD2" Residue "A ASP 197": "OD1" <-> "OD2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 201": "NH1" <-> "NH2" Residue "A PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A ASP 347": "OD1" <-> "OD2" Residue "A ARG 348": "NH1" <-> "NH2" Residue "A ARG 368": "NH1" <-> "NH2" Residue "A ASP 383": "OD1" <-> "OD2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 531": "OD1" <-> "OD2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 594": "OE1" <-> "OE2" Residue "A PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 70": "OE1" <-> "OE2" Residue "B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "E ASP 19": "OD1" <-> "OD2" Residue "E PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E GLU 53": "OE1" <-> "OE2" Residue "E PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 68": "NH1" <-> "NH2" Residue "E ASP 77": "OD1" <-> "OD2" Residue "E ARG 91": "NH1" <-> "NH2" Residue "E ARG 136": "NH1" <-> "NH2" Residue "E ASP 166": "OD1" <-> "OD2" Residue "E GLU 182": "OE1" <-> "OE2" Residue "E ASP 197": "OD1" <-> "OD2" Residue "E TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 201": "NH1" <-> "NH2" Residue "E ASP 211": "OD1" <-> "OD2" Residue "E PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 285": "OE1" <-> "OE2" Residue "E TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 306": "OD1" <-> "OD2" Residue "E TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 348": "NH1" <-> "NH2" Residue "E ARG 368": "NH1" <-> "NH2" Residue "E TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 419": "OD1" <-> "OD2" Residue "E ASP 430": "OD1" <-> "OD2" Residue "E ASP 451": "OD1" <-> "OD2" Residue "E PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 459": "OD1" <-> "OD2" Residue "E TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 483": "OE1" <-> "OE2" Residue "E ASP 491": "OD1" <-> "OD2" Residue "E ARG 492": "NH1" <-> "NH2" Residue "E PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 556": "OE1" <-> "OE2" Residue "E ASP 562": "OD1" <-> "OD2" Residue "E PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 99": "OD1" <-> "OD2" Residue "F TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 126": "OD1" <-> "OD2" Residue "F PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 233": "OE1" <-> "OE2" Residue "F PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 277": "OD1" <-> "OD2" Residue "F ASP 302": "OD1" <-> "OD2" Residue "I ASP 19": "OD1" <-> "OD2" Residue "I PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 49": "NH1" <-> "NH2" Residue "I ARG 52": "NH1" <-> "NH2" Residue "I PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 68": "NH1" <-> "NH2" Residue "I ASP 77": "OD1" <-> "OD2" Residue "I ARG 91": "NH1" <-> "NH2" Residue "I GLU 97": "OE1" <-> "OE2" Residue "I ARG 136": "NH1" <-> "NH2" Residue "I ASP 197": "OD1" <-> "OD2" Residue "I TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 201": "NH1" <-> "NH2" Residue "I PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 317": "OD1" <-> "OD2" Residue "I TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 348": "NH1" <-> "NH2" Residue "I ARG 368": "NH1" <-> "NH2" Residue "I TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 392": "OE1" <-> "OE2" Residue "I PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 492": "NH1" <-> "NH2" Residue "I PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 539": "OE1" <-> "OE2" Residue "I PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 556": "OE1" <-> "OE2" Residue "I ASP 562": "OD1" <-> "OD2" Residue "I PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 107": "OE1" <-> "OE2" Residue "J GLU 123": "OE1" <-> "OE2" Residue "J ASP 126": "OD1" <-> "OD2" Residue "J ASP 153": "OD1" <-> "OD2" Residue "J PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 232": "OD1" <-> "OD2" Residue "J GLU 233": "OE1" <-> "OE2" Residue "J GLU 289": "OE1" <-> "OE2" Residue "J ASP 298": "OD1" <-> "OD2" Residue "M ASP 19": "OD1" <-> "OD2" Residue "M PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 49": "NH1" <-> "NH2" Residue "M PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 52": "NH1" <-> "NH2" Residue "M PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 57": "OE1" <-> "OE2" Residue "M ARG 68": "NH1" <-> "NH2" Residue "M ASP 77": "OD1" <-> "OD2" Residue "M ARG 91": "NH1" <-> "NH2" Residue "M PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 136": "NH1" <-> "NH2" Residue "M GLU 182": "OE1" <-> "OE2" Residue "M ASP 197": "OD1" <-> "OD2" Residue "M TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 201": "NH1" <-> "NH2" Residue "M PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 285": "OE1" <-> "OE2" Residue "M GLU 298": "OE1" <-> "OE2" Residue "M ASP 347": "OD1" <-> "OD2" Residue "M ARG 348": "NH1" <-> "NH2" Residue "M ASP 355": "OD1" <-> "OD2" Residue "M ARG 368": "NH1" <-> "NH2" Residue "M ASP 383": "OD1" <-> "OD2" Residue "M TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 392": "OE1" <-> "OE2" Residue "M ASP 419": "OD1" <-> "OD2" Residue "M GLU 427": "OE1" <-> "OE2" Residue "M PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 492": "NH1" <-> "NH2" Residue "M ASP 493": "OD1" <-> "OD2" Residue "M PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 527": "OD1" <-> "OD2" Residue "M ASP 531": "OD1" <-> "OD2" Residue "M PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 556": "OE1" <-> "OE2" Residue "M PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 70": "OE1" <-> "OE2" Residue "N GLU 107": "OE1" <-> "OE2" Residue "N PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 126": "OD1" <-> "OD2" Residue "N PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 232": "OD1" <-> "OD2" Residue "N GLU 233": "OE1" <-> "OE2" Residue "N PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 276": "OE1" <-> "OE2" Residue "N ASP 284": "OD1" <-> "OD2" Residue "N ASP 302": "OD1" <-> "OD2" Residue "D ARG 74": "NH1" <-> "NH2" Residue "P ARG 74": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29048 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 4930 Classifications: {'peptide': 609} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 35, 'TRANS': 569} Chain breaks: 3 Chain: "B" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2240 Classifications: {'peptide': 295} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 282} Chain breaks: 2 Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Chain: "E" Number of atoms: 4933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4933 Classifications: {'peptide': 610} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 36, 'TRANS': 569} Chain breaks: 3 Chain: "F" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2233 Classifications: {'peptide': 294} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Chain: "I" Number of atoms: 4931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 4931 Classifications: {'peptide': 609} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 36, 'TRANS': 568} Chain breaks: 3 Chain: "J" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2240 Classifications: {'peptide': 295} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 282} Chain breaks: 2 Chain: "K" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 37 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "M" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 4930 Classifications: {'peptide': 609} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 35, 'TRANS': 569} Chain breaks: 3 Chain: "N" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2223 Classifications: {'peptide': 292} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 280} Chain breaks: 2 Chain: "O" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 37 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "H" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "P" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'ADN%rna2p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna2p': 1} Chain: "E" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'ADN%rna2p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna2p': 1} Chain: "I" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'ADN%rna2p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna2p': 1} Chain: "M" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'ADN%rna2p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 15.19, per 1000 atoms: 0.52 Number of scatterers: 29048 At special positions: 0 Unit cell: (146.91, 151.89, 159.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 140 16.00 O 5438 8.00 N 5013 7.00 C 18457 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.22 Conformation dependent library (CDL) restraints added in 5.3 seconds 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6910 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 93 helices and 52 sheets defined 21.1% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.69 Creating SS restraints... Processing helix chain 'A' and resid 26 through 36 Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 75 through 81 Processing helix chain 'A' and resid 97 through 117 Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 184 through 195 Processing helix chain 'A' and resid 215 through 223 Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 248 through 259 Processing helix chain 'A' and resid 278 through 290 removed outlier: 3.572A pdb=" N LEU A 284 " --> pdb=" O TYR A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 321 through 328 Processing helix chain 'A' and resid 331 through 348 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 370 through 381 Processing helix chain 'A' and resid 397 through 407 Processing helix chain 'A' and resid 410 through 412 No H-bonds generated for 'chain 'A' and resid 410 through 412' Processing helix chain 'A' and resid 446 through 451 Processing helix chain 'A' and resid 478 through 487 Processing helix chain 'A' and resid 496 through 499 removed outlier: 3.574A pdb=" N GLU A 499 " --> pdb=" O ALA A 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 496 through 499' Processing helix chain 'A' and resid 628 through 630 No H-bonds generated for 'chain 'A' and resid 628 through 630' Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'E' and resid 26 through 35 Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 75 through 81 Processing helix chain 'E' and resid 97 through 117 Processing helix chain 'E' and resid 132 through 142 Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 185 through 195 Processing helix chain 'E' and resid 215 through 222 Processing helix chain 'E' and resid 233 through 235 No H-bonds generated for 'chain 'E' and resid 233 through 235' Processing helix chain 'E' and resid 248 through 259 removed outlier: 3.582A pdb=" N LYS E 259 " --> pdb=" O PHE E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 290 removed outlier: 3.599A pdb=" N TYR E 280 " --> pdb=" O PHE E 277 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR E 283 " --> pdb=" O TYR E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 300 Processing helix chain 'E' and resid 321 through 328 removed outlier: 3.614A pdb=" N VAL E 326 " --> pdb=" O GLN E 322 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE E 327 " --> pdb=" O THR E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 348 Processing helix chain 'E' and resid 370 through 382 Processing helix chain 'E' and resid 395 through 407 removed outlier: 3.654A pdb=" N VAL E 399 " --> pdb=" O PRO E 395 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR E 400 " --> pdb=" O ASN E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 412 No H-bonds generated for 'chain 'E' and resid 410 through 412' Processing helix chain 'E' and resid 446 through 451 Processing helix chain 'E' and resid 478 through 486 Processing helix chain 'E' and resid 496 through 499 Processing helix chain 'E' and resid 628 through 630 No H-bonds generated for 'chain 'E' and resid 628 through 630' Processing helix chain 'F' and resid 64 through 66 No H-bonds generated for 'chain 'F' and resid 64 through 66' Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'I' and resid 26 through 36 removed outlier: 3.533A pdb=" N GLN I 36 " --> pdb=" O ALA I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 61 No H-bonds generated for 'chain 'I' and resid 59 through 61' Processing helix chain 'I' and resid 70 through 72 No H-bonds generated for 'chain 'I' and resid 70 through 72' Processing helix chain 'I' and resid 75 through 81 Processing helix chain 'I' and resid 97 through 117 Processing helix chain 'I' and resid 132 through 142 Processing helix chain 'I' and resid 185 through 195 Processing helix chain 'I' and resid 215 through 223 Processing helix chain 'I' and resid 233 through 235 No H-bonds generated for 'chain 'I' and resid 233 through 235' Processing helix chain 'I' and resid 248 through 259 Processing helix chain 'I' and resid 277 through 289 removed outlier: 3.779A pdb=" N LEU I 284 " --> pdb=" O TYR I 280 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN I 289 " --> pdb=" O GLU I 285 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 328 Processing helix chain 'I' and resid 331 through 346 Processing helix chain 'I' and resid 351 through 353 No H-bonds generated for 'chain 'I' and resid 351 through 353' Processing helix chain 'I' and resid 370 through 381 Processing helix chain 'I' and resid 395 through 407 removed outlier: 3.679A pdb=" N THR I 400 " --> pdb=" O ASN I 396 " (cutoff:3.500A) Processing helix chain 'I' and resid 410 through 412 No H-bonds generated for 'chain 'I' and resid 410 through 412' Processing helix chain 'I' and resid 446 through 452 removed outlier: 3.521A pdb=" N GLY I 452 " --> pdb=" O GLU I 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 478 through 487 Processing helix chain 'I' and resid 496 through 499 Processing helix chain 'I' and resid 628 through 630 No H-bonds generated for 'chain 'I' and resid 628 through 630' Processing helix chain 'J' and resid 64 through 66 No H-bonds generated for 'chain 'J' and resid 64 through 66' Processing helix chain 'J' and resid 70 through 72 No H-bonds generated for 'chain 'J' and resid 70 through 72' Processing helix chain 'M' and resid 26 through 35 Processing helix chain 'M' and resid 59 through 61 No H-bonds generated for 'chain 'M' and resid 59 through 61' Processing helix chain 'M' and resid 70 through 72 No H-bonds generated for 'chain 'M' and resid 70 through 72' Processing helix chain 'M' and resid 75 through 81 Processing helix chain 'M' and resid 97 through 117 Processing helix chain 'M' and resid 132 through 142 Processing helix chain 'M' and resid 185 through 195 Processing helix chain 'M' and resid 215 through 223 Processing helix chain 'M' and resid 248 through 259 Processing helix chain 'M' and resid 278 through 290 Processing helix chain 'M' and resid 297 through 301 Processing helix chain 'M' and resid 321 through 328 removed outlier: 3.747A pdb=" N VAL M 326 " --> pdb=" O GLN M 322 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE M 327 " --> pdb=" O THR M 323 " (cutoff:3.500A) Processing helix chain 'M' and resid 331 through 348 Processing helix chain 'M' and resid 351 through 353 No H-bonds generated for 'chain 'M' and resid 351 through 353' Processing helix chain 'M' and resid 370 through 382 Processing helix chain 'M' and resid 395 through 407 removed outlier: 3.759A pdb=" N THR M 400 " --> pdb=" O ASN M 396 " (cutoff:3.500A) Processing helix chain 'M' and resid 410 through 412 No H-bonds generated for 'chain 'M' and resid 410 through 412' Processing helix chain 'M' and resid 446 through 456 removed outlier: 4.678A pdb=" N HIS M 455 " --> pdb=" O ASP M 451 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N PHE M 456 " --> pdb=" O GLY M 452 " (cutoff:3.500A) Processing helix chain 'M' and resid 478 through 487 Processing helix chain 'M' and resid 497 through 499 No H-bonds generated for 'chain 'M' and resid 497 through 499' Processing helix chain 'M' and resid 628 through 630 No H-bonds generated for 'chain 'M' and resid 628 through 630' Processing helix chain 'N' and resid 64 through 66 No H-bonds generated for 'chain 'N' and resid 64 through 66' Processing helix chain 'N' and resid 70 through 72 No H-bonds generated for 'chain 'N' and resid 70 through 72' Processing sheet with id= A, first strand: chain 'A' and resid 264 through 266 removed outlier: 6.801A pdb=" N PHE A 40 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA A 121 " --> pdb=" O GLY A 84 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N MET A 150 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU A 124 " --> pdb=" O MET A 150 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N TRP A 152 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU A 126 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG A 154 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU A 206 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA A 229 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE A 208 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LEU A 231 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLN A 263 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N LEU A 231 " --> pdb=" O GLN A 263 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE A 265 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 462 through 464 removed outlier: 6.895A pdb=" N ARG A 385 " --> pdb=" O GLN A 359 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU A 361 " --> pdb=" O ARG A 385 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LYS A 387 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL A 363 " --> pdb=" O LYS A 387 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TYR A 389 " --> pdb=" O VAL A 363 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 520 through 522 Processing sheet with id= D, first strand: chain 'A' and resid 534 through 541 removed outlier: 6.409A pdb=" N ARG A 601 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL A 617 " --> pdb=" O ARG A 601 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N TRP A 603 " --> pdb=" O TRP A 615 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N TRP A 615 " --> pdb=" O TRP A 603 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N CYS A 605 " --> pdb=" O TYR A 613 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TYR A 613 " --> pdb=" O CYS A 605 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 546 through 548 Processing sheet with id= F, first strand: chain 'A' and resid 556 through 560 removed outlier: 6.877A pdb=" N ILE A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 75 through 79 removed outlier: 3.749A pdb=" N GLY B 56 " --> pdb=" O THR B 79 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N SER B 47 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LEU B 31 " --> pdb=" O SER B 47 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 83 through 88 removed outlier: 6.692A pdb=" N ALA B 97 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU B 86 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU B 95 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TRP B 88 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY B 93 " --> pdb=" O TRP B 88 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE B 119 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLU B 107 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N SER B 117 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 128 through 133 removed outlier: 6.843A pdb=" N GLY B 143 " --> pdb=" O SER B 129 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL B 131 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B 141 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N VAL B 133 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLN B 139 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ASP B 153 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N VAL B 159 " --> pdb=" O ASP B 153 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 203 through 205 removed outlier: 3.558A pdb=" N CYS B 172 " --> pdb=" O CYS B 186 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 250 through 252 removed outlier: 4.493A pdb=" N THR B 236 " --> pdb=" O ASP B 232 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 258 through 263 removed outlier: 6.666A pdb=" N LEU B 274 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU B 261 " --> pdb=" O ALA B 272 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA B 272 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 303 through 305 Processing sheet with id= N, first strand: chain 'E' and resid 264 through 266 removed outlier: 6.871A pdb=" N PHE E 40 " --> pdb=" O ARG E 18 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ALA E 121 " --> pdb=" O GLY E 84 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET E 150 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU E 124 " --> pdb=" O MET E 150 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N TRP E 152 " --> pdb=" O LEU E 124 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU E 126 " --> pdb=" O TRP E 152 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ARG E 154 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU E 206 " --> pdb=" O LYS E 227 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ALA E 229 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE E 208 " --> pdb=" O ALA E 229 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU E 231 " --> pdb=" O ILE E 208 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLN E 263 " --> pdb=" O ALA E 229 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU E 231 " --> pdb=" O GLN E 263 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE E 265 " --> pdb=" O LEU E 231 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 462 through 464 removed outlier: 6.883A pdb=" N ARG E 385 " --> pdb=" O GLN E 359 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N LEU E 361 " --> pdb=" O ARG E 385 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LYS E 387 " --> pdb=" O LEU E 361 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N VAL E 363 " --> pdb=" O LYS E 387 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR E 389 " --> pdb=" O VAL E 363 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 520 through 522 removed outlier: 3.588A pdb=" N GLY E 550 " --> pdb=" O ILE E 475 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 534 through 540 removed outlier: 6.607A pdb=" N ARG E 601 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL E 617 " --> pdb=" O ARG E 601 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N TRP E 603 " --> pdb=" O TRP E 615 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N TRP E 615 " --> pdb=" O TRP E 603 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N CYS E 605 " --> pdb=" O TYR E 613 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TYR E 613 " --> pdb=" O CYS E 605 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 546 through 548 Processing sheet with id= S, first strand: chain 'E' and resid 556 through 560 removed outlier: 6.925A pdb=" N ILE E 563 " --> pdb=" O LEU E 559 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 75 through 79 removed outlier: 3.866A pdb=" N GLY F 56 " --> pdb=" O THR F 79 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N SER F 47 " --> pdb=" O LEU F 31 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU F 31 " --> pdb=" O SER F 47 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 83 through 89 removed outlier: 6.634A pdb=" N ALA F 97 " --> pdb=" O ALA F 84 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU F 86 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU F 95 " --> pdb=" O LEU F 86 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TRP F 88 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLY F 93 " --> pdb=" O TRP F 88 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ALA F 102 " --> pdb=" O SER F 98 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLU F 107 " --> pdb=" O SER F 117 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N SER F 117 " --> pdb=" O GLU F 107 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 130 through 133 removed outlier: 5.961A pdb=" N ASP F 153 " --> pdb=" O VAL F 159 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N VAL F 159 " --> pdb=" O ASP F 153 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 203 through 205 removed outlier: 3.833A pdb=" N ARG F 191 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS F 172 " --> pdb=" O CYS F 186 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 250 through 252 removed outlier: 4.519A pdb=" N THR F 236 " --> pdb=" O ASP F 232 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 258 through 263 removed outlier: 6.654A pdb=" N LEU F 274 " --> pdb=" O THR F 259 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU F 261 " --> pdb=" O ALA F 272 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ALA F 272 " --> pdb=" O LEU F 261 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 322 through 326 removed outlier: 3.598A pdb=" N ASP F 302 " --> pdb=" O VAL F 316 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 264 through 266 removed outlier: 6.888A pdb=" N PHE I 40 " --> pdb=" O ARG I 18 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA I 121 " --> pdb=" O GLY I 84 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N MET I 150 " --> pdb=" O PHE I 122 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU I 124 " --> pdb=" O MET I 150 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N TRP I 152 " --> pdb=" O LEU I 124 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU I 126 " --> pdb=" O TRP I 152 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ARG I 154 " --> pdb=" O LEU I 126 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU I 206 " --> pdb=" O LYS I 227 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA I 229 " --> pdb=" O LEU I 206 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE I 208 " --> pdb=" O ALA I 229 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LEU I 231 " --> pdb=" O ILE I 208 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLN I 263 " --> pdb=" O ALA I 229 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU I 231 " --> pdb=" O GLN I 263 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE I 265 " --> pdb=" O LEU I 231 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'I' and resid 462 through 464 removed outlier: 6.941A pdb=" N ARG I 385 " --> pdb=" O GLN I 359 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU I 361 " --> pdb=" O ARG I 385 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LYS I 387 " --> pdb=" O LEU I 361 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL I 363 " --> pdb=" O LYS I 387 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR I 389 " --> pdb=" O VAL I 363 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'I' and resid 520 through 522 removed outlier: 3.682A pdb=" N GLY I 550 " --> pdb=" O ILE I 475 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'I' and resid 534 through 541 removed outlier: 3.549A pdb=" N ALA I 619 " --> pdb=" O CYS I 599 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ARG I 601 " --> pdb=" O VAL I 617 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL I 617 " --> pdb=" O ARG I 601 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N TRP I 603 " --> pdb=" O TRP I 615 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N TRP I 615 " --> pdb=" O TRP I 603 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N CYS I 605 " --> pdb=" O TYR I 613 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N TYR I 613 " --> pdb=" O CYS I 605 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'I' and resid 546 through 548 Processing sheet with id= AF, first strand: chain 'I' and resid 556 through 558 Processing sheet with id= AG, first strand: chain 'J' and resid 75 through 78 removed outlier: 6.352A pdb=" N SER J 47 " --> pdb=" O LEU J 31 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LEU J 31 " --> pdb=" O SER J 47 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'J' and resid 83 through 89 removed outlier: 6.744A pdb=" N ALA J 97 " --> pdb=" O ALA J 84 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU J 86 " --> pdb=" O LEU J 95 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU J 95 " --> pdb=" O LEU J 86 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TRP J 88 " --> pdb=" O GLY J 93 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLY J 93 " --> pdb=" O TRP J 88 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALA J 102 " --> pdb=" O SER J 98 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLU J 107 " --> pdb=" O SER J 117 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N SER J 117 " --> pdb=" O GLU J 107 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'J' and resid 130 through 133 removed outlier: 5.981A pdb=" N ASP J 153 " --> pdb=" O VAL J 159 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL J 159 " --> pdb=" O ASP J 153 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'J' and resid 203 through 205 removed outlier: 4.015A pdb=" N ARG J 191 " --> pdb=" O SER J 187 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N CYS J 172 " --> pdb=" O CYS J 186 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'J' and resid 250 through 252 removed outlier: 4.496A pdb=" N THR J 236 " --> pdb=" O ASP J 232 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'J' and resid 258 through 263 removed outlier: 6.723A pdb=" N LEU J 274 " --> pdb=" O THR J 259 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU J 261 " --> pdb=" O ALA J 272 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ALA J 272 " --> pdb=" O LEU J 261 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'J' and resid 321 through 326 removed outlier: 4.090A pdb=" N GLN J 321 " --> pdb=" O GLY J 317 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP J 302 " --> pdb=" O VAL J 316 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'M' and resid 264 through 267 removed outlier: 6.746A pdb=" N PHE M 40 " --> pdb=" O ARG M 18 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA M 121 " --> pdb=" O GLY M 84 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N MET M 150 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU M 124 " --> pdb=" O MET M 150 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N TRP M 152 " --> pdb=" O LEU M 124 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU M 126 " --> pdb=" O TRP M 152 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ARG M 154 " --> pdb=" O LEU M 126 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU M 206 " --> pdb=" O LYS M 227 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA M 229 " --> pdb=" O LEU M 206 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE M 208 " --> pdb=" O ALA M 229 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU M 231 " --> pdb=" O ILE M 208 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLN M 263 " --> pdb=" O ALA M 229 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N LEU M 231 " --> pdb=" O GLN M 263 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE M 265 " --> pdb=" O LEU M 231 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'M' and resid 462 through 464 removed outlier: 6.765A pdb=" N ARG M 385 " --> pdb=" O GLN M 359 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU M 361 " --> pdb=" O ARG M 385 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LYS M 387 " --> pdb=" O LEU M 361 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL M 363 " --> pdb=" O LYS M 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N TYR M 389 " --> pdb=" O VAL M 363 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'M' and resid 520 through 522 Processing sheet with id= AQ, first strand: chain 'M' and resid 534 through 541 removed outlier: 6.575A pdb=" N ARG M 601 " --> pdb=" O VAL M 617 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N VAL M 617 " --> pdb=" O ARG M 601 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N TRP M 603 " --> pdb=" O TRP M 615 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N TRP M 615 " --> pdb=" O TRP M 603 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N CYS M 605 " --> pdb=" O TYR M 613 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N TYR M 613 " --> pdb=" O CYS M 605 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'M' and resid 546 through 548 Processing sheet with id= AS, first strand: chain 'M' and resid 556 through 560 removed outlier: 6.922A pdb=" N ILE M 563 " --> pdb=" O LEU M 559 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'N' and resid 75 through 79 removed outlier: 3.984A pdb=" N GLY N 56 " --> pdb=" O THR N 79 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER N 47 " --> pdb=" O LEU N 31 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LEU N 31 " --> pdb=" O SER N 47 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'N' and resid 83 through 89 removed outlier: 6.759A pdb=" N ALA N 97 " --> pdb=" O ALA N 84 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU N 86 " --> pdb=" O LEU N 95 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU N 95 " --> pdb=" O LEU N 86 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TRP N 88 " --> pdb=" O GLY N 93 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLY N 93 " --> pdb=" O TRP N 88 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA N 102 " --> pdb=" O SER N 98 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE N 119 " --> pdb=" O LEU N 105 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLU N 107 " --> pdb=" O SER N 117 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N SER N 117 " --> pdb=" O GLU N 107 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'N' and resid 130 through 133 removed outlier: 6.243A pdb=" N ASP N 153 " --> pdb=" O VAL N 159 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N VAL N 159 " --> pdb=" O ASP N 153 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'N' and resid 191 through 196 removed outlier: 4.106A pdb=" N ARG N 191 " --> pdb=" O SER N 187 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'N' and resid 250 through 252 removed outlier: 4.364A pdb=" N THR N 236 " --> pdb=" O ASP N 232 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'N' and resid 261 through 263 Processing sheet with id= AZ, first strand: chain 'N' and resid 323 through 326 removed outlier: 3.698A pdb=" N ASP N 302 " --> pdb=" O VAL N 316 " (cutoff:3.500A) 929 hydrogen bonds defined for protein. 2601 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.91 Time building geometry restraints manager: 12.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4831 1.29 - 1.42: 7986 1.42 - 1.55: 16778 1.55 - 1.68: 5 1.68 - 1.81: 188 Bond restraints: 29788 Sorted by residual: bond pdb=" C ARG M 220 " pdb=" O ARG M 220 " ideal model delta sigma weight residual 1.237 1.323 -0.086 1.17e-02 7.31e+03 5.42e+01 bond pdb=" C ARG A 220 " pdb=" O ARG A 220 " ideal model delta sigma weight residual 1.237 1.311 -0.074 1.17e-02 7.31e+03 4.00e+01 bond pdb=" C TRP A 221 " pdb=" O TRP A 221 " ideal model delta sigma weight residual 1.237 1.164 0.073 1.17e-02 7.31e+03 3.88e+01 bond pdb=" C TRP M 221 " pdb=" O TRP M 221 " ideal model delta sigma weight residual 1.237 1.177 0.059 1.17e-02 7.31e+03 2.58e+01 bond pdb=" C ASP E 219 " pdb=" O ASP E 219 " ideal model delta sigma weight residual 1.237 1.296 -0.060 1.19e-02 7.06e+03 2.51e+01 ... (remaining 29783 not shown) Histogram of bond angle deviations from ideal: 97.79 - 105.12: 618 105.12 - 112.45: 15092 112.45 - 119.79: 10320 119.79 - 127.12: 13958 127.12 - 134.45: 520 Bond angle restraints: 40508 Sorted by residual: angle pdb=" N GLU M 224 " pdb=" CA GLU M 224 " pdb=" C GLU M 224 " ideal model delta sigma weight residual 110.07 121.90 -11.83 1.46e+00 4.69e-01 6.56e+01 angle pdb=" N GLU A 224 " pdb=" CA GLU A 224 " pdb=" C GLU A 224 " ideal model delta sigma weight residual 110.20 121.81 -11.61 1.44e+00 4.82e-01 6.50e+01 angle pdb=" C PHE M 440 " pdb=" N ALA M 441 " pdb=" CA ALA M 441 " ideal model delta sigma weight residual 121.54 132.95 -11.41 1.91e+00 2.74e-01 3.57e+01 angle pdb=" C PHE E 440 " pdb=" N ALA E 441 " pdb=" CA ALA E 441 " ideal model delta sigma weight residual 121.54 132.42 -10.88 1.91e+00 2.74e-01 3.25e+01 angle pdb=" N ASP I 162 " pdb=" CA ASP I 162 " pdb=" C ASP I 162 " ideal model delta sigma weight residual 114.12 106.45 7.67 1.39e+00 5.18e-01 3.04e+01 ... (remaining 40503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 16064 17.89 - 35.78: 1339 35.78 - 53.67: 249 53.67 - 71.56: 84 71.56 - 89.45: 28 Dihedral angle restraints: 17764 sinusoidal: 7139 harmonic: 10625 Sorted by residual: dihedral pdb=" CA TYR A 560 " pdb=" C TYR A 560 " pdb=" N GLN A 561 " pdb=" CA GLN A 561 " ideal model delta harmonic sigma weight residual -180.00 -152.15 -27.85 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA TYR M 560 " pdb=" C TYR M 560 " pdb=" N GLN M 561 " pdb=" CA GLN M 561 " ideal model delta harmonic sigma weight residual 180.00 -154.64 -25.36 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" C ILE F 147 " pdb=" N ILE F 147 " pdb=" CA ILE F 147 " pdb=" CB ILE F 147 " ideal model delta harmonic sigma weight residual -122.00 -134.59 12.59 0 2.50e+00 1.60e-01 2.54e+01 ... (remaining 17761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3709 0.080 - 0.161: 692 0.161 - 0.241: 35 0.241 - 0.321: 13 0.321 - 0.401: 4 Chirality restraints: 4453 Sorted by residual: chirality pdb=" CA HIS A 507 " pdb=" N HIS A 507 " pdb=" C HIS A 507 " pdb=" CB HIS A 507 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CA ASP E 419 " pdb=" N ASP E 419 " pdb=" C ASP E 419 " pdb=" CB ASP E 419 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CA ASP M 419 " pdb=" N ASP M 419 " pdb=" C ASP M 419 " pdb=" CB ASP M 419 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.35e+00 ... (remaining 4450 not shown) Planarity restraints: 5231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS J 145 " -0.026 2.00e-02 2.50e+03 5.15e-02 2.65e+01 pdb=" C LYS J 145 " 0.089 2.00e-02 2.50e+03 pdb=" O LYS J 145 " -0.034 2.00e-02 2.50e+03 pdb=" N ASP J 146 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR I 560 " 0.021 2.00e-02 2.50e+03 4.31e-02 1.86e+01 pdb=" C TYR I 560 " -0.075 2.00e-02 2.50e+03 pdb=" O TYR I 560 " 0.027 2.00e-02 2.50e+03 pdb=" N GLN I 561 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS N 145 " -0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C LYS N 145 " 0.066 2.00e-02 2.50e+03 pdb=" O LYS N 145 " -0.025 2.00e-02 2.50e+03 pdb=" N ASP N 146 " -0.022 2.00e-02 2.50e+03 ... (remaining 5228 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4104 2.75 - 3.29: 26205 3.29 - 3.83: 50753 3.83 - 4.36: 66305 4.36 - 4.90: 111855 Nonbonded interactions: 259222 Sorted by model distance: nonbonded pdb=" OE1 GLU J 226 " pdb=" OG1 THR J 242 " model vdw 2.214 2.440 nonbonded pdb=" OG SER B 135 " pdb=" O SER B 176 " model vdw 2.217 2.440 nonbonded pdb=" OH TYR A 334 " pdb=" OE1 GLU A 435 " model vdw 2.223 2.440 nonbonded pdb=" OD2 ASP A 70 " pdb=" OG1 THR I 400 " model vdw 2.246 2.440 nonbonded pdb=" O ARG I 76 " pdb=" OG1 THR I 80 " model vdw 2.247 2.440 ... (remaining 259217 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' and (resid 14 through 291 or resid 297 through 525 or resid 532 throu \ gh 637 or resid 701)) selection = (chain 'E' and (resid 14 through 171 or resid 180 through 291 or resid 297 throu \ gh 525 or resid 532 through 637 or resid 701)) selection = (chain 'I' and (resid 14 through 171 or resid 180 through 525 or resid 532 throu \ gh 637 or resid 701)) selection = (chain 'M' and (resid 14 through 291 or resid 297 through 525 or resid 532 throu \ gh 637 or resid 701)) } ncs_group { reference = (chain 'B' and resid 26 through 327) selection = (chain 'F' and resid 26 through 327) selection = (chain 'J' and resid 26 through 327) selection = (chain 'N' and resid 26 through 327) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' } ncs_group { reference = chain 'K' selection = chain 'O' } 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: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.130 Check model and map are aligned: 0.470 Set scattering table: 0.310 Process input model: 78.120 Find NCS groups from input model: 2.290 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:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.086 29788 Z= 0.595 Angle : 0.926 13.179 40508 Z= 0.533 Chirality : 0.061 0.401 4453 Planarity : 0.006 0.051 5231 Dihedral : 14.698 89.447 10854 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.85 % Favored : 97.04 % Rotamer: Outliers : 0.59 % Allowed : 1.22 % Favored : 98.18 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.13), residues: 3579 helix: -0.53 (0.17), residues: 795 sheet: -0.74 (0.15), residues: 1152 loop : -0.89 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 603 HIS 0.007 0.001 HIS J 296 PHE 0.045 0.003 PHE M 440 TYR 0.028 0.002 TYR I 342 ARG 0.012 0.001 ARG J 164 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 453 time to evaluate : 3.210 Fit side-chains revert: symmetry clash REVERT: A 610 LYS cc_start: 0.7977 (mmtt) cc_final: 0.7455 (mtpt) REVERT: E 317 ASP cc_start: 0.7374 (m-30) cc_final: 0.6953 (m-30) REVERT: E 476 SER cc_start: 0.8485 (t) cc_final: 0.8219 (t) REVERT: F 234 ASN cc_start: 0.8639 (t0) cc_final: 0.8414 (t0) REVERT: F 297 ARG cc_start: 0.8052 (mtm110) cc_final: 0.7728 (mtm-85) REVERT: I 35 LYS cc_start: 0.7793 (mmtm) cc_final: 0.7548 (tmtt) REVERT: M 383 ASP cc_start: 0.7361 (t0) cc_final: 0.7030 (t0) REVERT: N 99 ASP cc_start: 0.8227 (m-30) cc_final: 0.7986 (m-30) REVERT: H 76 ARG cc_start: 0.6036 (OUTLIER) cc_final: 0.5578 (ttm170) outliers start: 19 outliers final: 6 residues processed: 466 average time/residue: 1.5609 time to fit residues: 838.0712 Evaluate side-chains 356 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 349 time to evaluate : 3.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain I residue 562 ASP Chi-restraints excluded: chain M residue 506 LEU Chi-restraints excluded: chain N residue 148 CYS Chi-restraints excluded: chain H residue 76 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 301 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 279 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 324 optimal weight: 5.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN A 508 ASN A 525 ASN A 549 HIS B 190 ASN E 79 ASN E 141 HIS E 239 ASN E 322 GLN E 525 ASN F 256 GLN I 79 ASN I 141 HIS I 318 ASN I 454 GLN I 525 ASN I 588 GLN J 156 GLN J 205 GLN J 321 GLN M 79 ASN M 141 HIS M 525 ASN N 156 GLN N 256 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29788 Z= 0.228 Angle : 0.537 7.428 40508 Z= 0.282 Chirality : 0.045 0.138 4453 Planarity : 0.004 0.040 5231 Dihedral : 8.481 88.861 4021 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.12 % Favored : 97.76 % Rotamer: Outliers : 1.75 % Allowed : 9.39 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.14), residues: 3579 helix: 0.20 (0.18), residues: 806 sheet: -0.61 (0.15), residues: 1168 loop : -0.58 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP N 152 HIS 0.003 0.001 HIS E 216 PHE 0.022 0.002 PHE J 119 TYR 0.019 0.001 TYR M 481 ARG 0.008 0.000 ARG M 488 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 383 time to evaluate : 3.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7489 (mtt180) REVERT: A 197 ASP cc_start: 0.7997 (t0) cc_final: 0.7707 (t0) REVERT: A 325 GLU cc_start: 0.7579 (tt0) cc_final: 0.7228 (tm-30) REVERT: A 420 MET cc_start: 0.9007 (ptp) cc_final: 0.8720 (ptp) REVERT: A 576 MET cc_start: 0.8483 (ttp) cc_final: 0.8172 (ttp) REVERT: A 593 ARG cc_start: 0.7152 (ptt-90) cc_final: 0.6950 (mtm-85) REVERT: A 609 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7732 (mptt) REVERT: A 610 LYS cc_start: 0.7788 (mmtt) cc_final: 0.7417 (mtpt) REVERT: E 302 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7644 (mttm) REVERT: E 317 ASP cc_start: 0.7235 (m-30) cc_final: 0.6972 (m-30) REVERT: E 476 SER cc_start: 0.8381 (t) cc_final: 0.8134 (t) REVERT: E 489 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7335 (tt0) REVERT: F 234 ASN cc_start: 0.8691 (t0) cc_final: 0.8374 (t0) REVERT: F 297 ARG cc_start: 0.8023 (mtm110) cc_final: 0.7788 (mtm-85) REVERT: I 248 LYS cc_start: 0.7777 (mmpt) cc_final: 0.7551 (mmmt) REVERT: I 320 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7356 (tt0) REVERT: I 325 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7225 (tt0) REVERT: I 547 VAL cc_start: 0.7763 (OUTLIER) cc_final: 0.7543 (t) REVERT: J 104 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7597 (mt-10) REVERT: M 383 ASP cc_start: 0.7325 (t0) cc_final: 0.6978 (t0) REVERT: M 609 LYS cc_start: 0.8263 (mtpt) cc_final: 0.7847 (mttt) REVERT: N 99 ASP cc_start: 0.8178 (m-30) cc_final: 0.7880 (m-30) outliers start: 56 outliers final: 19 residues processed: 414 average time/residue: 1.5175 time to fit residues: 729.5682 Evaluate side-chains 372 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 346 time to evaluate : 3.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 302 LYS Chi-restraints excluded: chain E residue 489 GLU Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 320 GLU Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 597 THR Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain M residue 237 LEU Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 388 LEU Chi-restraints excluded: chain M residue 506 LEU Chi-restraints excluded: chain N residue 116 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 180 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 269 optimal weight: 0.9990 chunk 220 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 324 optimal weight: 3.9990 chunk 350 optimal weight: 9.9990 chunk 289 optimal weight: 8.9990 chunk 322 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 260 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN A 525 ASN B 69 ASN B 139 GLN E 79 ASN E 239 ASN E 322 GLN E 381 GLN E 525 ASN I 79 ASN I 318 ASN J 321 GLN M 56 GLN M 79 ASN M 394 ASN N 256 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 29788 Z= 0.313 Angle : 0.570 7.670 40508 Z= 0.296 Chirality : 0.046 0.143 4453 Planarity : 0.004 0.049 5231 Dihedral : 8.401 86.844 4006 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.74 % Favored : 97.15 % Rotamer: Outliers : 2.50 % Allowed : 11.15 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3579 helix: 0.38 (0.18), residues: 800 sheet: -0.67 (0.15), residues: 1176 loop : -0.48 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 152 HIS 0.007 0.001 HIS M 455 PHE 0.022 0.002 PHE J 119 TYR 0.015 0.002 TYR I 334 ARG 0.008 0.000 ARG M 488 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 350 time to evaluate : 3.438 Fit side-chains revert: symmetry clash REVERT: A 101 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7477 (mtt180) REVERT: A 197 ASP cc_start: 0.8021 (t0) cc_final: 0.7696 (t0) REVERT: A 325 GLU cc_start: 0.7684 (tt0) cc_final: 0.7298 (tm-30) REVERT: A 420 MET cc_start: 0.9016 (ptp) cc_final: 0.8746 (ptp) REVERT: A 576 MET cc_start: 0.8525 (ttp) cc_final: 0.8305 (ttp) REVERT: A 609 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7759 (mptt) REVERT: A 610 LYS cc_start: 0.7870 (mmtt) cc_final: 0.7478 (mtpt) REVERT: B 239 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8476 (tt) REVERT: E 68 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.7391 (ptp-170) REVERT: E 302 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7665 (mttm) REVERT: E 317 ASP cc_start: 0.7347 (m-30) cc_final: 0.7085 (m-30) REVERT: E 380 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7208 (mtpt) REVERT: E 476 SER cc_start: 0.8445 (t) cc_final: 0.8158 (t) REVERT: F 114 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8261 (mp) REVERT: F 234 ASN cc_start: 0.8719 (t0) cc_final: 0.8416 (t0) REVERT: F 294 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8224 (mt0) REVERT: F 297 ARG cc_start: 0.8010 (mtm110) cc_final: 0.7767 (mtm-85) REVERT: I 248 LYS cc_start: 0.7826 (mmpt) cc_final: 0.7554 (mmmt) REVERT: I 320 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7486 (tt0) REVERT: I 325 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7303 (tt0) REVERT: I 326 VAL cc_start: 0.8397 (t) cc_final: 0.8126 (p) REVERT: M 383 ASP cc_start: 0.7351 (t0) cc_final: 0.7003 (t0) REVERT: M 609 LYS cc_start: 0.8283 (mtpt) cc_final: 0.7823 (mttt) REVERT: N 99 ASP cc_start: 0.8281 (m-30) cc_final: 0.8019 (m-30) REVERT: N 223 GLN cc_start: 0.8421 (mp10) cc_final: 0.8209 (mp-120) outliers start: 80 outliers final: 34 residues processed: 402 average time/residue: 1.4505 time to fit residues: 680.2210 Evaluate side-chains 373 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 329 time to evaluate : 3.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 302 LYS Chi-restraints excluded: chain E residue 380 LYS Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 625 ILE Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 294 GLN Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 302 LYS Chi-restraints excluded: chain I residue 320 GLU Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 422 GLU Chi-restraints excluded: chain I residue 522 SER Chi-restraints excluded: chain I residue 597 THR Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 237 LEU Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 388 LEU Chi-restraints excluded: chain M residue 506 LEU Chi-restraints excluded: chain M residue 571 THR Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 161 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 320 optimal weight: 0.9980 chunk 244 optimal weight: 8.9990 chunk 168 optimal weight: 0.0060 chunk 35 optimal weight: 0.3980 chunk 154 optimal weight: 8.9990 chunk 218 optimal weight: 5.9990 chunk 325 optimal weight: 1.9990 chunk 345 optimal weight: 9.9990 chunk 170 optimal weight: 0.9980 chunk 308 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN B 78 GLN E 56 GLN E 79 ASN E 239 ASN E 322 GLN E 381 GLN E 455 HIS E 525 ASN I 79 ASN I 318 ASN J 321 GLN M 79 ASN N 256 GLN N 325 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29788 Z= 0.145 Angle : 0.469 7.235 40508 Z= 0.247 Chirality : 0.043 0.137 4453 Planarity : 0.004 0.037 5231 Dihedral : 8.045 85.726 4006 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.79 % Favored : 98.10 % Rotamer: Outliers : 1.88 % Allowed : 13.46 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3579 helix: 0.83 (0.19), residues: 806 sheet: -0.49 (0.15), residues: 1163 loop : -0.36 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP N 152 HIS 0.007 0.001 HIS M 455 PHE 0.019 0.001 PHE J 119 TYR 0.013 0.001 TYR M 116 ARG 0.009 0.000 ARG E 593 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 371 time to evaluate : 3.184 Fit side-chains revert: symmetry clash REVERT: A 101 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7478 (mtt180) REVERT: A 187 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.7093 (mmt) REVERT: A 197 ASP cc_start: 0.7910 (t0) cc_final: 0.7577 (t0) REVERT: A 325 GLU cc_start: 0.7514 (tt0) cc_final: 0.7158 (tm-30) REVERT: A 420 MET cc_start: 0.8996 (ptp) cc_final: 0.8688 (ptp) REVERT: A 602 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8485 (t80) REVERT: A 609 LYS cc_start: 0.8038 (mtpt) cc_final: 0.7747 (mptt) REVERT: A 610 LYS cc_start: 0.7741 (mmtt) cc_final: 0.7251 (mtpt) REVERT: B 148 CYS cc_start: 0.7565 (m) cc_final: 0.7001 (m) REVERT: E 70 ASP cc_start: 0.7888 (p0) cc_final: 0.7598 (p0) REVERT: E 302 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7685 (mttm) REVERT: E 388 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7912 (tt) REVERT: E 476 SER cc_start: 0.8360 (t) cc_final: 0.8081 (t) REVERT: E 506 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6940 (pt) REVERT: F 114 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8359 (mp) REVERT: F 234 ASN cc_start: 0.8665 (t0) cc_final: 0.8382 (t0) REVERT: F 297 ARG cc_start: 0.7942 (mtm110) cc_final: 0.7729 (mtm-85) REVERT: I 25 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7404 (mm-30) REVERT: I 320 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7390 (tt0) REVERT: I 326 VAL cc_start: 0.8305 (t) cc_final: 0.8097 (p) REVERT: M 407 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7381 (mt-10) REVERT: M 609 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7860 (mttt) REVERT: N 99 ASP cc_start: 0.8173 (m-30) cc_final: 0.7894 (m-30) outliers start: 60 outliers final: 21 residues processed: 409 average time/residue: 1.3887 time to fit residues: 667.2326 Evaluate side-chains 368 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 337 time to evaluate : 3.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 302 LYS Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 320 GLU Chi-restraints excluded: chain I residue 442 ASP Chi-restraints excluded: chain I residue 522 SER Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 237 LEU Chi-restraints excluded: chain M residue 407 GLU Chi-restraints excluded: chain M residue 411 SER Chi-restraints excluded: chain M residue 506 LEU Chi-restraints excluded: chain M residue 609 LYS Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 268 VAL Chi-restraints excluded: chain N residue 283 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 287 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 256 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 chunk 294 optimal weight: 0.9990 chunk 238 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 176 optimal weight: 0.9980 chunk 309 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN B 139 GLN E 56 GLN E 79 ASN E 381 GLN E 507 HIS E 525 ASN I 79 ASN ** I 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 318 ASN J 321 GLN M 394 ASN M 455 HIS N 256 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29788 Z= 0.165 Angle : 0.473 7.248 40508 Z= 0.248 Chirality : 0.044 0.137 4453 Planarity : 0.003 0.035 5231 Dihedral : 7.970 86.402 4006 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.04 % Favored : 97.85 % Rotamer: Outliers : 1.88 % Allowed : 14.72 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.14), residues: 3579 helix: 1.04 (0.19), residues: 807 sheet: -0.41 (0.15), residues: 1156 loop : -0.27 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 152 HIS 0.005 0.001 HIS F 325 PHE 0.017 0.001 PHE J 119 TYR 0.020 0.001 TYR M 481 ARG 0.009 0.000 ARG E 593 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 361 time to evaluate : 3.419 Fit side-chains revert: symmetry clash REVERT: A 101 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7492 (mtt180) REVERT: A 197 ASP cc_start: 0.7863 (t0) cc_final: 0.7544 (t0) REVERT: A 325 GLU cc_start: 0.7530 (tt0) cc_final: 0.7155 (tm-30) REVERT: A 420 MET cc_start: 0.8992 (ptp) cc_final: 0.8772 (ptp) REVERT: A 609 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7693 (mptt) REVERT: B 190 ASN cc_start: 0.8217 (t0) cc_final: 0.7949 (t0) REVERT: E 302 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7658 (mttm) REVERT: E 317 ASP cc_start: 0.7335 (m-30) cc_final: 0.7070 (m-30) REVERT: E 388 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7938 (tt) REVERT: E 476 SER cc_start: 0.8383 (t) cc_final: 0.8109 (t) REVERT: E 506 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.7001 (pt) REVERT: F 114 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8321 (mp) REVERT: F 234 ASN cc_start: 0.8628 (t0) cc_final: 0.8381 (t0) REVERT: F 297 ARG cc_start: 0.7934 (mtm110) cc_final: 0.7703 (mtm-85) REVERT: I 25 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7406 (mm-30) REVERT: I 326 VAL cc_start: 0.8401 (t) cc_final: 0.8133 (p) REVERT: M 290 ASN cc_start: 0.7205 (t0) cc_final: 0.6428 (t0) REVERT: M 609 LYS cc_start: 0.8283 (mtpt) cc_final: 0.7874 (mttt) REVERT: N 99 ASP cc_start: 0.8173 (m-30) cc_final: 0.7909 (m-30) outliers start: 60 outliers final: 30 residues processed: 397 average time/residue: 1.4158 time to fit residues: 659.5163 Evaluate side-chains 371 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 335 time to evaluate : 3.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 302 LYS Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 467 GLU Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 147 HIS Chi-restraints excluded: chain I residue 442 ASP Chi-restraints excluded: chain I residue 522 SER Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 237 LEU Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 388 LEU Chi-restraints excluded: chain M residue 411 SER Chi-restraints excluded: chain M residue 506 LEU Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 268 VAL Chi-restraints excluded: chain N residue 283 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 116 optimal weight: 10.0000 chunk 310 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 202 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 345 optimal weight: 5.9990 chunk 286 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 181 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 525 ASN E 56 GLN E 79 ASN E 239 ASN E 381 GLN E 525 ASN I 79 ASN ** I 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 318 ASN J 205 GLN J 321 GLN M 56 GLN M 455 HIS N 256 GLN N 325 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 29788 Z= 0.287 Angle : 0.540 7.603 40508 Z= 0.279 Chirality : 0.046 0.144 4453 Planarity : 0.004 0.040 5231 Dihedral : 8.171 89.057 4006 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.60 % Favored : 97.29 % Rotamer: Outliers : 2.57 % Allowed : 14.65 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.14), residues: 3579 helix: 0.83 (0.19), residues: 806 sheet: -0.46 (0.15), residues: 1164 loop : -0.31 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 186 HIS 0.007 0.001 HIS F 325 PHE 0.022 0.002 PHE J 119 TYR 0.022 0.002 TYR A 481 ARG 0.010 0.000 ARG E 593 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 336 time to evaluate : 3.789 Fit side-chains revert: symmetry clash REVERT: A 101 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7452 (mtt180) REVERT: A 187 MET cc_start: 0.7317 (OUTLIER) cc_final: 0.6371 (mmt) REVERT: A 197 ASP cc_start: 0.7902 (t0) cc_final: 0.7625 (t0) REVERT: A 325 GLU cc_start: 0.7611 (tt0) cc_final: 0.7218 (tm-30) REVERT: A 388 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8057 (tt) REVERT: A 420 MET cc_start: 0.8986 (ptp) cc_final: 0.8773 (ptp) REVERT: A 609 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7789 (mptt) REVERT: A 610 LYS cc_start: 0.7845 (mmtp) cc_final: 0.7458 (mtpt) REVERT: E 68 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.7155 (ptp-170) REVERT: E 302 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7662 (mttm) REVERT: E 317 ASP cc_start: 0.7347 (m-30) cc_final: 0.7126 (m-30) REVERT: E 388 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7941 (tt) REVERT: E 476 SER cc_start: 0.8453 (t) cc_final: 0.8182 (t) REVERT: E 495 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7571 (mt-10) REVERT: F 114 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8302 (mp) REVERT: F 234 ASN cc_start: 0.8653 (t0) cc_final: 0.8404 (t0) REVERT: F 294 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8255 (mt0) REVERT: F 297 ARG cc_start: 0.7947 (mtm110) cc_final: 0.7695 (mtm-85) REVERT: I 25 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7434 (mm-30) REVERT: I 248 LYS cc_start: 0.7798 (mmtt) cc_final: 0.7535 (mmmt) REVERT: I 326 VAL cc_start: 0.8454 (t) cc_final: 0.8174 (p) REVERT: M 57 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7274 (mt-10) REVERT: M 290 ASN cc_start: 0.7231 (t0) cc_final: 0.6481 (t0) REVERT: M 383 ASP cc_start: 0.7344 (t0) cc_final: 0.6872 (t0) REVERT: M 520 THR cc_start: 0.9018 (OUTLIER) cc_final: 0.8781 (m) REVERT: M 609 LYS cc_start: 0.8307 (mtpt) cc_final: 0.7853 (mttt) REVERT: N 99 ASP cc_start: 0.8256 (m-30) cc_final: 0.8004 (m-30) REVERT: N 223 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7215 (mm-40) outliers start: 82 outliers final: 42 residues processed: 389 average time/residue: 1.4736 time to fit residues: 667.8737 Evaluate side-chains 375 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 322 time to evaluate : 3.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 302 LYS Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 442 ASP Chi-restraints excluded: chain E residue 467 GLU Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 609 LYS Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 294 GLN Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 147 HIS Chi-restraints excluded: chain I residue 500 MET Chi-restraints excluded: chain I residue 522 SER Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 237 LEU Chi-restraints excluded: chain M residue 278 CYS Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 388 LEU Chi-restraints excluded: chain M residue 411 SER Chi-restraints excluded: chain M residue 506 LEU Chi-restraints excluded: chain M residue 520 THR Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 161 SER Chi-restraints excluded: chain N residue 223 GLN Chi-restraints excluded: chain N residue 225 SER Chi-restraints excluded: chain N residue 268 VAL Chi-restraints excluded: chain N residue 283 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 333 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 196 optimal weight: 0.2980 chunk 252 optimal weight: 6.9990 chunk 195 optimal weight: 1.9990 chunk 290 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 344 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 209 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 525 ASN E 79 ASN E 239 ASN E 381 GLN E 525 ASN I 79 ASN ** I 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 321 GLN M 455 HIS N 256 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 29788 Z= 0.295 Angle : 0.545 7.581 40508 Z= 0.283 Chirality : 0.046 0.142 4453 Planarity : 0.004 0.042 5231 Dihedral : 8.213 88.476 4006 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.43 % Favored : 97.46 % Rotamer: Outliers : 2.72 % Allowed : 14.93 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.14), residues: 3579 helix: 0.73 (0.18), residues: 805 sheet: -0.48 (0.15), residues: 1164 loop : -0.33 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 186 HIS 0.006 0.001 HIS F 325 PHE 0.022 0.002 PHE J 119 TYR 0.013 0.001 TYR I 334 ARG 0.011 0.000 ARG E 593 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 333 time to evaluate : 3.361 Fit side-chains revert: symmetry clash REVERT: A 101 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7453 (mtt180) REVERT: A 187 MET cc_start: 0.7289 (OUTLIER) cc_final: 0.6362 (mmt) REVERT: A 197 ASP cc_start: 0.7892 (t0) cc_final: 0.7614 (t0) REVERT: A 325 GLU cc_start: 0.7658 (tt0) cc_final: 0.7264 (tm-30) REVERT: A 388 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8035 (tt) REVERT: A 609 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7757 (mptt) REVERT: A 610 LYS cc_start: 0.7900 (mmtp) cc_final: 0.7499 (mtpt) REVERT: E 68 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.7135 (ptp-170) REVERT: E 302 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7667 (mttm) REVERT: E 317 ASP cc_start: 0.7320 (m-30) cc_final: 0.6937 (m-30) REVERT: E 388 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7929 (tt) REVERT: E 442 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7410 (p0) REVERT: E 476 SER cc_start: 0.8475 (t) cc_final: 0.8210 (t) REVERT: E 495 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7595 (mt-10) REVERT: F 114 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8324 (mp) REVERT: F 294 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8237 (mt0) REVERT: F 297 ARG cc_start: 0.7938 (mtm110) cc_final: 0.7683 (mtm-85) REVERT: I 25 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7444 (mm-30) REVERT: I 248 LYS cc_start: 0.7822 (mmtt) cc_final: 0.7536 (mmmt) REVERT: I 320 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7539 (tt0) REVERT: M 57 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7281 (mt-10) REVERT: M 101 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7510 (mtt-85) REVERT: M 290 ASN cc_start: 0.7218 (t0) cc_final: 0.6470 (t0) REVERT: M 383 ASP cc_start: 0.7345 (t0) cc_final: 0.6954 (t0) REVERT: M 609 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7854 (mttt) REVERT: N 99 ASP cc_start: 0.8287 (m-30) cc_final: 0.8014 (m-30) REVERT: N 223 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7297 (mm-40) outliers start: 87 outliers final: 48 residues processed: 389 average time/residue: 1.4825 time to fit residues: 673.3418 Evaluate side-chains 382 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 320 time to evaluate : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 302 LYS Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 442 ASP Chi-restraints excluded: chain E residue 467 GLU Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 609 LYS Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 294 GLN Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 147 HIS Chi-restraints excluded: chain I residue 320 GLU Chi-restraints excluded: chain I residue 442 ASP Chi-restraints excluded: chain I residue 500 MET Chi-restraints excluded: chain I residue 522 SER Chi-restraints excluded: chain I residue 597 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 101 ARG Chi-restraints excluded: chain M residue 237 LEU Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 388 LEU Chi-restraints excluded: chain M residue 411 SER Chi-restraints excluded: chain M residue 506 LEU Chi-restraints excluded: chain M residue 571 THR Chi-restraints excluded: chain M residue 609 LYS Chi-restraints excluded: chain M residue 635 ILE Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 161 SER Chi-restraints excluded: chain N residue 223 GLN Chi-restraints excluded: chain N residue 268 VAL Chi-restraints excluded: chain N residue 283 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 212 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 205 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 218 optimal weight: 0.9990 chunk 234 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 270 optimal weight: 7.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN E 79 ASN E 239 ASN E 525 ASN I 79 ASN J 321 GLN M 455 HIS N 256 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29788 Z= 0.210 Angle : 0.503 7.351 40508 Z= 0.263 Chirality : 0.045 0.155 4453 Planarity : 0.004 0.035 5231 Dihedral : 8.082 88.320 4006 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.18 % Favored : 97.71 % Rotamer: Outliers : 2.35 % Allowed : 15.75 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.14), residues: 3579 helix: 0.84 (0.19), residues: 811 sheet: -0.41 (0.15), residues: 1161 loop : -0.30 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 152 HIS 0.005 0.001 HIS F 325 PHE 0.020 0.001 PHE J 119 TYR 0.013 0.001 TYR M 116 ARG 0.010 0.000 ARG E 593 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 341 time to evaluate : 4.512 Fit side-chains revert: symmetry clash REVERT: A 101 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7502 (mtt180) REVERT: A 187 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6300 (mmt) REVERT: A 197 ASP cc_start: 0.7818 (t0) cc_final: 0.7549 (t0) REVERT: A 325 GLU cc_start: 0.7600 (tt0) cc_final: 0.7204 (tm-30) REVERT: A 388 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8087 (tt) REVERT: A 420 MET cc_start: 0.8988 (ptp) cc_final: 0.8765 (ptp) REVERT: A 609 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7761 (mptt) REVERT: A 610 LYS cc_start: 0.7876 (mmtp) cc_final: 0.7442 (mtpt) REVERT: B 239 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8491 (tt) REVERT: E 68 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.7059 (ptp-170) REVERT: E 302 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7650 (mttm) REVERT: E 317 ASP cc_start: 0.7336 (m-30) cc_final: 0.7071 (m-30) REVERT: E 388 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7934 (tt) REVERT: E 442 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7354 (p0) REVERT: E 476 SER cc_start: 0.8455 (t) cc_final: 0.8192 (t) REVERT: F 114 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8276 (mp) REVERT: F 297 ARG cc_start: 0.7944 (mtm110) cc_final: 0.7696 (mtm-85) REVERT: I 25 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7449 (mm-30) REVERT: I 248 LYS cc_start: 0.7754 (mmtt) cc_final: 0.7489 (mmmt) REVERT: I 285 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7236 (mt-10) REVERT: I 320 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7529 (tt0) REVERT: I 326 VAL cc_start: 0.8410 (t) cc_final: 0.8173 (p) REVERT: J 92 ARG cc_start: 0.7541 (mtt-85) cc_final: 0.6580 (mtp-110) REVERT: M 57 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7274 (mt-10) REVERT: M 290 ASN cc_start: 0.7211 (t0) cc_final: 0.6572 (t0) REVERT: M 320 GLU cc_start: 0.7967 (tt0) cc_final: 0.7759 (tt0) REVERT: M 383 ASP cc_start: 0.7318 (t0) cc_final: 0.6953 (t0) REVERT: M 520 THR cc_start: 0.9000 (OUTLIER) cc_final: 0.8687 (m) REVERT: M 576 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7201 (ttt) REVERT: M 609 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7830 (mttt) REVERT: N 99 ASP cc_start: 0.8255 (m-30) cc_final: 0.7963 (m-30) REVERT: N 223 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7238 (mm-40) outliers start: 75 outliers final: 43 residues processed: 387 average time/residue: 1.5200 time to fit residues: 694.5210 Evaluate side-chains 385 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 327 time to evaluate : 3.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 302 LYS Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 442 ASP Chi-restraints excluded: chain E residue 467 GLU Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 147 HIS Chi-restraints excluded: chain I residue 320 GLU Chi-restraints excluded: chain I residue 442 ASP Chi-restraints excluded: chain I residue 500 MET Chi-restraints excluded: chain I residue 522 SER Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 237 LEU Chi-restraints excluded: chain M residue 278 CYS Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 388 LEU Chi-restraints excluded: chain M residue 411 SER Chi-restraints excluded: chain M residue 506 LEU Chi-restraints excluded: chain M residue 520 THR Chi-restraints excluded: chain M residue 546 THR Chi-restraints excluded: chain M residue 576 MET Chi-restraints excluded: chain M residue 609 LYS Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 161 SER Chi-restraints excluded: chain N residue 223 GLN Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 268 VAL Chi-restraints excluded: chain N residue 283 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 313 optimal weight: 5.9990 chunk 329 optimal weight: 9.9990 chunk 300 optimal weight: 6.9990 chunk 320 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 251 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 289 optimal weight: 0.0570 chunk 303 optimal weight: 0.7980 chunk 319 optimal weight: 0.4980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN A 525 ASN E 79 ASN E 239 ASN E 507 HIS E 525 ASN I 56 GLN I 79 ASN I 454 GLN J 321 GLN M 455 HIS N 325 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 29788 Z= 0.138 Angle : 0.463 8.207 40508 Z= 0.243 Chirality : 0.043 0.135 4453 Planarity : 0.003 0.039 5231 Dihedral : 7.873 88.006 4006 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.90 % Favored : 97.99 % Rotamer: Outliers : 2.00 % Allowed : 16.28 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.14), residues: 3579 helix: 1.04 (0.19), residues: 824 sheet: -0.33 (0.15), residues: 1163 loop : -0.24 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 152 HIS 0.004 0.001 HIS J 296 PHE 0.016 0.001 PHE J 119 TYR 0.026 0.001 TYR A 481 ARG 0.011 0.000 ARG E 593 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 371 time to evaluate : 3.374 Fit side-chains REVERT: A 187 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6214 (mmt) REVERT: A 197 ASP cc_start: 0.7796 (t0) cc_final: 0.7514 (t0) REVERT: A 325 GLU cc_start: 0.7391 (tt0) cc_final: 0.7019 (tm-30) REVERT: A 420 MET cc_start: 0.8993 (ptp) cc_final: 0.8783 (ptp) REVERT: A 564 THR cc_start: 0.8187 (p) cc_final: 0.7879 (m) REVERT: A 609 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7704 (mptt) REVERT: A 610 LYS cc_start: 0.7706 (mmtp) cc_final: 0.7219 (mtmt) REVERT: B 190 ASN cc_start: 0.8145 (t0) cc_final: 0.7892 (t0) REVERT: E 68 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.6996 (ptp-170) REVERT: E 70 ASP cc_start: 0.7859 (p0) cc_final: 0.7564 (p0) REVERT: E 302 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7527 (mttm) REVERT: E 317 ASP cc_start: 0.7187 (m-30) cc_final: 0.6849 (m-30) REVERT: E 388 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7939 (tt) REVERT: E 442 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.7108 (p0) REVERT: E 476 SER cc_start: 0.8429 (t) cc_final: 0.8148 (t) REVERT: E 506 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6930 (pt) REVERT: F 294 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8250 (mt0) REVERT: F 297 ARG cc_start: 0.7904 (mtm110) cc_final: 0.7660 (mtm-85) REVERT: I 25 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7421 (mm-30) REVERT: I 320 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7322 (tt0) REVERT: I 326 VAL cc_start: 0.8419 (t) cc_final: 0.8163 (p) REVERT: J 92 ARG cc_start: 0.7532 (mtt-85) cc_final: 0.6621 (mtp-110) REVERT: M 57 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7250 (mt-10) REVERT: M 290 ASN cc_start: 0.7201 (t0) cc_final: 0.6622 (t0) REVERT: M 383 ASP cc_start: 0.7294 (t0) cc_final: 0.6898 (t0) REVERT: M 520 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8529 (m) REVERT: M 609 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7783 (mttt) REVERT: N 99 ASP cc_start: 0.8176 (m-30) cc_final: 0.7869 (m-30) outliers start: 64 outliers final: 28 residues processed: 410 average time/residue: 1.3766 time to fit residues: 662.4539 Evaluate side-chains 382 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 343 time to evaluate : 3.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 302 LYS Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 442 ASP Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 294 GLN Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 320 GLU Chi-restraints excluded: chain I residue 442 ASP Chi-restraints excluded: chain I residue 522 SER Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 147 HIS Chi-restraints excluded: chain M residue 237 LEU Chi-restraints excluded: chain M residue 278 CYS Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 388 LEU Chi-restraints excluded: chain M residue 411 SER Chi-restraints excluded: chain M residue 506 LEU Chi-restraints excluded: chain M residue 520 THR Chi-restraints excluded: chain M residue 546 THR Chi-restraints excluded: chain M residue 609 LYS Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 268 VAL Chi-restraints excluded: chain N residue 283 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 210 optimal weight: 5.9990 chunk 339 optimal weight: 9.9990 chunk 206 optimal weight: 0.0670 chunk 160 optimal weight: 0.9990 chunk 235 optimal weight: 8.9990 chunk 355 optimal weight: 0.0980 chunk 327 optimal weight: 2.9990 chunk 283 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 218 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 overall best weight: 1.4324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 507 HIS A 508 ASN A 525 ASN E 79 ASN E 525 ASN I 56 GLN I 79 ASN I 147 HIS I 627 ASN J 321 GLN M 271 HIS M 394 ASN M 455 HIS N 325 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29788 Z= 0.216 Angle : 0.506 7.373 40508 Z= 0.263 Chirality : 0.045 0.140 4453 Planarity : 0.004 0.039 5231 Dihedral : 7.990 89.911 4006 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.40 % Favored : 97.49 % Rotamer: Outliers : 1.47 % Allowed : 17.16 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3579 helix: 1.06 (0.19), residues: 811 sheet: -0.34 (0.15), residues: 1167 loop : -0.20 (0.16), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 186 HIS 0.006 0.001 HIS F 325 PHE 0.019 0.001 PHE J 119 TYR 0.026 0.001 TYR M 481 ARG 0.011 0.000 ARG E 593 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 341 time to evaluate : 3.317 Fit side-chains REVERT: A 187 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.6277 (mmt) REVERT: A 197 ASP cc_start: 0.7829 (t0) cc_final: 0.7553 (t0) REVERT: A 325 GLU cc_start: 0.7521 (tt0) cc_final: 0.7105 (tm-30) REVERT: A 420 MET cc_start: 0.8997 (ptp) cc_final: 0.8724 (ptp) REVERT: A 495 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7638 (mt-10) REVERT: A 564 THR cc_start: 0.8188 (p) cc_final: 0.7890 (m) REVERT: A 609 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7727 (mptt) REVERT: A 610 LYS cc_start: 0.7810 (mmtp) cc_final: 0.7397 (mtmt) REVERT: E 68 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.7098 (ptp-170) REVERT: E 317 ASP cc_start: 0.7338 (m-30) cc_final: 0.7101 (m-30) REVERT: E 388 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7950 (tt) REVERT: E 476 SER cc_start: 0.8425 (t) cc_final: 0.8154 (t) REVERT: E 506 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7001 (pt) REVERT: F 297 ARG cc_start: 0.7883 (mtm110) cc_final: 0.7657 (mtm-85) REVERT: I 25 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7436 (mm-30) REVERT: I 320 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7463 (tt0) REVERT: J 92 ARG cc_start: 0.7562 (mtt-85) cc_final: 0.6584 (mtp-110) REVERT: M 57 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7256 (mt-10) REVERT: M 290 ASN cc_start: 0.7125 (t0) cc_final: 0.6600 (t0) REVERT: M 320 GLU cc_start: 0.7720 (tt0) cc_final: 0.7438 (mm-30) REVERT: M 383 ASP cc_start: 0.7281 (t0) cc_final: 0.6924 (t0) REVERT: M 520 THR cc_start: 0.8982 (OUTLIER) cc_final: 0.8656 (m) REVERT: M 576 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7075 (ttt) REVERT: M 609 LYS cc_start: 0.8213 (mtpt) cc_final: 0.7836 (mttt) REVERT: N 99 ASP cc_start: 0.8222 (m-30) cc_final: 0.7924 (m-30) outliers start: 47 outliers final: 32 residues processed: 373 average time/residue: 1.4392 time to fit residues: 628.5657 Evaluate side-chains 372 residues out of total 3194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 332 time to evaluate : 3.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 147 HIS Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 297 ARG Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 442 ASP Chi-restraints excluded: chain E residue 467 GLU Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 320 GLU Chi-restraints excluded: chain I residue 442 ASP Chi-restraints excluded: chain I residue 500 MET Chi-restraints excluded: chain I residue 522 SER Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 237 LEU Chi-restraints excluded: chain M residue 278 CYS Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 388 LEU Chi-restraints excluded: chain M residue 411 SER Chi-restraints excluded: chain M residue 506 LEU Chi-restraints excluded: chain M residue 520 THR Chi-restraints excluded: chain M residue 546 THR Chi-restraints excluded: chain M residue 576 MET Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 161 SER Chi-restraints excluded: chain N residue 268 VAL Chi-restraints excluded: chain N residue 283 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 224 optimal weight: 4.9990 chunk 301 optimal weight: 0.4980 chunk 86 optimal weight: 9.9990 chunk 261 optimal weight: 10.0000 chunk 41 optimal weight: 0.0470 chunk 78 optimal weight: 7.9990 chunk 283 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 291 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 overall best weight: 2.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 525 ASN E 79 ASN E 239 ASN E 525 ASN I 56 GLN I 79 ASN J 321 GLN M 56 GLN M 455 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.158954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.131598 restraints weight = 30543.548| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.49 r_work: 0.3394 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 29788 Z= 0.302 Angle : 0.556 8.453 40508 Z= 0.288 Chirality : 0.046 0.151 4453 Planarity : 0.004 0.037 5231 Dihedral : 8.172 89.116 4006 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.60 % Favored : 97.29 % Rotamer: Outliers : 1.72 % Allowed : 17.03 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.14), residues: 3579 helix: 0.84 (0.19), residues: 809 sheet: -0.39 (0.15), residues: 1156 loop : -0.28 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 152 HIS 0.007 0.001 HIS E 147 PHE 0.022 0.002 PHE J 119 TYR 0.018 0.002 TYR A 342 ARG 0.011 0.000 ARG E 593 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10854.99 seconds wall clock time: 194 minutes 35.78 seconds (11675.78 seconds total)