Starting phenix.real_space_refine (version: dev) on Wed Dec 14 00:31:24 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ez0_28725/12_2022/8ez0_28725_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ez0_28725/12_2022/8ez0_28725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ez0_28725/12_2022/8ez0_28725.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ez0_28725/12_2022/8ez0_28725.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ez0_28725/12_2022/8ez0_28725_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ez0_28725/12_2022/8ez0_28725_neut.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3460 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 151": "OD1" <-> "OD2" Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 444": "OE1" <-> "OE2" Residue "A ASP 464": "OD1" <-> "OD2" Residue "A PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 151": "OD1" <-> "OD2" Residue "B ASP 157": "OD1" <-> "OD2" Residue "B GLU 239": "OE1" <-> "OE2" Residue "B TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 443": "OE1" <-> "OE2" Residue "B PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 535": "OD1" <-> "OD2" Residue "B ASP 622": "OD1" <-> "OD2" Residue "B GLU 635": "OE1" <-> "OE2" Residue "B PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 697": "OE1" <-> "OE2" Residue "B TYR 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 13": "OE1" <-> "OE2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 21": "OE1" <-> "OE2" Residue "F GLU 72": "OE1" <-> "OE2" Residue "F TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 72": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 14640 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6601 Classifications: {'peptide': 816} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 771} Chain breaks: 6 Chain: "B" Number of atoms: 6593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6593 Classifications: {'peptide': 815} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 770} Chain breaks: 7 Chain: "D" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Chain: "E" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Chain: "F" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 347 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain breaks: 1 Chain: "G" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 347 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain breaks: 1 Time building chain proxies: 8.87, per 1000 atoms: 0.61 Number of scatterers: 14640 At special positions: 0 Unit cell: (132.84, 122.04, 172.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 122 16.00 O 2716 8.00 N 2502 7.00 C 9300 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.04 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.02 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 862 " distance=2.03 Simple disulfide: pdb=" SG CYS A 788 " - pdb=" SG CYS A 797 " distance=2.04 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.04 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 862 " distance=2.03 Simple disulfide: pdb=" SG CYS B 788 " - pdb=" SG CYS B 797 " distance=2.04 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 62 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 66 " distance=2.03 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS E 62 " distance=2.03 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 75 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 66 " distance=2.03 Simple disulfide: pdb=" SG CYS F 7 " - pdb=" SG CYS F 62 " distance=2.03 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 75 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 66 " distance=2.03 Simple disulfide: pdb=" SG CYS G 7 " - pdb=" SG CYS G 62 " distance=2.03 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS G 75 " distance=2.03 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 66 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.94 Conformation dependent library (CDL) restraints added in 2.1 seconds 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3418 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 32 sheets defined 18.7% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 16 through 23 removed outlier: 3.914A pdb=" N ARG A 19 " --> pdb=" O ASN A 16 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU A 22 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.639A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 318 Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 350 through 358 Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.601A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 640 through 645 removed outlier: 3.778A pdb=" N PHE A 644 " --> pdb=" O ASP A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 716 Processing helix chain 'A' and resid 865 through 872 Processing helix chain 'B' and resid 16 through 23 removed outlier: 4.041A pdb=" N ARG B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU B 22 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 255 through 268 removed outlier: 3.643A pdb=" N CYS B 259 " --> pdb=" O ASN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 318 removed outlier: 3.546A pdb=" N GLU B 318 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 378 through 382 removed outlier: 4.493A pdb=" N PHE B 381 " --> pdb=" O SER B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.738A pdb=" N GLY B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 removed outlier: 3.578A pdb=" N ARG B 451 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLN B 452 " --> pdb=" O LYS B 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 448 through 452' Processing helix chain 'B' and resid 640 through 645 removed outlier: 3.574A pdb=" N PHE B 644 " --> pdb=" O ASP B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 716 Processing helix chain 'B' and resid 864 through 872 Processing helix chain 'D' and resid 8 through 19 removed outlier: 3.573A pdb=" N VAL D 12 " --> pdb=" O GLY D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 67 through 73 Processing helix chain 'E' and resid 8 through 19 removed outlier: 3.562A pdb=" N VAL E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 62 Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'F' and resid 8 through 19 removed outlier: 4.207A pdb=" N VAL F 12 " --> pdb=" O GLY F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 74 removed outlier: 3.819A pdb=" N TYR F 74 " --> pdb=" O GLN F 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 19 removed outlier: 4.211A pdb=" N VAL G 12 " --> pdb=" O GLY G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 Processing helix chain 'G' and resid 67 through 74 removed outlier: 3.547A pdb=" N TYR G 74 " --> pdb=" O GLN G 70 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 removed outlier: 6.571A pdb=" N MET A 11 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N LEU A 36 " --> pdb=" O MET A 11 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ILE A 13 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N MET A 38 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLN A 34 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU A 63 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU A 36 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG A 65 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A 93 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N GLU A 120 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE A 95 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ASN A 122 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL A 117 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL A 146 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE A 119 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN A 148 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LYS A 121 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.515A pdb=" N ILE A 29 " --> pdb=" O MET A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 Processing sheet with id=AA4, first strand: chain 'A' and resid 212 through 216 removed outlier: 5.823A pdb=" N LEU A 213 " --> pdb=" O CYS A 228 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N CYS A 228 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASN A 215 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AA6, first strand: chain 'A' and resid 278 through 280 Processing sheet with id=AA7, first strand: chain 'A' and resid 292 through 294 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 312 Processing sheet with id=AA9, first strand: chain 'A' and resid 319 through 321 removed outlier: 6.562A pdb=" N LYS A 319 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU A 368 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N LEU A 403 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE A 370 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LYS A 425 " --> pdb=" O TYR A 398 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE A 400 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 472 through 473 Processing sheet with id=AB2, first strand: chain 'A' and resid 486 through 487 Processing sheet with id=AB3, first strand: chain 'A' and resid 530 through 534 removed outlier: 3.532A pdb=" N GLY A 502 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A 508 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 601 through 609 removed outlier: 5.864A pdb=" N ASP A 602 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS A 618 " --> pdb=" O ASP A 602 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLN A 612 " --> pdb=" O ASN A 608 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 761 through 765 removed outlier: 3.948A pdb=" N GLY A 780 " --> pdb=" O GLN A 637 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 817 through 824 removed outlier: 5.115A pdb=" N GLN A 835 " --> pdb=" O PRO A 819 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 859 through 864 removed outlier: 3.544A pdb=" N GLU A 848 " --> pdb=" O ARG A 889 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG A 889 " --> pdb=" O GLU A 848 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 882 " --> pdb=" O VAL A 907 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.607A pdb=" N MET B 11 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LEU B 36 " --> pdb=" O MET B 11 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE B 13 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N MET B 38 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLN B 34 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU B 63 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU B 36 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ARG B 65 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU B 93 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N GLU B 120 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE B 95 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ASN B 122 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL B 117 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL B 146 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE B 119 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ASN B 148 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LYS B 121 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AC1, first strand: chain 'B' and resid 172 through 173 Processing sheet with id=AC2, first strand: chain 'B' and resid 212 through 216 removed outlier: 5.723A pdb=" N LEU B 213 " --> pdb=" O CYS B 228 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N CYS B 228 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASN B 215 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 231 through 233 removed outlier: 3.760A pdb=" N PHE B 231 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 238 " --> pdb=" O PHE B 231 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.728A pdb=" N HIS B 247 " --> pdb=" O CYS B 284 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 292 through 294 Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 312 Processing sheet with id=AC7, first strand: chain 'B' and resid 319 through 321 removed outlier: 6.513A pdb=" N LYS B 319 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 340 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ARG B 371 " --> pdb=" O LEU B 340 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE B 342 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=AC9, first strand: chain 'B' and resid 486 through 487 Processing sheet with id=AD1, first strand: chain 'B' and resid 530 through 534 removed outlier: 3.527A pdb=" N GLY B 502 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS B 508 " --> pdb=" O ALA B 565 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 601 through 609 removed outlier: 6.344A pdb=" N LYS B 616 " --> pdb=" O PRO B 603 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER B 605 " --> pdb=" O ILE B 614 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE B 614 " --> pdb=" O SER B 605 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N SER B 607 " --> pdb=" O GLN B 612 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N GLN B 612 " --> pdb=" O SER B 607 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 761 through 765 Processing sheet with id=AD4, first strand: chain 'B' and resid 821 through 824 Processing sheet with id=AD5, first strand: chain 'B' and resid 858 through 863 removed outlier: 3.541A pdb=" N ARG B 889 " --> pdb=" O GLU B 848 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG B 852 " --> pdb=" O SER B 885 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY B 882 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL B 907 " --> pdb=" O GLY B 882 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 936 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.11 Time building geometry restraints manager: 6.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4786 1.34 - 1.46: 3542 1.46 - 1.58: 6517 1.58 - 1.70: 0 1.70 - 1.82: 146 Bond restraints: 14991 Sorted by residual: bond pdb=" CA ASP A 142 " pdb=" CB ASP A 142 " ideal model delta sigma weight residual 1.530 1.556 -0.026 1.75e-02 3.27e+03 2.13e+00 bond pdb=" CB CYS B 182 " pdb=" SG CYS B 182 " ideal model delta sigma weight residual 1.808 1.767 0.041 3.30e-02 9.18e+02 1.54e+00 bond pdb=" CB ASP A 142 " pdb=" CG ASP A 142 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.53e+00 bond pdb=" C VAL B 158 " pdb=" N CYS B 159 " ideal model delta sigma weight residual 1.325 1.310 0.015 1.25e-02 6.40e+03 1.47e+00 bond pdb=" CA ASP B 250 " pdb=" CB ASP B 250 " ideal model delta sigma weight residual 1.530 1.550 -0.020 1.69e-02 3.50e+03 1.39e+00 ... (remaining 14986 not shown) Histogram of bond angle deviations from ideal: 97.90 - 105.15: 267 105.15 - 112.40: 7501 112.40 - 119.65: 5060 119.65 - 126.91: 7271 126.91 - 134.16: 213 Bond angle restraints: 20312 Sorted by residual: angle pdb=" N VAL A 377 " pdb=" CA VAL A 377 " pdb=" C VAL A 377 " ideal model delta sigma weight residual 113.53 109.56 3.97 9.80e-01 1.04e+00 1.64e+01 angle pdb=" N VAL A 140 " pdb=" CA VAL A 140 " pdb=" C VAL A 140 " ideal model delta sigma weight residual 112.96 109.24 3.72 1.00e+00 1.00e+00 1.38e+01 angle pdb=" CA ASP A 142 " pdb=" CB ASP A 142 " pdb=" CG ASP A 142 " ideal model delta sigma weight residual 112.60 116.07 -3.47 1.00e+00 1.00e+00 1.20e+01 angle pdb=" CA MET A 833 " pdb=" CB MET A 833 " pdb=" CG MET A 833 " ideal model delta sigma weight residual 114.10 120.65 -6.55 2.00e+00 2.50e-01 1.07e+01 angle pdb=" CB MET A 833 " pdb=" CG MET A 833 " pdb=" SD MET A 833 " ideal model delta sigma weight residual 112.70 122.19 -9.49 3.00e+00 1.11e-01 1.00e+01 ... (remaining 20307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 7873 18.06 - 36.11: 917 36.11 - 54.17: 233 54.17 - 72.22: 33 72.22 - 90.28: 22 Dihedral angle restraints: 9078 sinusoidal: 3782 harmonic: 5296 Sorted by residual: dihedral pdb=" CB CYS G 7 " pdb=" SG CYS G 7 " pdb=" SG CYS G 62 " pdb=" CB CYS G 62 " ideal model delta sinusoidal sigma weight residual 93.00 -176.72 -90.28 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS B 288 " pdb=" SG CYS B 288 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -172.30 86.30 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" CB CYS A 169 " pdb=" SG CYS A 169 " pdb=" SG CYS A 188 " pdb=" CB CYS A 188 " ideal model delta sinusoidal sigma weight residual 93.00 178.90 -85.90 1 1.00e+01 1.00e-02 8.91e+01 ... (remaining 9075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1393 0.034 - 0.068: 537 0.068 - 0.102: 186 0.102 - 0.136: 85 0.136 - 0.169: 6 Chirality restraints: 2207 Sorted by residual: chirality pdb=" CA ILE A 95 " pdb=" N ILE A 95 " pdb=" C ILE A 95 " pdb=" CB ILE A 95 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CA ILE B 119 " pdb=" N ILE B 119 " pdb=" C ILE B 119 " pdb=" CB ILE B 119 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CG LEU F 15 " pdb=" CB LEU F 15 " pdb=" CD1 LEU F 15 " pdb=" CD2 LEU F 15 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 2204 not shown) Planarity restraints: 2621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 250 " -0.012 2.00e-02 2.50e+03 2.45e-02 5.98e+00 pdb=" C ASP B 250 " 0.042 2.00e-02 2.50e+03 pdb=" O ASP B 250 " -0.016 2.00e-02 2.50e+03 pdb=" N TRP B 251 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 142 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" C ASP A 142 " 0.040 2.00e-02 2.50e+03 pdb=" O ASP A 142 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN A 143 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 580 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" C THR B 580 " 0.039 2.00e-02 2.50e+03 pdb=" O THR B 580 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR B 581 " -0.013 2.00e-02 2.50e+03 ... (remaining 2618 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 446 2.68 - 3.24: 14248 3.24 - 3.79: 22884 3.79 - 4.35: 29909 4.35 - 4.90: 48842 Nonbonded interactions: 116329 Sorted by model distance: nonbonded pdb=" O ILE B 29 " pdb=" OG1 THR B 58 " model vdw 2.130 2.440 nonbonded pdb=" OH TYR A 144 " pdb=" OE2 GLU B 700 " model vdw 2.152 2.440 nonbonded pdb=" OG SER B 880 " pdb=" OH TYR B 884 " model vdw 2.160 2.440 nonbonded pdb=" O GLY G 56 " pdb=" OH TYR G 74 " model vdw 2.161 2.440 nonbonded pdb=" O GLN F 60 " pdb=" OG SER F 64 " model vdw 2.162 2.440 ... (remaining 116324 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 406 or resid 408 through 910)) selection = chain 'B' } ncs_group { reference = (chain 'D' and (resid 4 through 26 or resid 56 through 76)) selection = (chain 'E' and (resid 4 through 26 or resid 56 through 76)) selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 122 5.16 5 C 9300 2.51 5 N 2502 2.21 5 O 2716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 7.270 Check model and map are aligned: 0.220 Convert atoms to be neutral: 0.120 Process input model: 41.940 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 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 : 0.004 0.041 14991 Z= 0.256 Angle : 0.631 9.489 20312 Z= 0.341 Chirality : 0.044 0.169 2207 Planarity : 0.004 0.034 2621 Dihedral : 15.908 89.022 5522 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.20), residues: 1769 helix: -0.70 (0.31), residues: 292 sheet: -0.80 (0.29), residues: 333 loop : -1.32 (0.19), residues: 1144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 1.941 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 100 average time/residue: 0.2302 time to fit residues: 37.5532 Evaluate side-chains 94 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 1.683 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1801 time to fit residues: 2.6414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 139 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 103 optimal weight: 0.0870 chunk 161 optimal weight: 40.0000 overall best weight: 2.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN A 90 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 ASN A 860 HIS B 90 ASN B 108 ASN ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN F 70 GLN F 76 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 14991 Z= 0.411 Angle : 0.632 7.072 20312 Z= 0.327 Chirality : 0.045 0.163 2207 Planarity : 0.004 0.034 2621 Dihedral : 4.842 20.144 1978 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.20), residues: 1769 helix: -0.69 (0.30), residues: 295 sheet: -1.07 (0.28), residues: 347 loop : -1.37 (0.19), residues: 1127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 95 time to evaluate : 1.904 Fit side-chains revert: symmetry clash outliers start: 52 outliers final: 21 residues processed: 139 average time/residue: 0.2261 time to fit residues: 50.8892 Evaluate side-chains 111 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 1.853 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1577 time to fit residues: 8.2291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 134 optimal weight: 0.5980 chunk 110 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 161 optimal weight: 40.0000 chunk 174 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 160 optimal weight: 40.0000 chunk 55 optimal weight: 9.9990 chunk 129 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN B 108 ASN B 143 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 14991 Z= 0.186 Angle : 0.546 7.990 20312 Z= 0.281 Chirality : 0.043 0.151 2207 Planarity : 0.003 0.033 2621 Dihedral : 4.623 20.938 1978 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer Outliers : 2.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.20), residues: 1769 helix: -0.60 (0.30), residues: 296 sheet: -0.83 (0.29), residues: 343 loop : -1.27 (0.19), residues: 1130 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 100 time to evaluate : 1.832 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 11 residues processed: 131 average time/residue: 0.2129 time to fit residues: 45.3228 Evaluate side-chains 100 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 1.829 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1359 time to fit residues: 5.1904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 40.0000 chunk 121 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 77 optimal weight: 0.0670 chunk 108 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 172 optimal weight: 7.9990 chunk 154 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 143 optimal weight: 0.0980 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 14991 Z= 0.169 Angle : 0.543 10.963 20312 Z= 0.276 Chirality : 0.043 0.151 2207 Planarity : 0.003 0.032 2621 Dihedral : 4.516 20.082 1978 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.20), residues: 1769 helix: -0.65 (0.30), residues: 304 sheet: -0.77 (0.29), residues: 343 loop : -1.21 (0.19), residues: 1122 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 105 time to evaluate : 1.861 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 123 average time/residue: 0.2149 time to fit residues: 43.4088 Evaluate side-chains 109 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 1.839 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1434 time to fit residues: 5.2970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN ** B 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.052 14991 Z= 0.487 Angle : 0.674 8.964 20312 Z= 0.343 Chirality : 0.046 0.158 2207 Planarity : 0.004 0.036 2621 Dihedral : 4.856 20.304 1978 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.31 % Favored : 91.52 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.20), residues: 1769 helix: -0.65 (0.30), residues: 294 sheet: -1.13 (0.28), residues: 359 loop : -1.34 (0.19), residues: 1116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 89 time to evaluate : 1.863 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 19 residues processed: 121 average time/residue: 0.2212 time to fit residues: 43.8964 Evaluate side-chains 101 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 1.899 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1380 time to fit residues: 7.3489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 0.0060 chunk 34 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 172 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 166 optimal weight: 0.9980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 14991 Z= 0.173 Angle : 0.555 8.954 20312 Z= 0.283 Chirality : 0.043 0.149 2207 Planarity : 0.004 0.037 2621 Dihedral : 4.606 20.130 1978 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.20), residues: 1769 helix: -0.58 (0.30), residues: 301 sheet: -0.97 (0.28), residues: 348 loop : -1.22 (0.19), residues: 1120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 1.904 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 115 average time/residue: 0.2301 time to fit residues: 43.4863 Evaluate side-chains 95 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 1.874 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1422 time to fit residues: 4.5780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 0.0970 chunk 98 optimal weight: 6.9990 chunk 125 optimal weight: 0.0470 chunk 97 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 overall best weight: 2.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 14991 Z= 0.356 Angle : 0.607 8.429 20312 Z= 0.309 Chirality : 0.045 0.155 2207 Planarity : 0.004 0.036 2621 Dihedral : 4.710 20.796 1978 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.20), residues: 1769 helix: -0.52 (0.31), residues: 294 sheet: -1.03 (0.28), residues: 353 loop : -1.31 (0.19), residues: 1122 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 85 time to evaluate : 1.723 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 101 average time/residue: 0.2260 time to fit residues: 37.7085 Evaluate side-chains 91 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 1.919 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1408 time to fit residues: 4.5233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 0.0770 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 156 optimal weight: 40.0000 chunk 164 optimal weight: 0.0470 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 14991 Z= 0.179 Angle : 0.557 11.460 20312 Z= 0.282 Chirality : 0.043 0.149 2207 Planarity : 0.004 0.040 2621 Dihedral : 4.535 20.033 1978 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.20), residues: 1769 helix: -0.40 (0.31), residues: 298 sheet: -0.93 (0.28), residues: 353 loop : -1.26 (0.19), residues: 1118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 1.889 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 105 average time/residue: 0.2770 time to fit residues: 48.7543 Evaluate side-chains 95 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 2.211 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2385 time to fit residues: 5.7503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 20.0000 chunk 159 optimal weight: 7.9990 chunk 164 optimal weight: 0.0370 chunk 96 optimal weight: 8.9990 chunk 69 optimal weight: 20.0000 chunk 125 optimal weight: 0.0470 chunk 49 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 169 optimal weight: 5.9990 overall best weight: 1.1960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 14991 Z= 0.227 Angle : 0.572 9.678 20312 Z= 0.287 Chirality : 0.044 0.175 2207 Planarity : 0.004 0.035 2621 Dihedral : 4.510 20.099 1978 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.20), residues: 1769 helix: -0.54 (0.30), residues: 303 sheet: -0.81 (0.28), residues: 344 loop : -1.25 (0.19), residues: 1122 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 1.715 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 100 average time/residue: 0.2304 time to fit residues: 37.9236 Evaluate side-chains 95 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 1.981 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1540 time to fit residues: 4.5877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 chunk 163 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 109 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 150 optimal weight: 40.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 14991 Z= 0.204 Angle : 0.558 8.788 20312 Z= 0.282 Chirality : 0.044 0.182 2207 Planarity : 0.003 0.035 2621 Dihedral : 4.502 19.635 1978 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.20), residues: 1769 helix: -0.49 (0.30), residues: 305 sheet: -0.77 (0.28), residues: 344 loop : -1.23 (0.19), residues: 1120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 1.858 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 96 average time/residue: 0.2344 time to fit residues: 36.5740 Evaluate side-chains 89 residues out of total 1651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 2.039 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1690 time to fit residues: 2.9080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 141 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 17 optimal weight: 0.0770 chunk 26 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN B 108 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.118049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.079173 restraints weight = 39301.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.081789 restraints weight = 20668.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.083425 restraints weight = 14419.380| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 14991 Z= 0.179 Angle : 0.561 10.502 20312 Z= 0.282 Chirality : 0.043 0.180 2207 Planarity : 0.003 0.034 2621 Dihedral : 4.426 19.750 1978 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.20), residues: 1769 helix: -0.49 (0.30), residues: 305 sheet: -0.69 (0.29), residues: 334 loop : -1.20 (0.19), residues: 1130 =============================================================================== Job complete usr+sys time: 2483.81 seconds wall clock time: 46 minutes 29.37 seconds (2789.37 seconds total)