Starting phenix.real_space_refine on Mon Mar 25 02:41:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3v_34475/03_2024/8h3v_34475_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3v_34475/03_2024/8h3v_34475.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3v_34475/03_2024/8h3v_34475.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3v_34475/03_2024/8h3v_34475.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3v_34475/03_2024/8h3v_34475_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h3v_34475/03_2024/8h3v_34475_neut.pdb" } resolution = 4.5 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= 0.007 sd= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 208 5.49 5 S 149 5.16 5 C 28368 2.51 5 N 8180 2.21 5 O 9143 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 108": "OD1" <-> "OD2" Residue "A PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 124": "OD1" <-> "OD2" Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 474": "OD1" <-> "OD2" Residue "A TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 515": "OE1" <-> "OE2" Residue "A ASP 525": "OD1" <-> "OD2" Residue "A ARG 571": "NH1" <-> "NH2" Residue "A TYR 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 648": "OD1" <-> "OD2" Residue "A ASP 671": "OD1" <-> "OD2" Residue "A TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 746": "OD1" <-> "OD2" Residue "A GLU 778": "OE1" <-> "OE2" Residue "A ASP 780": "OD1" <-> "OD2" Residue "A PHE 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 850": "OD1" <-> "OD2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 942": "OE1" <-> "OE2" Residue "A ASP 946": "OD1" <-> "OD2" Residue "B TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 199": "NH1" <-> "NH2" Residue "B ASP 206": "OD1" <-> "OD2" Residue "B GLU 227": "OE1" <-> "OE2" Residue "B TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 310": "OD1" <-> "OD2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "B GLU 392": "OE1" <-> "OE2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B GLU 486": "OE1" <-> "OE2" Residue "B PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 594": "OD1" <-> "OD2" Residue "B GLU 638": "OE1" <-> "OE2" Residue "B PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 815": "OD1" <-> "OD2" Residue "B PHE 999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1025": "OE1" <-> "OE2" Residue "B PHE 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1205": "OD1" <-> "OD2" Residue "B PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1237": "OE1" <-> "OE2" Residue "B TYR 1254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C GLU 137": "OE1" <-> "OE2" Residue "C ASP 167": "OD1" <-> "OD2" Residue "C ASP 186": "OD1" <-> "OD2" Residue "D GLU 84": "OE1" <-> "OE2" Residue "D PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "D ASP 186": "OD1" <-> "OD2" Residue "D GLU 208": "OE1" <-> "OE2" Residue "D ASP 226": "OD1" <-> "OD2" Residue "E PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 10": "OD1" <-> "OD2" Residue "E GLU 60": "OE1" <-> "OE2" Residue "E GLU 296": "OE1" <-> "OE2" Residue "E GLU 378": "OE1" <-> "OE2" Residue "E PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 471": "OD1" <-> "OD2" Residue "E GLU 523": "OE1" <-> "OE2" Residue "E ASP 539": "OD1" <-> "OD2" Residue "E PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 561": "OD1" <-> "OD2" Residue "E ASP 563": "OD1" <-> "OD2" Residue "E ASP 570": "OD1" <-> "OD2" Residue "E GLU 621": "OE1" <-> "OE2" Residue "F GLU 48": "OE1" <-> "OE2" Residue "G GLU 99": "OE1" <-> "OE2" Residue "G GLU 122": "OE1" <-> "OE2" Residue "G ASP 130": "OD1" <-> "OD2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 199": "OD1" <-> "OD2" Residue "G TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 295": "OD1" <-> "OD2" Residue "G ASP 321": "OD1" <-> "OD2" Residue "G ASP 327": "OD1" <-> "OD2" Residue "G ASP 345": "OD1" <-> "OD2" Residue "S PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 129": "OD1" <-> "OD2" Residue "S ARG 155": "NH1" <-> "NH2" Residue "S GLU 168": "OE1" <-> "OE2" Residue "S ASP 227": "OD1" <-> "OD2" Residue "S ASP 283": "OD1" <-> "OD2" Residue "T PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 34": "NH1" <-> "NH2" Residue "T GLU 80": "OE1" <-> "OE2" Residue "T TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 118": "OE1" <-> "OE2" Residue "T ASP 129": "OD1" <-> "OD2" Residue "T ARG 155": "NH1" <-> "NH2" Residue "T TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 214": "OE1" <-> "OE2" Residue "T ASP 227": "OD1" <-> "OD2" Residue "U ARG 34": "NH1" <-> "NH2" Residue "U GLU 91": "OE1" <-> "OE2" Residue "U PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 129": "OD1" <-> "OD2" Residue "U ASP 137": "OD1" <-> "OD2" Residue "U ASP 141": "OD1" <-> "OD2" Residue "U PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 155": "NH1" <-> "NH2" Residue "U GLU 160": "OE1" <-> "OE2" Residue "U GLU 165": "OE1" <-> "OE2" Residue "U TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 187": "OE1" <-> "OE2" Residue "U PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 198": "OD1" <-> "OD2" Residue "U PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 237": "OE1" <-> "OE2" Residue "V PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 137": "OD1" <-> "OD2" Residue "V TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 187": "OE1" <-> "OE2" Residue "V PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 124": "NH1" <-> "NH2" Residue "X PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 166": "OD1" <-> "OD2" Residue "X ARG 187": "NH1" <-> "NH2" Residue "Y PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 99": "OE1" <-> "OE2" Residue "Y ARG 124": "NH1" <-> "NH2" Residue "Y PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 187": "NH1" <-> "NH2" Residue "Y ASP 196": "OD1" <-> "OD2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 46048 Number of models: 1 Model: "" Number of chains: 15 Chain: "1" Number of atoms: 2302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2302 Classifications: {'DNA': 112} Link IDs: {'rna3p': 111} Chain: "2" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1967 Classifications: {'DNA': 96} Link IDs: {'rna3p': 95} Chain breaks: 1 Chain: "A" Number of atoms: 8473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8473 Classifications: {'peptide': 1077} Link IDs: {'PTRANS': 61, 'TRANS': 1015} Chain: "B" Number of atoms: 9292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1217, 9292 Classifications: {'peptide': 1217} Link IDs: {'PTRANS': 52, 'TRANS': 1164} Chain breaks: 3 Chain: "C" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1762 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 9, 'TRANS': 216} Chain: "D" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1762 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 9, 'TRANS': 216} Chain: "E" Number of atoms: 4918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4918 Classifications: {'peptide': 619} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 585} Chain: "F" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 474 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "G" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2600 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 303} Chain: "S" Number of atoms: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2389 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 17, 'TRANS': 286} Chain: "T" Number of atoms: 2320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2320 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 16, 'TRANS': 277} Chain breaks: 1 Chain: "U" Number of atoms: 2320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2320 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 16, 'TRANS': 277} Chain breaks: 1 Chain: "V" Number of atoms: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2389 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 17, 'TRANS': 286} Chain: "X" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1540 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain: "Y" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1540 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Time building chain proxies: 23.87, per 1000 atoms: 0.52 Number of scatterers: 46048 At special positions: 0 Unit cell: (194.74, 218.28, 162.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 149 16.00 P 208 15.00 O 9143 8.00 N 8180 7.00 C 28368 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 295 " distance=2.92 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 295 " distance=1.94 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.00 Simple disulfide: pdb=" SG CYS E 71 " - pdb=" SG CYS E 73 " distance=1.81 Simple disulfide: pdb=" SG CYS E 71 " - pdb=" SG CYS E 86 " distance=2.20 Simple disulfide: pdb=" SG CYS E 73 " - pdb=" SG CYS E 86 " distance=2.05 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: 22.69 Conformation dependent library (CDL) restraints added in 7.9 seconds 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9902 Finding SS restraints... Secondary structure from input PDB file: 178 helices and 42 sheets defined 32.3% alpha, 3.0% beta 66 base pairs and 148 stacking pairs defined. Time for finding SS restraints: 16.67 Creating SS restraints... Processing helix chain 'A' and resid 32 through 45 removed outlier: 4.003A pdb=" N LEU A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.536A pdb=" N SER A 52 " --> pdb=" O GLU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 87 Processing helix chain 'A' and resid 207 through 212 Processing helix chain 'A' and resid 249 through 261 Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'A' and resid 270 through 282 Processing helix chain 'A' and resid 293 through 309 removed outlier: 3.945A pdb=" N ILE A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 4.070A pdb=" N GLN A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 378 removed outlier: 3.656A pdb=" N VAL A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 400 removed outlier: 3.521A pdb=" N ARG A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 430 removed outlier: 3.844A pdb=" N ARG A 429 " --> pdb=" O SER A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 548 Processing helix chain 'A' and resid 554 through 560 removed outlier: 4.057A pdb=" N GLN A 560 " --> pdb=" O GLY A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 563 No H-bonds generated for 'chain 'A' and resid 561 through 563' Processing helix chain 'A' and resid 579 through 587 Processing helix chain 'A' and resid 614 through 619 Processing helix chain 'A' and resid 706 through 711 removed outlier: 3.554A pdb=" N GLN A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 749 Processing helix chain 'A' and resid 784 through 793 Processing helix chain 'A' and resid 821 through 825 removed outlier: 3.641A pdb=" N GLN A 824 " --> pdb=" O THR A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 911 Processing helix chain 'A' and resid 926 through 943 removed outlier: 3.757A pdb=" N ARG A 930 " --> pdb=" O GLU A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1023 Processing helix chain 'A' and resid 1032 through 1040 Processing helix chain 'A' and resid 1044 through 1057 removed outlier: 3.515A pdb=" N VAL A1056 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1082 Processing helix chain 'B' and resid 9 through 22 removed outlier: 3.726A pdb=" N LEU B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 31 Processing helix chain 'B' and resid 34 through 48 Processing helix chain 'B' and resid 60 through 81 removed outlier: 4.336A pdb=" N SER B 64 " --> pdb=" O PRO B 60 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 115 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 134 through 141 Processing helix chain 'B' and resid 168 through 196 removed outlier: 3.999A pdb=" N TYR B 172 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 205 Processing helix chain 'B' and resid 265 through 275 Processing helix chain 'B' and resid 295 through 299 Processing helix chain 'B' and resid 314 through 322 removed outlier: 3.727A pdb=" N ILE B 318 " --> pdb=" O ALA B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 696 through 703 removed outlier: 3.744A pdb=" N VAL B 700 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG B 703 " --> pdb=" O VAL B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 813 Processing helix chain 'B' and resid 1011 through 1019 removed outlier: 4.166A pdb=" N GLU B1015 " --> pdb=" O LEU B1011 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU B1016 " --> pdb=" O PRO B1012 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B1017 " --> pdb=" O ARG B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1026 removed outlier: 4.112A pdb=" N ALA B1026 " --> pdb=" O PRO B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1090 through 1101 Processing helix chain 'B' and resid 1106 through 1132 removed outlier: 3.909A pdb=" N VAL B1128 " --> pdb=" O GLU B1124 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1149 removed outlier: 3.647A pdb=" N THR B1149 " --> pdb=" O VAL B1145 " (cutoff:3.500A) Processing helix chain 'B' and resid 1156 through 1161 Processing helix chain 'B' and resid 1170 through 1180 Processing helix chain 'B' and resid 1196 through 1204 removed outlier: 4.148A pdb=" N LEU B1202 " --> pdb=" O THR B1198 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN B1203 " --> pdb=" O LYS B1199 " (cutoff:3.500A) Processing helix chain 'B' and resid 1217 through 1222 removed outlier: 3.959A pdb=" N THR B1221 " --> pdb=" O THR B1217 " (cutoff:3.500A) Processing helix chain 'B' and resid 1223 through 1227 Processing helix chain 'B' and resid 1234 through 1240 Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 33 through 47 removed outlier: 3.627A pdb=" N ASN C 38 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 79 Processing helix chain 'C' and resid 185 through 189 Processing helix chain 'C' and resid 205 through 208 Processing helix chain 'C' and resid 209 through 222 removed outlier: 3.972A pdb=" N GLY C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C 217 " --> pdb=" O ALA C 213 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL C 218 " --> pdb=" O ALA C 214 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP C 219 " --> pdb=" O GLY C 215 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 220 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 44 removed outlier: 3.759A pdb=" N VAL D 36 " --> pdb=" O GLN D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 81 Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 205 through 208 Processing helix chain 'D' and resid 209 through 222 Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 97 through 102 removed outlier: 3.617A pdb=" N ARG E 102 " --> pdb=" O ARG E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 118 Processing helix chain 'E' and resid 123 through 128 Processing helix chain 'E' and resid 129 through 131 No H-bonds generated for 'chain 'E' and resid 129 through 131' Processing helix chain 'E' and resid 132 through 140 Processing helix chain 'E' and resid 164 through 169 removed outlier: 4.469A pdb=" N GLU E 169 " --> pdb=" O ASP E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 176 removed outlier: 4.027A pdb=" N GLN E 173 " --> pdb=" O ILE E 170 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ILE E 174 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 198 removed outlier: 3.740A pdb=" N LEU E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 215 removed outlier: 4.059A pdb=" N GLU E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY E 214 " --> pdb=" O ARG E 210 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER E 215 " --> pdb=" O GLU E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 236 removed outlier: 3.643A pdb=" N PHE E 234 " --> pdb=" O VAL E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 244 Processing helix chain 'E' and resid 253 through 257 removed outlier: 3.799A pdb=" N LEU E 256 " --> pdb=" O PRO E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 288 removed outlier: 3.753A pdb=" N LEU E 286 " --> pdb=" O ARG E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 293 Processing helix chain 'E' and resid 299 through 308 removed outlier: 3.923A pdb=" N ARG E 304 " --> pdb=" O ARG E 300 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET E 305 " --> pdb=" O ASN E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 315 Processing helix chain 'E' and resid 333 through 337 removed outlier: 3.703A pdb=" N ILE E 337 " --> pdb=" O LEU E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 349 Processing helix chain 'E' and resid 376 through 380 Processing helix chain 'E' and resid 381 through 383 No H-bonds generated for 'chain 'E' and resid 381 through 383' Processing helix chain 'E' and resid 384 through 395 removed outlier: 3.812A pdb=" N ARG E 391 " --> pdb=" O PHE E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 411 Processing helix chain 'E' and resid 412 through 422 removed outlier: 4.622A pdb=" N TRP E 416 " --> pdb=" O ASP E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 441 Processing helix chain 'E' and resid 480 through 489 removed outlier: 3.625A pdb=" N GLN E 484 " --> pdb=" O SER E 480 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA E 485 " --> pdb=" O LEU E 481 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU E 489 " --> pdb=" O ALA E 485 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 522 Processing helix chain 'E' and resid 538 through 547 removed outlier: 4.183A pdb=" N ILE E 542 " --> pdb=" O LEU E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 609 through 616 Processing helix chain 'E' and resid 617 through 625 removed outlier: 4.156A pdb=" N GLU E 621 " --> pdb=" O LYS E 617 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 20 removed outlier: 3.700A pdb=" N ASP F 20 " --> pdb=" O ARG F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 45 Processing helix chain 'F' and resid 50 through 55 removed outlier: 3.961A pdb=" N MET F 55 " --> pdb=" O ASP F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 67 removed outlier: 3.725A pdb=" N ARG F 60 " --> pdb=" O LYS F 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 90 Processing helix chain 'G' and resid 98 through 124 removed outlier: 4.091A pdb=" N GLU G 102 " --> pdb=" O ASP G 98 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 135 Processing helix chain 'G' and resid 140 through 162 removed outlier: 4.316A pdb=" N HIS G 149 " --> pdb=" O ARG G 145 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ARG G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL G 159 " --> pdb=" O LYS G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 173 Processing helix chain 'G' and resid 181 through 196 removed outlier: 4.490A pdb=" N GLY G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY G 190 " --> pdb=" O GLU G 186 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE G 192 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU G 196 " --> pdb=" O ILE G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 225 removed outlier: 3.541A pdb=" N THR G 219 " --> pdb=" O ARG G 215 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG G 220 " --> pdb=" O GLN G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 237 Processing helix chain 'G' and resid 238 through 240 No H-bonds generated for 'chain 'G' and resid 238 through 240' Processing helix chain 'G' and resid 241 through 250 Processing helix chain 'G' and resid 260 through 266 Processing helix chain 'G' and resid 269 through 279 Processing helix chain 'G' and resid 311 through 325 removed outlier: 3.600A pdb=" N ASN G 316 " --> pdb=" O GLN G 312 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU G 317 " --> pdb=" O VAL G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 335 Processing helix chain 'G' and resid 336 through 340 removed outlier: 3.603A pdb=" N LEU G 339 " --> pdb=" O VAL G 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 358 Processing helix chain 'G' and resid 362 through 375 removed outlier: 4.694A pdb=" N ARG G 366 " --> pdb=" O ARG G 362 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN G 367 " --> pdb=" O GLU G 363 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 15 Processing helix chain 'S' and resid 18 through 23 Processing helix chain 'S' and resid 32 through 40 removed outlier: 3.694A pdb=" N SER S 38 " --> pdb=" O ARG S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 67 through 80 removed outlier: 3.610A pdb=" N CYS S 71 " --> pdb=" O ALA S 67 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU S 80 " --> pdb=" O THR S 76 " (cutoff:3.500A) Processing helix chain 'S' and resid 105 through 116 Processing helix chain 'S' and resid 128 through 136 Processing helix chain 'S' and resid 185 through 190 removed outlier: 3.548A pdb=" N VAL S 189 " --> pdb=" O TRP S 185 " (cutoff:3.500A) Processing helix chain 'S' and resid 200 through 212 removed outlier: 3.905A pdb=" N GLU S 208 " --> pdb=" O ARG S 204 " (cutoff:3.500A) Processing helix chain 'S' and resid 225 through 230 Processing helix chain 'S' and resid 287 through 298 Processing helix chain 'T' and resid 4 through 13 removed outlier: 4.011A pdb=" N ALA T 8 " --> pdb=" O GLU T 4 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA T 11 " --> pdb=" O GLN T 7 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE T 12 " --> pdb=" O ALA T 8 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 43 removed outlier: 4.026A pdb=" N GLN T 37 " --> pdb=" O SER T 33 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER T 38 " --> pdb=" O ARG T 34 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP T 42 " --> pdb=" O SER T 38 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 64 Processing helix chain 'T' and resid 64 through 84 removed outlier: 3.765A pdb=" N LEU T 81 " --> pdb=" O ALA T 77 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLY T 82 " --> pdb=" O THR T 78 " (cutoff:3.500A) Processing helix chain 'T' and resid 105 through 115 Processing helix chain 'T' and resid 130 through 138 Processing helix chain 'T' and resid 175 through 182 removed outlier: 4.207A pdb=" N ALA T 178 " --> pdb=" O HIS T 175 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ARG T 182 " --> pdb=" O ALA T 179 " (cutoff:3.500A) Processing helix chain 'T' and resid 200 through 211 Processing helix chain 'T' and resid 225 through 235 Processing helix chain 'T' and resid 246 through 251 Processing helix chain 'T' and resid 287 through 299 removed outlier: 3.553A pdb=" N PHE T 293 " --> pdb=" O PRO T 289 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 14 removed outlier: 4.018A pdb=" N ALA U 11 " --> pdb=" O GLN U 7 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 23 Processing helix chain 'U' and resid 31 through 41 removed outlier: 5.035A pdb=" N GLN U 37 " --> pdb=" O SER U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 64 Processing helix chain 'U' and resid 64 through 84 removed outlier: 4.787A pdb=" N GLY U 82 " --> pdb=" O THR U 78 " (cutoff:3.500A) Processing helix chain 'U' and resid 105 through 111 Processing helix chain 'U' and resid 129 through 134 Processing helix chain 'U' and resid 175 through 180 removed outlier: 3.520A pdb=" N ALA U 179 " --> pdb=" O HIS U 175 " (cutoff:3.500A) Processing helix chain 'U' and resid 187 through 191 removed outlier: 4.008A pdb=" N ARG U 190 " --> pdb=" O GLU U 187 " (cutoff:3.500A) Processing helix chain 'U' and resid 202 through 211 Processing helix chain 'U' and resid 225 through 230 Processing helix chain 'U' and resid 281 through 285 Processing helix chain 'U' and resid 287 through 296 Processing helix chain 'V' and resid 2 through 11 Processing helix chain 'V' and resid 11 through 16 Processing helix chain 'V' and resid 19 through 25 Processing helix chain 'V' and resid 32 through 44 removed outlier: 3.711A pdb=" N SER V 38 " --> pdb=" O ARG V 34 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP V 42 " --> pdb=" O SER V 38 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY V 44 " --> pdb=" O GLU V 40 " (cutoff:3.500A) Processing helix chain 'V' and resid 66 through 78 removed outlier: 3.966A pdb=" N ALA V 77 " --> pdb=" O GLU V 73 " (cutoff:3.500A) Processing helix chain 'V' and resid 104 through 110 Processing helix chain 'V' and resid 128 through 135 Processing helix chain 'V' and resid 175 through 179 Processing helix chain 'V' and resid 200 through 208 Processing helix chain 'V' and resid 227 through 232 Processing helix chain 'V' and resid 243 through 251 removed outlier: 3.899A pdb=" N GLU V 249 " --> pdb=" O SER V 245 " (cutoff:3.500A) Processing helix chain 'V' and resid 287 through 292 Processing helix chain 'V' and resid 292 through 301 removed outlier: 3.970A pdb=" N ARG V 298 " --> pdb=" O TRP V 294 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU V 299 " --> pdb=" O GLN V 295 " (cutoff:3.500A) Processing helix chain 'X' and resid 77 through 81 Processing helix chain 'X' and resid 104 through 114 removed outlier: 4.554A pdb=" N VAL X 108 " --> pdb=" O PRO X 104 " (cutoff:3.500A) Processing helix chain 'X' and resid 118 through 129 Processing helix chain 'X' and resid 129 through 141 removed outlier: 3.517A pdb=" N MET X 136 " --> pdb=" O GLN X 132 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA X 141 " --> pdb=" O ILE X 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 145 through 155 Processing helix chain 'X' and resid 177 through 182 Processing helix chain 'X' and resid 191 through 200 Processing helix chain 'X' and resid 205 through 209 Processing helix chain 'X' and resid 215 through 220 removed outlier: 3.710A pdb=" N SER X 219 " --> pdb=" O PRO X 215 " (cutoff:3.500A) Processing helix chain 'Y' and resid 77 through 81 Processing helix chain 'Y' and resid 104 through 114 removed outlier: 4.320A pdb=" N VAL Y 108 " --> pdb=" O PRO Y 104 " (cutoff:3.500A) Processing helix chain 'Y' and resid 119 through 141 removed outlier: 3.575A pdb=" N ARG Y 124 " --> pdb=" O MET Y 120 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLN Y 132 " --> pdb=" O SER Y 128 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N MET Y 135 " --> pdb=" O LEU Y 131 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA Y 141 " --> pdb=" O ILE Y 137 " (cutoff:3.500A) Processing helix chain 'Y' and resid 145 through 160 removed outlier: 3.922A pdb=" N ARG Y 158 " --> pdb=" O LEU Y 154 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE Y 160 " --> pdb=" O LEU Y 156 " (cutoff:3.500A) Processing helix chain 'Y' and resid 177 through 182 removed outlier: 3.589A pdb=" N GLU Y 181 " --> pdb=" O GLN Y 177 " (cutoff:3.500A) Processing helix chain 'Y' and resid 191 through 199 removed outlier: 3.706A pdb=" N GLU Y 199 " --> pdb=" O GLY Y 195 " (cutoff:3.500A) Processing helix chain 'Y' and resid 214 through 220 removed outlier: 3.812A pdb=" N LEU Y 218 " --> pdb=" O LYS Y 214 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 removed outlier: 3.751A pdb=" N VAL A 136 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA5, first strand: chain 'A' and resid 149 through 152 removed outlier: 4.015A pdb=" N GLU A 152 " --> pdb=" O THR A 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA7, first strand: chain 'A' and resid 508 through 509 Processing sheet with id=AA8, first strand: chain 'A' and resid 608 through 610 removed outlier: 4.538A pdb=" N VAL A 608 " --> pdb=" O ILE A 635 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 702 Processing sheet with id=AB2, first strand: chain 'A' and resid 715 through 720 removed outlier: 4.338A pdb=" N VAL A 840 " --> pdb=" O GLU A 720 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 736 through 737 removed outlier: 3.715A pdb=" N GLY A 771 " --> pdb=" O THR A 737 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 818 through 820 removed outlier: 3.592A pdb=" N ARG A 818 " --> pdb=" O ARG A 837 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG A 837 " --> pdb=" O ARG A 818 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE A 820 " --> pdb=" O VAL A 835 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 992 through 993 removed outlier: 3.692A pdb=" N ARG A 993 " --> pdb=" O SER E 357 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER E 357 " --> pdb=" O ARG A 993 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 3 through 4 removed outlier: 6.846A pdb=" N PHE B 3 " --> pdb=" O GLU E 565 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 439 through 443 Processing sheet with id=AB8, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AB9, first strand: chain 'B' and resid 461 through 462 Processing sheet with id=AC1, first strand: chain 'B' and resid 502 through 504 Processing sheet with id=AC2, first strand: chain 'B' and resid 512 through 513 removed outlier: 3.612A pdb=" N THR B 513 " --> pdb=" O THR B 874 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 551 through 552 Processing sheet with id=AC4, first strand: chain 'B' and resid 635 through 642 removed outlier: 4.678A pdb=" N ARG B 682 " --> pdb=" O VAL B 639 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LYS B 641 " --> pdb=" O ILE B 680 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ILE B 680 " --> pdb=" O LYS B 641 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 660 through 661 Processing sheet with id=AC6, first strand: chain 'B' and resid 765 through 766 removed outlier: 3.677A pdb=" N SER B 765 " --> pdb=" O GLU B 800 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1152 through 1154 Processing sheet with id=AC8, first strand: chain 'C' and resid 50 through 52 Processing sheet with id=AC9, first strand: chain 'C' and resid 55 through 56 Processing sheet with id=AD1, first strand: chain 'C' and resid 176 through 177 Processing sheet with id=AD2, first strand: chain 'C' and resid 180 through 182 Processing sheet with id=AD3, first strand: chain 'D' and resid 6 through 7 removed outlier: 3.769A pdb=" N ILE D 24 " --> pdb=" O GLU D 7 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU D 25 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 194 " --> pdb=" O LEU D 25 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP D 192 " --> pdb=" O PRO D 27 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 50 through 52 Processing sheet with id=AD5, first strand: chain 'E' and resid 428 through 429 Processing sheet with id=AD6, first strand: chain 'E' and resid 431 through 432 Processing sheet with id=AD7, first strand: chain 'E' and resid 556 through 558 Processing sheet with id=AD8, first strand: chain 'S' and resid 93 through 94 removed outlier: 7.856A pdb=" N LEU S 121 " --> pdb=" O GLU U 222 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 161 through 163 removed outlier: 3.531A pdb=" N TYR S 163 " --> pdb=" O VAL S 276 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'U' and resid 163 through 165 removed outlier: 4.259A pdb=" N ARG U 274 " --> pdb=" O GLU U 165 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'V' and resid 145 through 146 removed outlier: 3.561A pdb=" N VAL V 145 " --> pdb=" O VAL V 277 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'V' and resid 263 through 264 removed outlier: 5.053A pdb=" N ASN V 263 " --> pdb=" O GLY V 271 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'X' and resid 51 through 54 Processing sheet with id=AE5, first strand: chain 'Y' and resid 26 through 27 Processing sheet with id=AE6, first strand: chain 'Y' and resid 51 through 54 1028 hydrogen bonds defined for protein. 2802 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 153 hydrogen bonds 298 hydrogen bond angles 0 basepair planarities 66 basepair parallelities 148 stacking parallelities Total time for adding SS restraints: 19.09 Time building geometry restraints manager: 24.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.38: 18033 1.38 - 1.78: 29001 1.78 - 2.17: 205 2.17 - 2.56: 0 2.56 - 2.95: 1 Bond restraints: 47240 Sorted by residual: bond pdb=" O3' DC 1 45 " pdb=" P DA 1 46 " ideal model delta sigma weight residual 1.607 2.949 -1.342 1.50e-02 4.44e+03 8.00e+03 bond pdb=" C GLY U 154 " pdb=" N ARG U 155 " ideal model delta sigma weight residual 1.332 1.733 -0.401 1.40e-02 5.10e+03 8.19e+02 bond pdb=" CA GLN G 87 " pdb=" C GLN G 87 " ideal model delta sigma weight residual 1.524 1.132 0.393 1.48e-02 4.57e+03 7.03e+02 bond pdb=" N PRO E 150 " pdb=" CD PRO E 150 " ideal model delta sigma weight residual 1.473 1.148 0.325 1.40e-02 5.10e+03 5.39e+02 bond pdb=" N PRO U 176 " pdb=" CD PRO U 176 " ideal model delta sigma weight residual 1.473 1.148 0.325 1.40e-02 5.10e+03 5.37e+02 ... (remaining 47235 not shown) Histogram of bond angle deviations from ideal: 41.71 - 67.83: 2 67.83 - 93.94: 66 93.94 - 120.05: 47695 120.05 - 146.17: 17084 146.17 - 172.28: 3 Bond angle restraints: 64850 Sorted by residual: angle pdb=" C3' DC 1 45 " pdb=" O3' DC 1 45 " pdb=" P DA 1 46 " ideal model delta sigma weight residual 120.20 41.71 78.49 1.50e+00 4.44e-01 2.74e+03 angle pdb=" O3' DC 1 45 " pdb=" P DA 1 46 " pdb=" OP2 DA 1 46 " ideal model delta sigma weight residual 108.00 172.28 -64.28 3.00e+00 1.11e-01 4.59e+02 angle pdb=" O3' DC 1 45 " pdb=" P DA 1 46 " pdb=" O5' DA 1 46 " ideal model delta sigma weight residual 104.00 73.89 30.11 1.50e+00 4.44e-01 4.03e+02 angle pdb=" CA MET T 157 " pdb=" CB MET T 157 " pdb=" CG MET T 157 " ideal model delta sigma weight residual 114.10 152.37 -38.27 2.00e+00 2.50e-01 3.66e+02 angle pdb=" C PRO G 309 " pdb=" CA PRO G 309 " pdb=" CB PRO G 309 " ideal model delta sigma weight residual 111.56 87.93 23.63 1.27e+00 6.20e-01 3.46e+02 ... (remaining 64845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.44: 26229 32.44 - 64.87: 2174 64.87 - 97.31: 114 97.31 - 129.75: 1 129.75 - 162.18: 4 Dihedral angle restraints: 28522 sinusoidal: 13178 harmonic: 15344 Sorted by residual: dihedral pdb=" C MET T 157 " pdb=" N MET T 157 " pdb=" CA MET T 157 " pdb=" CB MET T 157 " ideal model delta harmonic sigma weight residual -122.60 -167.49 44.89 0 2.50e+00 1.60e-01 3.22e+02 dihedral pdb=" N MET T 157 " pdb=" C MET T 157 " pdb=" CA MET T 157 " pdb=" CB MET T 157 " ideal model delta harmonic sigma weight residual 122.80 166.92 -44.12 0 2.50e+00 1.60e-01 3.12e+02 dihedral pdb=" C PRO G 309 " pdb=" N PRO G 309 " pdb=" CA PRO G 309 " pdb=" CB PRO G 309 " ideal model delta harmonic sigma weight residual -120.70 -87.72 -32.98 0 2.50e+00 1.60e-01 1.74e+02 ... (remaining 28519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.514: 7418 0.514 - 1.027: 47 1.027 - 1.541: 0 1.541 - 2.054: 1 2.054 - 2.568: 1 Chirality restraints: 7467 Sorted by residual: chirality pdb=" C3' DG 1 13 " pdb=" C4' DG 1 13 " pdb=" O3' DG 1 13 " pdb=" C2' DG 1 13 " both_signs ideal model delta sigma weight residual False -2.66 -0.09 -2.57 2.00e-01 2.50e+01 1.65e+02 chirality pdb=" CA MET T 157 " pdb=" N MET T 157 " pdb=" C MET T 157 " pdb=" CB MET T 157 " both_signs ideal model delta sigma weight residual False 2.51 0.57 1.94 2.00e-01 2.50e+01 9.39e+01 chirality pdb=" CA ILE T 167 " pdb=" N ILE T 167 " pdb=" C ILE T 167 " pdb=" CB ILE T 167 " both_signs ideal model delta sigma weight residual False 2.43 1.42 1.01 2.00e-01 2.50e+01 2.56e+01 ... (remaining 7464 not shown) Planarity restraints: 7705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU S 84 " 0.086 2.00e-02 2.50e+03 1.70e-01 2.90e+02 pdb=" C LEU S 84 " -0.293 2.00e-02 2.50e+03 pdb=" O LEU S 84 " 0.125 2.00e-02 2.50e+03 pdb=" N ILE S 85 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU U 84 " -0.085 2.00e-02 2.50e+03 1.68e-01 2.82e+02 pdb=" C LEU U 84 " 0.290 2.00e-02 2.50e+03 pdb=" O LEU U 84 " -0.123 2.00e-02 2.50e+03 pdb=" N ILE U 85 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL T 195 " 0.066 2.00e-02 2.50e+03 1.32e-01 1.73e+02 pdb=" C VAL T 195 " -0.228 2.00e-02 2.50e+03 pdb=" O VAL T 195 " 0.083 2.00e-02 2.50e+03 pdb=" N PHE T 196 " 0.078 2.00e-02 2.50e+03 ... (remaining 7702 not shown) Histogram of nonbonded interaction distances: 0.97 - 1.76: 60 1.76 - 2.54: 3954 2.54 - 3.33: 75659 3.33 - 4.11: 136149 4.11 - 4.90: 207172 Warning: very small nonbonded interaction distances. Nonbonded interactions: 422994 Sorted by model distance: nonbonded pdb=" CA PRO A 875 " pdb=" OH TYR A 960 " model vdw 0.972 3.470 nonbonded pdb=" O GLN T 193 " pdb=" CD1 LEU T 217 " model vdw 0.987 3.460 nonbonded pdb=" OE1 GLN U 5 " pdb=" CD GLN U 35 " model vdw 1.004 3.270 nonbonded pdb=" OH TYR V 180 " pdb=" CZ TYR V 191 " model vdw 1.155 3.260 nonbonded pdb=" CD GLN U 5 " pdb=" OE1 GLN U 35 " model vdw 1.183 3.270 ... (remaining 422989 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 'C' selection = chain 'D' } ncs_group { reference = (chain 'S' and (resid 1 through 262 or resid 272 through 303)) selection = chain 'T' selection = chain 'U' selection = (chain 'V' and (resid 1 through 262 or resid 272 through 303)) } ncs_group { reference = chain 'X' selection = chain 'Y' } 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=0.10 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.520 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: 0.030 Extract box with map and model: 11.840 Check model and map are aligned: 0.630 Set scattering table: 0.390 Process input model: 135.340 Find NCS groups from input model: 2.000 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6105 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 : 0.030 1.342 47240 Z= 1.934 Angle : 2.794 78.487 64850 Z= 1.615 Chirality : 0.140 2.568 7467 Planarity : 0.022 0.436 7705 Dihedral : 20.268 162.182 18602 Min Nonbonded Distance : 0.972 Molprobity Statistics. All-atom Clashscore : 180.47 Ramachandran Plot: Outliers : 5.50 % Allowed : 33.81 % Favored : 60.69 % Rotamer: Outliers : 7.38 % Allowed : 10.65 % Favored : 81.97 % Cbeta Deviations : 1.70 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.02 % Twisted General : 5.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.34 (0.07), residues: 5289 helix: -4.66 (0.07), residues: 1395 sheet: -4.96 (0.22), residues: 263 loop : -5.39 (0.07), residues: 3631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.008 TRP C 199 HIS 0.072 0.007 HIS A 991 PHE 0.126 0.007 PHE G 301 TYR 0.186 0.008 TYR G 85 ARG 0.097 0.002 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1219 residues out of total 4565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 337 poor density : 882 time to evaluate : 5.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 GLU cc_start: 0.8033 (mt-10) cc_final: 0.6730 (tm-30) REVERT: A 431 CYS cc_start: 0.8167 (t) cc_final: 0.6461 (p) REVERT: A 541 MET cc_start: 0.7258 (mmp) cc_final: 0.6989 (mmp) REVERT: B 77 GLU cc_start: 0.8275 (mt-10) cc_final: 0.8038 (tm-30) REVERT: B 151 GLN cc_start: 0.5853 (mm-40) cc_final: 0.5202 (pp30) REVERT: B 648 VAL cc_start: 0.5636 (OUTLIER) cc_final: 0.5352 (m) REVERT: B 1119 THR cc_start: 0.7161 (p) cc_final: 0.6842 (m) REVERT: B 1128 VAL cc_start: 0.8999 (t) cc_final: 0.8778 (p) REVERT: C 77 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.6796 (mm-30) REVERT: C 169 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7473 (pt) REVERT: D 36 VAL cc_start: 0.9038 (OUTLIER) cc_final: 0.8624 (m) REVERT: D 51 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8109 (t) REVERT: D 72 ARG cc_start: 0.8628 (mtp180) cc_final: 0.8259 (ttp80) REVERT: D 183 VAL cc_start: 0.7818 (t) cc_final: 0.7596 (t) REVERT: E 273 ASN cc_start: 0.7780 (p0) cc_final: 0.7309 (p0) REVERT: E 420 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7302 (tm-30) REVERT: E 587 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7769 (tt) REVERT: E 602 ILE cc_start: 0.6162 (OUTLIER) cc_final: 0.4723 (mm) REVERT: G 113 LEU cc_start: 0.8368 (mt) cc_final: 0.7978 (tt) REVERT: G 165 LEU cc_start: 0.2480 (OUTLIER) cc_final: 0.1812 (pp) REVERT: G 173 TYR cc_start: 0.7044 (m-80) cc_final: 0.6726 (m-10) REVERT: G 184 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7594 (tt) REVERT: S 151 LEU cc_start: 0.0564 (OUTLIER) cc_final: -0.0087 (mp) REVERT: S 278 MET cc_start: -0.4996 (mmm) cc_final: -0.5235 (mtt) REVERT: S 287 ILE cc_start: 0.0363 (OUTLIER) cc_final: 0.0131 (pt) REVERT: T 99 SER cc_start: 0.2299 (OUTLIER) cc_final: 0.2021 (t) REVERT: T 167 ILE cc_start: -0.0513 (OUTLIER) cc_final: -0.0875 (tt) REVERT: T 208 GLU cc_start: 0.6277 (OUTLIER) cc_final: 0.5742 (pt0) REVERT: T 278 MET cc_start: 0.0870 (ptm) cc_final: 0.0018 (ptm) REVERT: U 182 ARG cc_start: 0.8691 (mtp180) cc_final: 0.8328 (mtm-85) REVERT: V 18 PHE cc_start: -0.2528 (OUTLIER) cc_final: -0.2839 (m-10) REVERT: V 25 CYS cc_start: -0.2055 (OUTLIER) cc_final: -0.3381 (t) REVERT: V 157 MET cc_start: 0.3823 (mmm) cc_final: 0.3331 (tpt) REVERT: Y 196 ASP cc_start: 0.6552 (OUTLIER) cc_final: 0.6233 (t0) outliers start: 337 outliers final: 90 residues processed: 1147 average time/residue: 0.6247 time to fit residues: 1139.0759 Evaluate side-chains 583 residues out of total 4565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 476 time to evaluate : 4.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 460 optimal weight: 30.0000 chunk 413 optimal weight: 30.0000 chunk 229 optimal weight: 30.0000 chunk 141 optimal weight: 30.0000 chunk 278 optimal weight: 0.8980 chunk 220 optimal weight: 1.9990 chunk 427 optimal weight: 4.9990 chunk 165 optimal weight: 8.9990 chunk 259 optimal weight: 7.9990 chunk 317 optimal weight: 0.9980 chunk 494 optimal weight: 0.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 GLN A 389 GLN ** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 ASN ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 ASN ** A1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 HIS ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1068 ASN ** B1089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1112 HIS ** B1118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1147 GLN ** C 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN ** D 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 HIS ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 HIS E 101 HIS ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 GLN E 281 ASN E 371 HIS E 385 GLN ** E 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 GLN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 HIS G 251 GLN ** S 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 53 HIS S 89 GLN S 147 ASN ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 282 GLN S 292 HIS T 98 HIS T 110 GLN ** T 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 218 GLN T 286 GLN U 53 HIS ** U 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 174 ASN V 193 GLN ** Y 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 47240 Z= 0.448 Angle : 1.317 22.997 64850 Z= 0.676 Chirality : 0.065 0.689 7467 Planarity : 0.011 0.181 7705 Dihedral : 21.020 165.779 8207 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 48.99 Ramachandran Plot: Outliers : 1.49 % Allowed : 20.46 % Favored : 78.05 % Rotamer: Outliers : 1.91 % Allowed : 10.23 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.35 % Twisted General : 1.58 % 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: -6.24 (0.08), residues: 5289 helix: -3.76 (0.09), residues: 1482 sheet: -4.27 (0.23), residues: 288 loop : -4.65 (0.08), residues: 3519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP B 98 HIS 0.020 0.003 HIS V 175 PHE 0.048 0.004 PHE Y 75 TYR 0.041 0.004 TYR U 200 ARG 0.029 0.002 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 4565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 724 time to evaluate : 5.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6094 (tm-30) REVERT: A 378 PHE cc_start: 0.7096 (m-10) cc_final: 0.6748 (m-80) REVERT: A 413 GLU cc_start: 0.8264 (pm20) cc_final: 0.7259 (pt0) REVERT: A 535 VAL cc_start: 0.8874 (m) cc_final: 0.8666 (m) REVERT: A 581 GLN cc_start: 0.7800 (pm20) cc_final: 0.6759 (pp30) REVERT: A 584 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.7080 (mtm180) REVERT: A 646 ASN cc_start: 0.7639 (t0) cc_final: 0.7404 (t0) REVERT: A 694 GLU cc_start: 0.7417 (pm20) cc_final: 0.6812 (tt0) REVERT: A 748 LEU cc_start: 0.8741 (tt) cc_final: 0.8434 (mt) REVERT: A 900 GLU cc_start: 0.8631 (pm20) cc_final: 0.8055 (pm20) REVERT: A 947 TRP cc_start: 0.8360 (p-90) cc_final: 0.8100 (p-90) REVERT: A 1076 GLU cc_start: 0.8460 (pt0) cc_final: 0.7917 (pt0) REVERT: B 125 MET cc_start: 0.8701 (mpp) cc_final: 0.8051 (mpp) REVERT: B 261 ASN cc_start: 0.7574 (m-40) cc_final: 0.6703 (t0) REVERT: B 353 MET cc_start: 0.5059 (tpt) cc_final: 0.4593 (mpp) REVERT: B 538 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7614 (pm20) REVERT: B 693 MET cc_start: 0.8442 (mpp) cc_final: 0.8126 (mpp) REVERT: B 1119 THR cc_start: 0.8155 (p) cc_final: 0.7043 (m) REVERT: B 1121 LEU cc_start: 0.9192 (mt) cc_final: 0.8670 (mt) REVERT: B 1202 LEU cc_start: 0.8339 (mp) cc_final: 0.7893 (mp) REVERT: B 1237 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7355 (mm-30) REVERT: C 74 ASP cc_start: 0.7787 (t0) cc_final: 0.7561 (p0) REVERT: C 77 GLU cc_start: 0.7908 (pm20) cc_final: 0.6581 (mm-30) REVERT: C 80 MET cc_start: 0.8791 (mmm) cc_final: 0.8480 (mmp) REVERT: D 82 MET cc_start: 0.7058 (mmp) cc_final: 0.6694 (mmm) REVERT: D 183 VAL cc_start: 0.8290 (t) cc_final: 0.7704 (t) REVERT: E 129 LEU cc_start: 0.8001 (mt) cc_final: 0.6869 (mt) REVERT: E 146 VAL cc_start: 0.8878 (m) cc_final: 0.8546 (p) REVERT: E 240 LYS cc_start: 0.8321 (mttp) cc_final: 0.7858 (mtpt) REVERT: E 273 ASN cc_start: 0.8309 (p0) cc_final: 0.7552 (p0) REVERT: E 350 LEU cc_start: 0.7771 (tp) cc_final: 0.7534 (tp) REVERT: E 371 HIS cc_start: 0.5979 (m-70) cc_final: 0.5587 (m-70) REVERT: E 379 MET cc_start: 0.7806 (ptp) cc_final: 0.7484 (mtm) REVERT: E 400 ASN cc_start: 0.5566 (t0) cc_final: 0.5075 (t0) REVERT: E 468 PHE cc_start: 0.8754 (m-80) cc_final: 0.8154 (m-10) REVERT: E 482 GLU cc_start: 0.7246 (pm20) cc_final: 0.6825 (pm20) REVERT: E 513 MET cc_start: 0.8131 (mtt) cc_final: 0.7651 (mtt) REVERT: F 62 ILE cc_start: 0.8873 (mm) cc_final: 0.8583 (tt) REVERT: G 118 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8418 (pp20) REVERT: G 185 GLN cc_start: 0.8142 (mm110) cc_final: 0.7877 (tp40) REVERT: G 266 MET cc_start: 0.6390 (mtt) cc_final: 0.6042 (mtt) REVERT: S 278 MET cc_start: -0.6533 (mmm) cc_final: -0.6905 (mmm) REVERT: U 182 ARG cc_start: 0.7990 (mtp180) cc_final: 0.7396 (mtm-85) REVERT: U 278 MET cc_start: 0.2876 (mtp) cc_final: 0.0961 (mmt) REVERT: X 90 TYR cc_start: 0.5776 (m-80) cc_final: 0.5315 (m-80) outliers start: 87 outliers final: 19 residues processed: 802 average time/residue: 0.5696 time to fit residues: 755.7030 Evaluate side-chains 482 residues out of total 4565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 460 time to evaluate : 5.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 275 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 411 optimal weight: 8.9990 chunk 337 optimal weight: 0.8980 chunk 136 optimal weight: 5.9990 chunk 495 optimal weight: 50.0000 chunk 535 optimal weight: 5.9990 chunk 441 optimal weight: 9.9990 chunk 491 optimal weight: 9.9990 chunk 169 optimal weight: 0.0570 chunk 397 optimal weight: 2.9990 overall best weight: 2.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN A 389 GLN ** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 HIS ** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** A1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 GLN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 HIS ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN D 102 ASN ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 385 GLN ** E 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 579 ASN F 13 GLN ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 110 GLN ** T 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 120 GLN ** U 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 148 ASN V 269 ASN X 132 GLN X 142 HIS X 176 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.6951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 47240 Z= 0.380 Angle : 1.091 21.495 64850 Z= 0.561 Chirality : 0.056 0.445 7467 Planarity : 0.009 0.167 7705 Dihedral : 20.421 169.123 8207 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 39.77 Ramachandran Plot: Outliers : 0.95 % Allowed : 19.98 % Favored : 79.07 % Rotamer: Outliers : 0.42 % Allowed : 8.89 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.61 % 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: -5.47 (0.09), residues: 5289 helix: -3.09 (0.10), residues: 1512 sheet: -3.86 (0.23), residues: 333 loop : -4.15 (0.09), residues: 3444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP E 416 HIS 0.013 0.002 HIS T 98 PHE 0.030 0.003 PHE U 229 TYR 0.037 0.003 TYR B 653 ARG 0.021 0.001 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 4565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 638 time to evaluate : 5.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.6730 (m-80) cc_final: 0.6523 (m-80) REVERT: A 128 PHE cc_start: 0.8338 (m-10) cc_final: 0.8036 (m-10) REVERT: A 258 ASP cc_start: 0.9009 (p0) cc_final: 0.8725 (p0) REVERT: A 344 GLU cc_start: 0.7418 (mt-10) cc_final: 0.6374 (tm-30) REVERT: A 413 GLU cc_start: 0.8443 (pm20) cc_final: 0.7502 (pt0) REVERT: A 523 GLN cc_start: 0.6467 (pm20) cc_final: 0.6096 (pm20) REVERT: A 535 VAL cc_start: 0.8917 (m) cc_final: 0.8549 (m) REVERT: A 541 MET cc_start: 0.8820 (mmm) cc_final: 0.8526 (mmm) REVERT: A 637 TYR cc_start: 0.7480 (OUTLIER) cc_final: 0.6559 (p90) REVERT: A 646 ASN cc_start: 0.7775 (t0) cc_final: 0.7434 (t0) REVERT: A 694 GLU cc_start: 0.7356 (pm20) cc_final: 0.7002 (tt0) REVERT: A 876 ASP cc_start: 0.8728 (p0) cc_final: 0.8021 (t0) REVERT: A 922 MET cc_start: 0.6740 (ttt) cc_final: 0.6511 (ttt) REVERT: A 960 TYR cc_start: 0.7332 (p90) cc_final: 0.7039 (p90) REVERT: A 1003 GLN cc_start: 0.8532 (tm-30) cc_final: 0.8002 (tm-30) REVERT: A 1050 GLU cc_start: 0.8620 (tt0) cc_final: 0.8216 (tt0) REVERT: B 51 ILE cc_start: 0.8858 (pt) cc_final: 0.8615 (mp) REVERT: B 120 ASN cc_start: 0.7726 (t0) cc_final: 0.7400 (t0) REVERT: B 225 MET cc_start: 0.8074 (ttt) cc_final: 0.7824 (ttt) REVERT: B 261 ASN cc_start: 0.7843 (m-40) cc_final: 0.7184 (p0) REVERT: B 353 MET cc_start: 0.4902 (tpt) cc_final: 0.4653 (mpp) REVERT: B 1127 MET cc_start: 0.8067 (tmm) cc_final: 0.7816 (tmm) REVERT: C 76 LEU cc_start: 0.8702 (mp) cc_final: 0.8265 (mp) REVERT: C 100 LEU cc_start: 0.8622 (mt) cc_final: 0.8406 (mt) REVERT: C 138 MET cc_start: 0.8715 (tpt) cc_final: 0.8460 (tpp) REVERT: C 166 ILE cc_start: 0.6950 (tt) cc_final: 0.6610 (tp) REVERT: C 199 TRP cc_start: 0.7933 (m100) cc_final: 0.7585 (m100) REVERT: D 183 VAL cc_start: 0.8359 (t) cc_final: 0.7262 (m) REVERT: D 193 ARG cc_start: 0.8324 (ttm170) cc_final: 0.7948 (ptp-110) REVERT: D 222 ASN cc_start: 0.5486 (t0) cc_final: 0.5179 (m110) REVERT: E 70 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6173 (tt0) REVERT: E 81 HIS cc_start: 0.7450 (t-90) cc_final: 0.7102 (t-90) REVERT: E 129 LEU cc_start: 0.8128 (mt) cc_final: 0.7702 (mt) REVERT: E 233 ASN cc_start: 0.8740 (m-40) cc_final: 0.7919 (m-40) REVERT: E 242 GLU cc_start: 0.9042 (pm20) cc_final: 0.8708 (pm20) REVERT: E 273 ASN cc_start: 0.8697 (p0) cc_final: 0.7908 (p0) REVERT: E 296 GLU cc_start: 0.8733 (pm20) cc_final: 0.8408 (pm20) REVERT: E 302 GLU cc_start: 0.7720 (mm-30) cc_final: 0.6727 (mm-30) REVERT: E 321 ARG cc_start: 0.8216 (ptt180) cc_final: 0.7837 (ptt90) REVERT: E 338 ILE cc_start: 0.8190 (pt) cc_final: 0.7507 (pt) REVERT: E 339 GLU cc_start: 0.8195 (mp0) cc_final: 0.5823 (tt0) REVERT: E 348 ASN cc_start: 0.7499 (m110) cc_final: 0.7108 (t0) REVERT: E 407 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.7992 (mt) REVERT: E 468 PHE cc_start: 0.8566 (m-80) cc_final: 0.8358 (m-10) REVERT: E 513 MET cc_start: 0.8372 (mtt) cc_final: 0.8117 (mtt) REVERT: E 616 ASN cc_start: 0.8035 (m110) cc_final: 0.7738 (t0) REVERT: G 98 ASP cc_start: 0.7471 (p0) cc_final: 0.7165 (p0) REVERT: G 300 ASP cc_start: 0.7080 (m-30) cc_final: 0.6718 (m-30) REVERT: T 202 MET cc_start: -0.6177 (ptm) cc_final: -0.6462 (ttp) REVERT: U 1 MET cc_start: 0.1345 (ttm) cc_final: 0.0446 (mtp) REVERT: U 182 ARG cc_start: 0.7812 (mtp180) cc_final: 0.7219 (mtm-85) REVERT: U 278 MET cc_start: 0.2779 (mtp) cc_final: -0.0032 (mmt) outliers start: 19 outliers final: 6 residues processed: 653 average time/residue: 0.5721 time to fit residues: 624.1546 Evaluate side-chains 451 residues out of total 4565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 443 time to evaluate : 5.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 489 optimal weight: 6.9990 chunk 372 optimal weight: 0.8980 chunk 257 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 236 optimal weight: 0.9990 chunk 332 optimal weight: 2.9990 chunk 497 optimal weight: 9.9990 chunk 526 optimal weight: 10.0000 chunk 259 optimal weight: 0.9990 chunk 471 optimal weight: 0.9980 chunk 141 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS A 228 GLN A 389 GLN A 450 HIS ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 GLN B 462 GLN ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 HIS ** B 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 854 GLN ** B1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN E 114 HIS ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS E 385 GLN E 549 GLN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 GLN ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 282 GLN ** V 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 176 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.7855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 47240 Z= 0.267 Angle : 0.978 20.330 64850 Z= 0.498 Chirality : 0.052 0.470 7467 Planarity : 0.008 0.162 7705 Dihedral : 20.099 169.351 8207 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 31.57 Ramachandran Plot: Outliers : 0.89 % Allowed : 17.05 % Favored : 82.06 % Rotamer: Outliers : 0.13 % Allowed : 6.53 % Favored : 93.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.57 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.97 (0.10), residues: 5289 helix: -2.63 (0.11), residues: 1517 sheet: -3.54 (0.25), residues: 304 loop : -3.87 (0.09), residues: 3468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP E 416 HIS 0.010 0.002 HIS F 16 PHE 0.041 0.003 PHE X 152 TYR 0.025 0.002 TYR V 200 ARG 0.022 0.001 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 4565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 646 time to evaluate : 5.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8623 (pp) cc_final: 0.8285 (mp) REVERT: A 258 ASP cc_start: 0.8851 (p0) cc_final: 0.8616 (p0) REVERT: A 344 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6507 (tm-30) REVERT: A 413 GLU cc_start: 0.8291 (pm20) cc_final: 0.7670 (pt0) REVERT: A 520 THR cc_start: 0.7129 (p) cc_final: 0.6927 (p) REVERT: A 526 TYR cc_start: 0.7294 (m-80) cc_final: 0.7011 (m-10) REVERT: A 646 ASN cc_start: 0.7670 (t0) cc_final: 0.7325 (t0) REVERT: A 694 GLU cc_start: 0.7130 (pm20) cc_final: 0.6709 (tt0) REVERT: A 922 MET cc_start: 0.6538 (ttt) cc_final: 0.6215 (ttt) REVERT: A 936 LEU cc_start: 0.8742 (mt) cc_final: 0.8503 (tp) REVERT: A 947 TRP cc_start: 0.8840 (p-90) cc_final: 0.7275 (p-90) REVERT: A 960 TYR cc_start: 0.7210 (p90) cc_final: 0.6930 (p90) REVERT: A 1050 GLU cc_start: 0.8648 (tt0) cc_final: 0.8279 (tt0) REVERT: B 55 ASP cc_start: 0.8005 (t0) cc_final: 0.7594 (t0) REVERT: B 261 ASN cc_start: 0.7627 (m-40) cc_final: 0.6888 (p0) REVERT: B 1127 MET cc_start: 0.7904 (tmm) cc_final: 0.7550 (tmm) REVERT: B 1237 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7339 (mm-30) REVERT: C 64 GLU cc_start: 0.7107 (tm-30) cc_final: 0.6647 (tm-30) REVERT: C 74 ASP cc_start: 0.7636 (t0) cc_final: 0.7177 (p0) REVERT: C 77 GLU cc_start: 0.7809 (pm20) cc_final: 0.6654 (mm-30) REVERT: C 137 GLU cc_start: 0.7728 (pm20) cc_final: 0.7444 (pm20) REVERT: D 80 MET cc_start: 0.7908 (tpt) cc_final: 0.7633 (tpt) REVERT: D 81 ARG cc_start: 0.8441 (mtt-85) cc_final: 0.7423 (mmt-90) REVERT: D 183 VAL cc_start: 0.8343 (t) cc_final: 0.7414 (m) REVERT: D 193 ARG cc_start: 0.8163 (ttm110) cc_final: 0.7938 (ptp-110) REVERT: D 224 LEU cc_start: 0.7631 (tp) cc_final: 0.7366 (tt) REVERT: E 70 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6023 (tt0) REVERT: E 81 HIS cc_start: 0.7144 (t-90) cc_final: 0.6851 (t-90) REVERT: E 240 LYS cc_start: 0.8544 (mttm) cc_final: 0.8217 (mtpp) REVERT: E 242 GLU cc_start: 0.8879 (pm20) cc_final: 0.8614 (pm20) REVERT: E 273 ASN cc_start: 0.8787 (p0) cc_final: 0.8031 (p0) REVERT: E 348 ASN cc_start: 0.7200 (m110) cc_final: 0.6901 (t0) REVERT: E 473 MET cc_start: 0.8871 (ptp) cc_final: 0.8505 (ptm) REVERT: E 616 ASN cc_start: 0.7783 (m110) cc_final: 0.7303 (t0) REVERT: G 78 THR cc_start: 0.8161 (t) cc_final: 0.7818 (m) REVERT: G 113 LEU cc_start: 0.7413 (tp) cc_final: 0.7116 (tp) REVERT: G 158 MET cc_start: 0.7661 (ppp) cc_final: 0.7248 (ppp) REVERT: G 345 ASP cc_start: 0.6045 (m-30) cc_final: 0.5739 (p0) REVERT: U 1 MET cc_start: 0.1270 (ttm) cc_final: 0.0615 (mtp) REVERT: U 182 ARG cc_start: 0.7435 (mtp180) cc_final: 0.6738 (mpp-170) REVERT: U 278 MET cc_start: 0.1659 (mtp) cc_final: -0.0984 (mmt) REVERT: V 146 MET cc_start: 0.0353 (mtt) cc_final: -0.0071 (mtt) REVERT: X 187 ARG cc_start: 0.3060 (tpt170) cc_final: 0.2670 (tpt170) outliers start: 6 outliers final: 2 residues processed: 652 average time/residue: 0.5443 time to fit residues: 597.5698 Evaluate side-chains 454 residues out of total 4565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 452 time to evaluate : 4.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 438 optimal weight: 0.8980 chunk 299 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 392 optimal weight: 40.0000 chunk 217 optimal weight: 40.0000 chunk 449 optimal weight: 10.0000 chunk 364 optimal weight: 3.9990 chunk 0 optimal weight: 60.0000 chunk 268 optimal weight: 3.9990 chunk 472 optimal weight: 40.0000 chunk 132 optimal weight: 0.9980 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN A 333 GLN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 ASN ** A1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1203 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN D 93 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN E 233 ASN E 328 ASN E 372 GLN ** E 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 476 HIS ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 132 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.8609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 47240 Z= 0.437 Angle : 1.053 19.402 64850 Z= 0.537 Chirality : 0.054 0.359 7467 Planarity : 0.008 0.171 7705 Dihedral : 20.172 175.457 8207 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 35.98 Ramachandran Plot: Outliers : 0.89 % Allowed : 19.13 % Favored : 79.98 % Rotamer: Outliers : 0.09 % Allowed : 6.11 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.85 (0.10), residues: 5289 helix: -2.51 (0.11), residues: 1522 sheet: -3.26 (0.25), residues: 329 loop : -3.82 (0.09), residues: 3438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP G 133 HIS 0.014 0.002 HIS A1087 PHE 0.041 0.003 PHE D 221 TYR 0.032 0.003 TYR A 600 ARG 0.024 0.001 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 4565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 557 time to evaluate : 5.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.7408 (m-10) cc_final: 0.7052 (m-80) REVERT: A 188 ASP cc_start: 0.6944 (m-30) cc_final: 0.6624 (m-30) REVERT: A 258 ASP cc_start: 0.8979 (p0) cc_final: 0.8768 (p0) REVERT: A 344 GLU cc_start: 0.7584 (mt-10) cc_final: 0.6674 (tm-30) REVERT: A 526 TYR cc_start: 0.7812 (m-80) cc_final: 0.7403 (m-10) REVERT: A 566 LEU cc_start: 0.9523 (mp) cc_final: 0.9322 (mp) REVERT: A 646 ASN cc_start: 0.8084 (t0) cc_final: 0.7811 (t0) REVERT: A 885 ASN cc_start: 0.9084 (t0) cc_final: 0.8822 (t0) REVERT: A 922 MET cc_start: 0.6946 (ttt) cc_final: 0.6575 (ttt) REVERT: A 1050 GLU cc_start: 0.8848 (tt0) cc_final: 0.8267 (tt0) REVERT: B 1127 MET cc_start: 0.7881 (tmm) cc_final: 0.7609 (tmm) REVERT: B 1174 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.7672 (tp30) REVERT: B 1207 PHE cc_start: 0.8552 (t80) cc_final: 0.8331 (t80) REVERT: C 64 GLU cc_start: 0.7556 (tm-30) cc_final: 0.7150 (tm-30) REVERT: C 74 ASP cc_start: 0.8038 (t0) cc_final: 0.7650 (p0) REVERT: C 76 LEU cc_start: 0.8818 (mp) cc_final: 0.8392 (mp) REVERT: C 137 GLU cc_start: 0.7848 (pm20) cc_final: 0.7643 (pm20) REVERT: C 167 ASP cc_start: 0.5876 (p0) cc_final: 0.5496 (p0) REVERT: D 80 MET cc_start: 0.8032 (tpt) cc_final: 0.7552 (tpt) REVERT: D 183 VAL cc_start: 0.8846 (t) cc_final: 0.7512 (m) REVERT: D 193 ARG cc_start: 0.8371 (ttm110) cc_final: 0.8068 (ptp-110) REVERT: E 51 LYS cc_start: 0.8643 (ptpp) cc_final: 0.8340 (mttt) REVERT: E 70 GLU cc_start: 0.7540 (mm-30) cc_final: 0.6412 (tt0) REVERT: E 81 HIS cc_start: 0.7032 (t-90) cc_final: 0.6829 (t-90) REVERT: E 89 CYS cc_start: 0.8366 (t) cc_final: 0.8001 (p) REVERT: E 240 LYS cc_start: 0.8923 (mttm) cc_final: 0.8419 (mtpt) REVERT: E 273 ASN cc_start: 0.9164 (p0) cc_final: 0.8640 (p0) REVERT: E 305 MET cc_start: 0.8297 (tpt) cc_final: 0.8064 (tpp) REVERT: E 328 ASN cc_start: 0.6402 (OUTLIER) cc_final: 0.5745 (t0) REVERT: E 339 GLU cc_start: 0.8569 (mp0) cc_final: 0.6596 (tt0) REVERT: E 348 ASN cc_start: 0.7692 (m110) cc_final: 0.6896 (t0) REVERT: E 387 PHE cc_start: 0.8620 (m-80) cc_final: 0.8411 (m-10) REVERT: E 473 MET cc_start: 0.8896 (ptp) cc_final: 0.8620 (ptm) REVERT: E 475 VAL cc_start: 0.9336 (t) cc_final: 0.9096 (t) REVERT: E 513 MET cc_start: 0.8311 (mtt) cc_final: 0.8025 (mtt) REVERT: G 78 THR cc_start: 0.7951 (t) cc_final: 0.7658 (m) REVERT: G 158 MET cc_start: 0.8091 (ppp) cc_final: 0.7674 (ppp) REVERT: G 196 GLU cc_start: 0.7782 (pm20) cc_final: 0.7352 (mp0) REVERT: G 287 GLU cc_start: 0.8235 (tp30) cc_final: 0.7711 (tp30) REVERT: U 1 MET cc_start: 0.1178 (ttm) cc_final: 0.0584 (mtp) REVERT: U 182 ARG cc_start: 0.7371 (mtp180) cc_final: 0.6654 (mpp-170) outliers start: 4 outliers final: 1 residues processed: 560 average time/residue: 0.5569 time to fit residues: 520.8300 Evaluate side-chains 399 residues out of total 4565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 396 time to evaluate : 4.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 177 optimal weight: 0.8980 chunk 474 optimal weight: 40.0000 chunk 104 optimal weight: 0.9980 chunk 309 optimal weight: 8.9990 chunk 130 optimal weight: 0.9980 chunk 527 optimal weight: 20.0000 chunk 437 optimal weight: 0.4980 chunk 244 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 174 optimal weight: 7.9990 chunk 276 optimal weight: 0.0470 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN A1004 GLN ** A1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 368 HIS ** B 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 GLN D 38 ASN D 93 GLN ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 ASN ** E 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 176 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.9075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 47240 Z= 0.245 Angle : 0.923 19.525 64850 Z= 0.468 Chirality : 0.050 0.371 7467 Planarity : 0.007 0.146 7705 Dihedral : 19.950 171.667 8207 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 28.88 Ramachandran Plot: Outliers : 0.81 % Allowed : 16.26 % Favored : 82.93 % Rotamer: Outliers : 0.02 % Allowed : 3.44 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.53 (0.10), residues: 5289 helix: -2.16 (0.12), residues: 1534 sheet: -3.31 (0.23), residues: 354 loop : -3.62 (0.09), residues: 3401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP G 133 HIS 0.007 0.001 HIS C 63 PHE 0.033 0.002 PHE D 221 TYR 0.039 0.002 TYR D 178 ARG 0.031 0.001 ARG E 488 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 4565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 588 time to evaluate : 4.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.8336 (mtm-85) cc_final: 0.7827 (mmm-85) REVERT: A 137 ILE cc_start: 0.8618 (mt) cc_final: 0.8351 (mm) REVERT: A 187 ILE cc_start: 0.8864 (pt) cc_final: 0.8416 (pt) REVERT: A 188 ASP cc_start: 0.6845 (m-30) cc_final: 0.6502 (m-30) REVERT: A 330 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7864 (mp0) REVERT: A 344 GLU cc_start: 0.6968 (mt-10) cc_final: 0.6388 (tm-30) REVERT: A 391 ASN cc_start: 0.9373 (t0) cc_final: 0.9077 (t0) REVERT: A 446 SER cc_start: 0.8867 (t) cc_final: 0.8576 (p) REVERT: A 526 TYR cc_start: 0.7681 (m-80) cc_final: 0.7481 (m-80) REVERT: A 541 MET cc_start: 0.8888 (mmp) cc_final: 0.8232 (mmm) REVERT: A 566 LEU cc_start: 0.9519 (mp) cc_final: 0.9313 (mp) REVERT: A 573 LEU cc_start: 0.9098 (tp) cc_final: 0.8447 (tp) REVERT: A 646 ASN cc_start: 0.7771 (t0) cc_final: 0.7365 (t0) REVERT: A 704 ILE cc_start: 0.8919 (tp) cc_final: 0.8637 (tp) REVERT: A 706 GLU cc_start: 0.7257 (pt0) cc_final: 0.6731 (tt0) REVERT: A 815 VAL cc_start: 0.8767 (p) cc_final: 0.8121 (p) REVERT: A 850 ASP cc_start: 0.8338 (m-30) cc_final: 0.7943 (m-30) REVERT: A 876 ASP cc_start: 0.8815 (p0) cc_final: 0.8516 (p0) REVERT: A 922 MET cc_start: 0.6715 (ttt) cc_final: 0.6336 (ttt) REVERT: A 956 LYS cc_start: 0.8979 (mppt) cc_final: 0.8452 (mttt) REVERT: A 1017 PHE cc_start: 0.7084 (t80) cc_final: 0.6347 (t80) REVERT: A 1037 LEU cc_start: 0.9188 (tp) cc_final: 0.8846 (tp) REVERT: A 1050 GLU cc_start: 0.8447 (tt0) cc_final: 0.8108 (tt0) REVERT: B 37 LYS cc_start: 0.8207 (mmtt) cc_final: 0.7254 (mmtt) REVERT: B 77 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7731 (tp30) REVERT: B 125 MET cc_start: 0.8909 (mpp) cc_final: 0.8373 (mtm) REVERT: B 201 VAL cc_start: 0.8466 (t) cc_final: 0.8122 (t) REVERT: B 261 ASN cc_start: 0.8153 (m-40) cc_final: 0.7116 (p0) REVERT: B 1127 MET cc_start: 0.7747 (tmm) cc_final: 0.7485 (tmm) REVERT: B 1207 PHE cc_start: 0.8336 (t80) cc_final: 0.8049 (t80) REVERT: C 64 GLU cc_start: 0.7515 (tm-30) cc_final: 0.7277 (tm-30) REVERT: C 74 ASP cc_start: 0.8019 (t0) cc_final: 0.7729 (p0) REVERT: C 76 LEU cc_start: 0.8519 (mp) cc_final: 0.8096 (mp) REVERT: D 80 MET cc_start: 0.7680 (tpt) cc_final: 0.7268 (tpt) REVERT: D 100 LEU cc_start: 0.8286 (mt) cc_final: 0.7681 (pt) REVERT: D 183 VAL cc_start: 0.8506 (t) cc_final: 0.8124 (m) REVERT: E 89 CYS cc_start: 0.8111 (t) cc_final: 0.7704 (p) REVERT: E 233 ASN cc_start: 0.8783 (m-40) cc_final: 0.8332 (m-40) REVERT: E 273 ASN cc_start: 0.9003 (p0) cc_final: 0.8642 (p0) REVERT: E 305 MET cc_start: 0.8334 (tpt) cc_final: 0.7949 (tpp) REVERT: E 377 ARG cc_start: 0.8737 (ttm-80) cc_final: 0.8207 (tpp80) REVERT: E 407 LEU cc_start: 0.8412 (pp) cc_final: 0.7991 (mt) REVERT: E 616 ASN cc_start: 0.7897 (m110) cc_final: 0.6928 (t0) REVERT: F 62 ILE cc_start: 0.8696 (mm) cc_final: 0.8440 (mt) REVERT: G 85 TYR cc_start: 0.7900 (m-80) cc_final: 0.7571 (m-80) REVERT: G 156 ASP cc_start: 0.8108 (m-30) cc_final: 0.7798 (m-30) REVERT: G 158 MET cc_start: 0.7863 (ppp) cc_final: 0.7388 (ppp) REVERT: U 182 ARG cc_start: 0.7358 (mtp180) cc_final: 0.6679 (mpp-170) REVERT: U 278 MET cc_start: 0.0614 (mtp) cc_final: -0.3100 (mmt) REVERT: V 157 MET cc_start: 0.3865 (mmp) cc_final: 0.3651 (mmm) outliers start: 1 outliers final: 0 residues processed: 589 average time/residue: 0.5565 time to fit residues: 549.1705 Evaluate side-chains 423 residues out of total 4565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 423 time to evaluate : 5.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 508 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 300 optimal weight: 8.9990 chunk 385 optimal weight: 5.9990 chunk 298 optimal weight: 5.9990 chunk 443 optimal weight: 20.0000 chunk 294 optimal weight: 0.0020 chunk 525 optimal weight: 2.9990 chunk 328 optimal weight: 0.6980 chunk 320 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 overall best weight: 1.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN ** A1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN D 93 GLN E 101 HIS ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 372 GLN E 385 GLN ** E 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 19 GLN S 193 GLN ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 174 ASN ** T 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 148 ASN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 91 HIS Y 176 HIS Y 206 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.9519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 47240 Z= 0.287 Angle : 0.914 18.701 64850 Z= 0.465 Chirality : 0.050 0.379 7467 Planarity : 0.007 0.151 7705 Dihedral : 19.851 173.195 8207 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 29.36 Ramachandran Plot: Outliers : 0.76 % Allowed : 17.36 % Favored : 81.89 % Rotamer: Outliers : 0.07 % Allowed : 3.55 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.33 (0.10), residues: 5289 helix: -1.97 (0.12), residues: 1556 sheet: -3.08 (0.25), residues: 323 loop : -3.54 (0.09), residues: 3410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP E 416 HIS 0.011 0.001 HIS C 63 PHE 0.027 0.002 PHE D 221 TYR 0.039 0.002 TYR A 698 ARG 0.017 0.001 ARG C 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 4565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 542 time to evaluate : 5.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.7014 (m-30) cc_final: 0.6731 (m-30) REVERT: A 258 ASP cc_start: 0.8584 (p0) cc_final: 0.8264 (p0) REVERT: A 330 GLU cc_start: 0.8222 (mt-10) cc_final: 0.8000 (mp0) REVERT: A 344 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6583 (tm-30) REVERT: A 488 LEU cc_start: 0.5897 (tt) cc_final: 0.5687 (tp) REVERT: A 526 TYR cc_start: 0.7687 (m-80) cc_final: 0.7455 (m-80) REVERT: A 541 MET cc_start: 0.8860 (mmp) cc_final: 0.8259 (mmm) REVERT: A 555 MET cc_start: 0.7960 (ppp) cc_final: 0.6454 (ppp) REVERT: A 559 MET cc_start: 0.8409 (tpp) cc_final: 0.7317 (mmm) REVERT: A 704 ILE cc_start: 0.8900 (tp) cc_final: 0.8645 (tp) REVERT: A 850 ASP cc_start: 0.8431 (m-30) cc_final: 0.8155 (m-30) REVERT: A 885 ASN cc_start: 0.8611 (t0) cc_final: 0.8386 (t0) REVERT: A 956 LYS cc_start: 0.9125 (mppt) cc_final: 0.8630 (mttt) REVERT: A 1050 GLU cc_start: 0.8478 (tt0) cc_final: 0.8030 (tt0) REVERT: B 37 LYS cc_start: 0.8062 (mmtt) cc_final: 0.7195 (mmtt) REVERT: B 38 ASP cc_start: 0.7723 (m-30) cc_final: 0.6992 (t0) REVERT: B 77 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7921 (tm-30) REVERT: B 216 THR cc_start: 0.8410 (m) cc_final: 0.7987 (p) REVERT: B 776 TYR cc_start: 0.5661 (t80) cc_final: 0.5341 (t80) REVERT: C 74 ASP cc_start: 0.8089 (t0) cc_final: 0.7682 (p0) REVERT: C 76 LEU cc_start: 0.8533 (mp) cc_final: 0.8055 (mp) REVERT: C 93 GLN cc_start: 0.8652 (mt0) cc_final: 0.8300 (mt0) REVERT: D 80 MET cc_start: 0.7951 (tpt) cc_final: 0.7467 (tpt) REVERT: D 100 LEU cc_start: 0.8187 (mt) cc_final: 0.7518 (pt) REVERT: D 183 VAL cc_start: 0.9066 (t) cc_final: 0.8662 (p) REVERT: E 89 CYS cc_start: 0.8403 (t) cc_final: 0.8000 (p) REVERT: E 164 GLU cc_start: 0.7053 (mt-10) cc_final: 0.6748 (mt-10) REVERT: E 233 ASN cc_start: 0.8811 (m-40) cc_final: 0.8307 (m-40) REVERT: E 240 LYS cc_start: 0.8844 (mttm) cc_final: 0.8149 (mtpt) REVERT: E 273 ASN cc_start: 0.9099 (p0) cc_final: 0.8855 (p0) REVERT: E 339 GLU cc_start: 0.8116 (mp0) cc_final: 0.6809 (tt0) REVERT: E 473 MET cc_start: 0.8226 (ptm) cc_final: 0.7952 (ptp) REVERT: E 524 ASN cc_start: 0.7274 (t0) cc_final: 0.6782 (t0) REVERT: E 551 ASP cc_start: 0.7754 (t70) cc_final: 0.7352 (t70) REVERT: G 156 ASP cc_start: 0.8245 (m-30) cc_final: 0.7891 (m-30) REVERT: G 158 MET cc_start: 0.7907 (ppp) cc_final: 0.7475 (ppp) REVERT: U 182 ARG cc_start: 0.7247 (mtp180) cc_final: 0.6560 (mpp-170) REVERT: U 278 MET cc_start: -0.0138 (mtp) cc_final: -0.3293 (mmt) REVERT: V 278 MET cc_start: 0.6640 (ptm) cc_final: 0.6179 (ptm) outliers start: 3 outliers final: 1 residues processed: 545 average time/residue: 0.5599 time to fit residues: 510.8845 Evaluate side-chains 408 residues out of total 4565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 407 time to evaluate : 5.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 324 optimal weight: 0.4980 chunk 209 optimal weight: 50.0000 chunk 313 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 333 optimal weight: 0.8980 chunk 357 optimal weight: 0.0270 chunk 259 optimal weight: 0.0970 chunk 48 optimal weight: 3.9990 chunk 412 optimal weight: 40.0000 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS A 389 GLN ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 HIS ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN B 321 GLN ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 989 GLN ** B1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 HIS ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 GLN E 371 HIS E 372 GLN E 385 GLN ** E 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 132 GLN X 176 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.9872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 47240 Z= 0.219 Angle : 0.882 21.425 64850 Z= 0.445 Chirality : 0.048 0.388 7467 Planarity : 0.006 0.131 7705 Dihedral : 19.760 171.886 8207 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 26.10 Ramachandran Plot: Outliers : 0.76 % Allowed : 15.47 % Favored : 83.78 % Rotamer: Outliers : 0.02 % Allowed : 2.04 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.10), residues: 5289 helix: -1.76 (0.12), residues: 1551 sheet: -2.84 (0.26), residues: 329 loop : -3.40 (0.10), residues: 3409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP C 199 HIS 0.018 0.001 HIS C 19 PHE 0.050 0.002 PHE B1097 TYR 0.028 0.002 TYR A 698 ARG 0.013 0.001 ARG E 438 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 4565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 568 time to evaluate : 5.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.8180 (mtm-85) cc_final: 0.7933 (mmm-85) REVERT: A 187 ILE cc_start: 0.8818 (pt) cc_final: 0.8466 (pt) REVERT: A 188 ASP cc_start: 0.6999 (m-30) cc_final: 0.6717 (m-30) REVERT: A 258 ASP cc_start: 0.8390 (p0) cc_final: 0.8087 (p0) REVERT: A 330 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7897 (mp0) REVERT: A 344 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6131 (tm-30) REVERT: A 534 ILE cc_start: 0.8661 (mp) cc_final: 0.8354 (mp) REVERT: A 541 MET cc_start: 0.8958 (mmp) cc_final: 0.8350 (mmm) REVERT: A 555 MET cc_start: 0.8026 (ppp) cc_final: 0.6513 (ppp) REVERT: A 602 ASP cc_start: 0.8962 (t70) cc_final: 0.8338 (t70) REVERT: A 646 ASN cc_start: 0.7667 (t0) cc_final: 0.7181 (t0) REVERT: A 702 ILE cc_start: 0.8923 (mm) cc_final: 0.8649 (mm) REVERT: A 704 ILE cc_start: 0.8850 (tp) cc_final: 0.8553 (tp) REVERT: A 850 ASP cc_start: 0.8231 (m-30) cc_final: 0.7793 (m-30) REVERT: A 876 ASP cc_start: 0.8840 (p0) cc_final: 0.7799 (t70) REVERT: A 956 LYS cc_start: 0.8971 (mppt) cc_final: 0.8557 (mttt) REVERT: A 1017 PHE cc_start: 0.6843 (t80) cc_final: 0.6352 (t80) REVERT: A 1050 GLU cc_start: 0.8474 (tt0) cc_final: 0.8140 (tt0) REVERT: B 38 ASP cc_start: 0.7718 (m-30) cc_final: 0.6858 (t0) REVERT: B 216 THR cc_start: 0.8408 (m) cc_final: 0.7832 (p) REVERT: B 353 MET cc_start: 0.4550 (tpt) cc_final: 0.4041 (mpp) REVERT: B 776 TYR cc_start: 0.5537 (t80) cc_final: 0.5299 (t80) REVERT: C 74 ASP cc_start: 0.8017 (t0) cc_final: 0.7551 (p0) REVERT: C 77 GLU cc_start: 0.7688 (pm20) cc_final: 0.6675 (mm-30) REVERT: C 93 GLN cc_start: 0.8509 (mt0) cc_final: 0.8213 (mt0) REVERT: C 199 TRP cc_start: 0.8110 (m100) cc_final: 0.7890 (m100) REVERT: D 80 MET cc_start: 0.7630 (tpt) cc_final: 0.7166 (tpt) REVERT: D 100 LEU cc_start: 0.8152 (mt) cc_final: 0.7517 (pt) REVERT: E 89 CYS cc_start: 0.8078 (t) cc_final: 0.7823 (p) REVERT: E 103 MET cc_start: 0.7846 (mmm) cc_final: 0.7367 (mmp) REVERT: E 164 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6795 (mt-10) REVERT: E 233 ASN cc_start: 0.8845 (m-40) cc_final: 0.8370 (m-40) REVERT: E 244 MET cc_start: 0.8533 (tpt) cc_final: 0.8306 (tpp) REVERT: E 258 PRO cc_start: 0.9054 (Cg_endo) cc_final: 0.8733 (Cg_exo) REVERT: E 273 ASN cc_start: 0.8954 (p0) cc_final: 0.8719 (p0) REVERT: E 305 MET cc_start: 0.8142 (tpt) cc_final: 0.7806 (tpp) REVERT: E 339 GLU cc_start: 0.7450 (mp0) cc_final: 0.7131 (tt0) REVERT: E 524 ASN cc_start: 0.7086 (t0) cc_final: 0.6832 (t0) REVERT: F 62 ILE cc_start: 0.8495 (mm) cc_final: 0.7975 (mm) REVERT: G 156 ASP cc_start: 0.8071 (m-30) cc_final: 0.7704 (m-30) REVERT: U 182 ARG cc_start: 0.7045 (mtp180) cc_final: 0.6351 (mpp-170) REVERT: U 278 MET cc_start: -0.1261 (mtp) cc_final: -0.4058 (mmt) REVERT: V 278 MET cc_start: 0.6362 (ptm) cc_final: 0.6027 (ptm) outliers start: 1 outliers final: 0 residues processed: 569 average time/residue: 0.5361 time to fit residues: 518.7893 Evaluate side-chains 426 residues out of total 4565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 426 time to evaluate : 5.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 477 optimal weight: 10.0000 chunk 503 optimal weight: 40.0000 chunk 459 optimal weight: 30.0000 chunk 489 optimal weight: 2.9990 chunk 294 optimal weight: 0.9990 chunk 213 optimal weight: 0.5980 chunk 384 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 442 optimal weight: 9.9990 chunk 462 optimal weight: 20.0000 chunk 487 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 347 GLN ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 HIS E 101 HIS E 114 HIS ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN E 372 GLN E 385 GLN ** E 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 176 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 1.0140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 47240 Z= 0.271 Angle : 0.888 18.704 64850 Z= 0.450 Chirality : 0.049 0.391 7467 Planarity : 0.007 0.121 7705 Dihedral : 19.724 173.884 8207 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 27.92 Ramachandran Plot: Outliers : 0.78 % Allowed : 16.32 % Favored : 82.91 % Rotamer: Outliers : 0.02 % Allowed : 1.49 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.10), residues: 5289 helix: -1.67 (0.12), residues: 1580 sheet: -2.81 (0.26), residues: 320 loop : -3.37 (0.09), residues: 3389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 199 HIS 0.007 0.001 HIS V 175 PHE 0.037 0.002 PHE A1028 TYR 0.060 0.002 TYR D 178 ARG 0.015 0.001 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 4565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 535 time to evaluate : 5.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.7102 (m-30) cc_final: 0.6576 (m-30) REVERT: A 258 ASP cc_start: 0.8583 (p0) cc_final: 0.8217 (p0) REVERT: A 330 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7785 (mp0) REVERT: A 344 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6546 (tm-30) REVERT: A 555 MET cc_start: 0.7974 (ppp) cc_final: 0.6516 (ppp) REVERT: A 602 ASP cc_start: 0.9016 (t70) cc_final: 0.8457 (t70) REVERT: A 646 ASN cc_start: 0.7719 (t0) cc_final: 0.7388 (t0) REVERT: A 704 ILE cc_start: 0.8935 (tp) cc_final: 0.8724 (tp) REVERT: A 757 ILE cc_start: 0.8311 (tp) cc_final: 0.8106 (tp) REVERT: A 850 ASP cc_start: 0.8406 (m-30) cc_final: 0.7975 (m-30) REVERT: A 885 ASN cc_start: 0.8652 (t0) cc_final: 0.8360 (t0) REVERT: A 956 LYS cc_start: 0.9118 (mppt) cc_final: 0.8670 (mttt) REVERT: A 1050 GLU cc_start: 0.8490 (tt0) cc_final: 0.8200 (tt0) REVERT: B 38 ASP cc_start: 0.7680 (m-30) cc_final: 0.7325 (t70) REVERT: B 125 MET cc_start: 0.8578 (mpp) cc_final: 0.8370 (mpp) REVERT: B 273 GLU cc_start: 0.7342 (tm-30) cc_final: 0.6989 (tm-30) REVERT: B 353 MET cc_start: 0.4346 (tpt) cc_final: 0.3970 (mpp) REVERT: C 74 ASP cc_start: 0.8067 (t0) cc_final: 0.7768 (p0) REVERT: C 93 GLN cc_start: 0.8562 (mt0) cc_final: 0.8240 (mt0) REVERT: D 80 MET cc_start: 0.7934 (tpt) cc_final: 0.7426 (tpt) REVERT: D 100 LEU cc_start: 0.8141 (mt) cc_final: 0.7614 (pt) REVERT: E 89 CYS cc_start: 0.8335 (t) cc_final: 0.8109 (p) REVERT: E 164 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6549 (mt-10) REVERT: E 233 ASN cc_start: 0.8797 (m-40) cc_final: 0.8224 (m-40) REVERT: E 240 LYS cc_start: 0.8692 (mttm) cc_final: 0.8174 (mtpp) REVERT: E 258 PRO cc_start: 0.9122 (Cg_endo) cc_final: 0.8913 (Cg_exo) REVERT: E 273 ASN cc_start: 0.9044 (p0) cc_final: 0.8834 (p0) REVERT: E 305 MET cc_start: 0.8111 (tpt) cc_final: 0.7893 (tpp) REVERT: E 339 GLU cc_start: 0.7903 (mp0) cc_final: 0.6962 (tt0) REVERT: E 405 LYS cc_start: 0.7676 (pptt) cc_final: 0.7366 (pttt) REVERT: E 524 ASN cc_start: 0.7402 (t0) cc_final: 0.7008 (t0) REVERT: G 156 ASP cc_start: 0.8096 (m-30) cc_final: 0.7641 (m-30) REVERT: U 182 ARG cc_start: 0.7006 (mtp180) cc_final: 0.6294 (mpp-170) REVERT: U 278 MET cc_start: -0.1973 (mtp) cc_final: -0.4342 (mmt) REVERT: V 278 MET cc_start: 0.5930 (ptm) cc_final: 0.5667 (ptm) outliers start: 1 outliers final: 0 residues processed: 536 average time/residue: 0.5186 time to fit residues: 476.1015 Evaluate side-chains 405 residues out of total 4565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 5.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 321 optimal weight: 0.9980 chunk 517 optimal weight: 9.9990 chunk 315 optimal weight: 0.8980 chunk 245 optimal weight: 0.0970 chunk 359 optimal weight: 5.9990 chunk 542 optimal weight: 10.0000 chunk 499 optimal weight: 5.9990 chunk 432 optimal weight: 30.0000 chunk 44 optimal weight: 9.9990 chunk 333 optimal weight: 2.9990 chunk 265 optimal weight: 0.8980 overall best weight: 1.1780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 ASN ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** A1053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 347 GLN ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 HIS ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 372 GLN E 385 GLN ** E 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 1.0405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 47240 Z= 0.239 Angle : 0.866 20.134 64850 Z= 0.438 Chirality : 0.048 0.411 7467 Planarity : 0.006 0.116 7705 Dihedral : 19.663 173.822 8207 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 25.63 Ramachandran Plot: Outliers : 0.74 % Allowed : 15.52 % Favored : 83.74 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.10), residues: 5289 helix: -1.55 (0.12), residues: 1572 sheet: -2.68 (0.27), residues: 311 loop : -3.30 (0.10), residues: 3406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 199 HIS 0.012 0.001 HIS C 63 PHE 0.034 0.002 PHE B1097 TYR 0.035 0.002 TYR E 607 ARG 0.015 0.001 ARG E 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10578 Ramachandran restraints generated. 5289 Oldfield, 0 Emsley, 5289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 4565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 541 time to evaluate : 5.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.8286 (mtm-85) cc_final: 0.7908 (mmm-85) REVERT: A 188 ASP cc_start: 0.7037 (m-30) cc_final: 0.6625 (m-30) REVERT: A 258 ASP cc_start: 0.8399 (p0) cc_final: 0.8025 (p0) REVERT: A 330 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7801 (mp0) REVERT: A 344 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6640 (tm-30) REVERT: A 555 MET cc_start: 0.7819 (ppp) cc_final: 0.6319 (ppp) REVERT: A 602 ASP cc_start: 0.9030 (t70) cc_final: 0.8310 (t70) REVERT: A 704 ILE cc_start: 0.8931 (tp) cc_final: 0.8659 (tp) REVERT: A 801 ASP cc_start: 0.7365 (p0) cc_final: 0.7132 (p0) REVERT: A 850 ASP cc_start: 0.8320 (m-30) cc_final: 0.7943 (m-30) REVERT: A 876 ASP cc_start: 0.8831 (p0) cc_final: 0.8581 (p0) REVERT: A 931 ILE cc_start: 0.9232 (mt) cc_final: 0.8992 (mm) REVERT: A 956 LYS cc_start: 0.9090 (mppt) cc_final: 0.8606 (mttt) REVERT: A 1050 GLU cc_start: 0.8428 (tt0) cc_final: 0.8173 (tt0) REVERT: B 38 ASP cc_start: 0.7822 (m-30) cc_final: 0.7304 (t70) REVERT: B 353 MET cc_start: 0.4231 (tpt) cc_final: 0.4026 (mpp) REVERT: B 420 LYS cc_start: 0.4728 (mtmm) cc_final: 0.2739 (tptp) REVERT: B 724 TYR cc_start: 0.6550 (t80) cc_final: 0.6195 (t80) REVERT: B 776 TYR cc_start: 0.6435 (t80) cc_final: 0.5837 (t80) REVERT: C 74 ASP cc_start: 0.7997 (t0) cc_final: 0.7545 (p0) REVERT: C 77 GLU cc_start: 0.7819 (pm20) cc_final: 0.6590 (mm-30) REVERT: C 80 MET cc_start: 0.7853 (mmp) cc_final: 0.7489 (tpp) REVERT: C 93 GLN cc_start: 0.8443 (mt0) cc_final: 0.8159 (mt0) REVERT: C 199 TRP cc_start: 0.8184 (m100) cc_final: 0.7928 (m100) REVERT: C 205 SER cc_start: 0.8480 (t) cc_final: 0.7803 (m) REVERT: D 80 MET cc_start: 0.7636 (tpt) cc_final: 0.6979 (tpt) REVERT: D 98 ARG cc_start: 0.7201 (mmt-90) cc_final: 0.6765 (mmp80) REVERT: E 89 CYS cc_start: 0.8293 (t) cc_final: 0.7991 (p) REVERT: E 103 MET cc_start: 0.7844 (mmm) cc_final: 0.7420 (mmp) REVERT: E 233 ASN cc_start: 0.8783 (m-40) cc_final: 0.8305 (m-40) REVERT: E 240 LYS cc_start: 0.8562 (mttm) cc_final: 0.8342 (mmtm) REVERT: E 258 PRO cc_start: 0.9031 (Cg_endo) cc_final: 0.8719 (Cg_exo) REVERT: E 305 MET cc_start: 0.8160 (tpt) cc_final: 0.7954 (tpp) REVERT: E 339 GLU cc_start: 0.7608 (mp0) cc_final: 0.7167 (tt0) REVERT: E 405 LYS cc_start: 0.7786 (pptt) cc_final: 0.7508 (pttt) REVERT: E 524 ASN cc_start: 0.7419 (t0) cc_final: 0.7050 (t0) REVERT: F 62 ILE cc_start: 0.8538 (mm) cc_final: 0.7958 (mm) REVERT: G 156 ASP cc_start: 0.8152 (m-30) cc_final: 0.7557 (m-30) REVERT: T 202 MET cc_start: -0.6944 (ptm) cc_final: -0.7464 (ttp) REVERT: U 182 ARG cc_start: 0.6958 (mtp180) cc_final: 0.6256 (mpp-170) REVERT: U 278 MET cc_start: -0.2091 (mtp) cc_final: -0.4472 (mmt) outliers start: 0 outliers final: 0 residues processed: 541 average time/residue: 0.5402 time to fit residues: 498.5067 Evaluate side-chains 417 residues out of total 4565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 417 time to evaluate : 5.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 545 random chunks: chunk 343 optimal weight: 1.9990 chunk 460 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 398 optimal weight: 30.0000 chunk 63 optimal weight: 0.0040 chunk 120 optimal weight: 0.9990 chunk 433 optimal weight: 0.6980 chunk 181 optimal weight: 4.9990 chunk 444 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 79 optimal weight: 0.4980 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 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 ASN ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN A1053 ASN B 321 GLN B 347 GLN ** B1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN ** D 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 HIS ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 ASN ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 372 GLN E 385 GLN ** E 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 98 HIS ** T 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 176 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.170456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.133436 restraints weight = 142815.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.130849 restraints weight = 178987.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.131901 restraints weight = 144723.800| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3879 r_free = 0.3879 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3879 r_free = 0.3879 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 1.0644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 47240 Z= 0.215 Angle : 0.850 20.312 64850 Z= 0.428 Chirality : 0.047 0.417 7467 Planarity : 0.006 0.112 7705 Dihedral : 19.576 173.654 8207 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 24.16 Ramachandran Plot: Outliers : 0.70 % Allowed : 14.97 % Favored : 84.33 % Rotamer: Outliers : 0.02 % Allowed : 0.72 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.11), residues: 5289 helix: -1.47 (0.12), residues: 1572 sheet: -2.70 (0.25), residues: 346 loop : -3.21 (0.10), residues: 3371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 199 HIS 0.008 0.001 HIS C 63 PHE 0.030 0.002 PHE B1097 TYR 0.026 0.002 TYR S 104 ARG 0.010 0.001 ARG A 607 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10829.58 seconds wall clock time: 195 minutes 51.37 seconds (11751.37 seconds total)