Starting phenix.real_space_refine on Mon Aug 5 17:40:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8u_36962/08_2024/8k8u_36962.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8u_36962/08_2024/8k8u_36962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8u_36962/08_2024/8k8u_36962.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8u_36962/08_2024/8k8u_36962.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8u_36962/08_2024/8k8u_36962.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8u_36962/08_2024/8k8u_36962.cif" } resolution = 3.05 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= 0.002 sd= 0.109 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: 6 Type Number sf(0) Gaussians P 29 5.49 5 Mg 3 5.21 5 S 71 5.16 5 C 8860 2.51 5 N 2327 2.21 5 O 2679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 900": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 992": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 997": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1004": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 13969 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 8201 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 37, 'TRANS': 966} Chain: "B" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1772 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Chain: "C" Number of atoms: 3411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3411 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 10, 'TRANS': 407} Chain breaks: 1 Chain: "E" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 231 Classifications: {'DNA': 12} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 321 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 33 Unusual residues: {' MG': 3, 'CTP': 1} Classifications: {'undetermined': 4, 'water': 2} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.66, per 1000 atoms: 0.69 Number of scatterers: 13969 At special positions: 0 Unit cell: (102.178, 127.179, 144.571, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 71 16.00 P 29 15.00 Mg 3 11.99 O 2679 8.00 N 2327 7.00 C 8860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.61 Conformation dependent library (CDL) restraints added in 2.6 seconds 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3142 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 19 sheets defined 40.1% alpha, 22.1% beta 12 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 5.04 Creating SS restraints... Processing helix chain 'A' and resid 44 through 48 Processing helix chain 'A' and resid 108 through 117 Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 209 through 219 Processing helix chain 'A' and resid 240 through 253 Processing helix chain 'A' and resid 267 through 280 removed outlier: 3.791A pdb=" N LEU A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 380 through 390 removed outlier: 3.515A pdb=" N THR A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 448 through 473 removed outlier: 3.756A pdb=" N CYS A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.882A pdb=" N VAL A 493 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 552 through 562 removed outlier: 3.636A pdb=" N ASN A 556 " --> pdb=" O SER A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 576 through 591 removed outlier: 4.215A pdb=" N GLN A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 643 removed outlier: 4.074A pdb=" N ARG A 625 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN A 643 " --> pdb=" O LYS A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 672 removed outlier: 4.481A pdb=" N TYR A 668 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A 669 " --> pdb=" O ASN A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 703 Processing helix chain 'A' and resid 764 through 782 Processing helix chain 'A' and resid 837 through 857 Processing helix chain 'A' and resid 862 through 883 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.110A pdb=" N MET A 891 " --> pdb=" O GLU A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 918 Processing helix chain 'A' and resid 947 through 949 No H-bonds generated for 'chain 'A' and resid 947 through 949' Processing helix chain 'A' and resid 967 through 981 removed outlier: 3.812A pdb=" N TYR A 971 " --> pdb=" O PHE A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 997 Processing helix chain 'B' and resid 16 through 18 No H-bonds generated for 'chain 'B' and resid 16 through 18' Processing helix chain 'B' and resid 19 through 38 removed outlier: 4.038A pdb=" N SER B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N GLN B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLU B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N SER B 35 " --> pdb=" O ASN B 31 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N TRP B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 37 " --> pdb=" O VAL B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 50 through 55 removed outlier: 3.502A pdb=" N GLN B 55 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 101 Processing helix chain 'B' and resid 133 through 150 removed outlier: 5.955A pdb=" N LYS B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ILE B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 184 through 188 removed outlier: 3.895A pdb=" N HIS B 187 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN B 188 " --> pdb=" O ARG B 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 184 through 188' Processing helix chain 'B' and resid 193 through 205 removed outlier: 3.545A pdb=" N ASN B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 214 Processing helix chain 'C' and resid 4 through 19 removed outlier: 3.782A pdb=" N SER C 19 " --> pdb=" O SER C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 43 Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 107 through 119 removed outlier: 3.737A pdb=" N ARG C 111 " --> pdb=" O PRO C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 158 Processing helix chain 'C' and resid 177 through 187 Processing helix chain 'C' and resid 249 through 256 removed outlier: 3.749A pdb=" N LEU C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 298 Processing helix chain 'C' and resid 315 through 323 removed outlier: 3.714A pdb=" N ASN C 321 " --> pdb=" O LYS C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 341 through 351 removed outlier: 3.504A pdb=" N LYS C 345 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG C 346 " --> pdb=" O GLY C 342 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LYS C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE C 348 " --> pdb=" O VAL C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 361 removed outlier: 3.718A pdb=" N LEU C 361 " --> pdb=" O SER C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 373 Processing helix chain 'C' and resid 391 through 396 removed outlier: 3.811A pdb=" N CYS C 394 " --> pdb=" O ASN C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 406 removed outlier: 3.607A pdb=" N ASN C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 425 removed outlier: 3.770A pdb=" N PHE C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 126 removed outlier: 5.806A pdb=" N CYS A 5 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG A 23 " --> pdb=" O CYS A 5 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N CYS A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43 removed outlier: 6.478A pdb=" N SER A 84 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ARG A 64 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ALA A 86 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LYS A 62 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N MET A 88 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73 removed outlier: 6.741A pdb=" N ILE A 614 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL A 571 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE A 612 " --> pdb=" O VAL A 571 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL A 573 " --> pdb=" O SER A 610 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N SER A 610 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU A 611 " --> pdb=" O CYS A 601 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223 removed outlier: 6.544A pdb=" N LEU A 222 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N SER A 184 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA A 168 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N THR A 186 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ALA A 166 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR A 188 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N PHE A 164 " --> pdb=" O TYR A 188 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N TYR A 190 " --> pdb=" O TYR A 162 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR A 162 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU A 163 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 285 through 287 Processing sheet with id=AA6, first strand: chain 'A' and resid 299 through 305 removed outlier: 6.507A pdb=" N TYR A 300 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE A 318 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG A 302 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR A 316 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLN A 304 " --> pdb=" O ALA A 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 363 removed outlier: 6.622A pdb=" N THR A 369 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ARG A 363 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS A 416 " --> pdb=" O LYS A 408 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LYS A 408 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL A 418 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS A 404 " --> pdb=" O SER A 420 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 732 through 734 removed outlier: 3.506A pdb=" N PHE A 743 " --> pdb=" O LEU A 707 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N PHE A 756 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLY A 750 " --> pdb=" O SER A 754 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER A 754 " --> pdb=" O GLY A 750 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL A 545 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL A 794 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE A 547 " --> pdb=" O GLU A 792 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N TYR A 795 " --> pdb=" O TYR A 811 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TYR A 811 " --> pdb=" O TYR A 795 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ASN A 797 " --> pdb=" O MET A 809 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N MET A 809 " --> pdb=" O ASN A 797 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS A 805 " --> pdb=" O GLN A 801 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 892 through 895 removed outlier: 4.657A pdb=" N TYR A 929 " --> pdb=" O ILE A 954 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AB2, first strand: chain 'B' and resid 2 through 5 Processing sheet with id=AB3, first strand: chain 'B' and resid 116 through 120 removed outlier: 3.649A pdb=" N VAL B 64 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 107 through 108 Processing sheet with id=AB5, first strand: chain 'C' and resid 69 through 71 removed outlier: 3.519A pdb=" N THR C 174 " --> pdb=" O ILE C 71 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 166 through 169 removed outlier: 4.134A pdb=" N LEU C 166 " --> pdb=" O PHE C 78 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE C 78 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 95 through 97 removed outlier: 6.774A pdb=" N ARG C 128 " --> pdb=" O GLU C 139 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 214 through 227 removed outlier: 4.542A pdb=" N SER C 273 " --> pdb=" O LYS C 244 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 301 through 304 Processing sheet with id=AC1, first strand: chain 'C' and resid 375 through 380 removed outlier: 6.638A pdb=" N ARG C 376 " --> pdb=" O PHE C 387 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE C 387 " --> pdb=" O ARG C 376 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS C 378 " --> pdb=" O VAL C 385 " (cutoff:3.500A) 588 hydrogen bonds defined for protein. 1677 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 62 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 5.93 Time building geometry restraints manager: 6.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2500 1.32 - 1.44: 3767 1.44 - 1.57: 7893 1.57 - 1.69: 56 1.69 - 1.81: 108 Bond restraints: 14324 Sorted by residual: bond pdb=" N PRO C 73 " pdb=" CD PRO C 73 " ideal model delta sigma weight residual 1.473 1.422 0.051 1.40e-02 5.10e+03 1.31e+01 bond pdb=" N PRO B 44 " pdb=" CD PRO B 44 " ideal model delta sigma weight residual 1.474 1.424 0.050 1.40e-02 5.10e+03 1.29e+01 bond pdb=" C ASP C 72 " pdb=" N PRO C 73 " ideal model delta sigma weight residual 1.330 1.374 -0.044 1.25e-02 6.40e+03 1.22e+01 bond pdb=" N PRO A 555 " pdb=" CD PRO A 555 " ideal model delta sigma weight residual 1.473 1.510 -0.037 1.40e-02 5.10e+03 6.89e+00 bond pdb=" N PRO A 52 " pdb=" CD PRO A 52 " ideal model delta sigma weight residual 1.473 1.510 -0.037 1.40e-02 5.10e+03 6.85e+00 ... (remaining 14319 not shown) Histogram of bond angle deviations from ideal: 99.99 - 106.74: 494 106.74 - 113.50: 7650 113.50 - 120.26: 5797 120.26 - 127.01: 5346 127.01 - 133.77: 190 Bond angle restraints: 19477 Sorted by residual: angle pdb=" C ASP B 205 " pdb=" N ASN B 206 " pdb=" CA ASN B 206 " ideal model delta sigma weight residual 122.34 127.51 -5.17 1.39e+00 5.18e-01 1.38e+01 angle pdb=" C ILE A 623 " pdb=" CA ILE A 623 " pdb=" CB ILE A 623 " ideal model delta sigma weight residual 114.00 109.30 4.70 1.31e+00 5.83e-01 1.29e+01 angle pdb=" N GLY C 312 " pdb=" CA GLY C 312 " pdb=" C GLY C 312 " ideal model delta sigma weight residual 112.25 117.05 -4.80 1.34e+00 5.57e-01 1.28e+01 angle pdb=" C PHE A 164 " pdb=" N LEU A 165 " pdb=" CA LEU A 165 " ideal model delta sigma weight residual 122.29 116.60 5.69 1.65e+00 3.67e-01 1.19e+01 angle pdb=" N PRO C 73 " pdb=" CA PRO C 73 " pdb=" C PRO C 73 " ideal model delta sigma weight residual 111.22 115.91 -4.69 1.40e+00 5.10e-01 1.12e+01 ... (remaining 19472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.82: 8260 23.82 - 47.65: 238 47.65 - 71.47: 76 71.47 - 95.30: 6 95.30 - 119.12: 1 Dihedral angle restraints: 8581 sinusoidal: 3710 harmonic: 4871 Sorted by residual: dihedral pdb=" O3B CTP A1104 " pdb=" O3A CTP A1104 " pdb=" PB CTP A1104 " pdb=" PA CTP A1104 " ideal model delta sinusoidal sigma weight residual -39.29 79.82 -119.12 1 2.00e+01 2.50e-03 3.57e+01 dihedral pdb=" CA TYR A 188 " pdb=" C TYR A 188 " pdb=" N CYS A 189 " pdb=" CA CYS A 189 " ideal model delta harmonic sigma weight residual 180.00 160.15 19.85 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA VAL A 310 " pdb=" C VAL A 310 " pdb=" N CYS A 311 " pdb=" CA CYS A 311 " ideal model delta harmonic sigma weight residual -180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 8578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1395 0.035 - 0.070: 326 0.070 - 0.106: 245 0.106 - 0.141: 135 0.141 - 0.176: 52 Chirality restraints: 2153 Sorted by residual: chirality pdb=" CA VAL B 77 " pdb=" N VAL B 77 " pdb=" C VAL B 77 " pdb=" CB VAL B 77 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.75e-01 chirality pdb=" CA ILE C 71 " pdb=" N ILE C 71 " pdb=" C ILE C 71 " pdb=" CB ILE C 71 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.65e-01 chirality pdb=" CA VAL A 360 " pdb=" N VAL A 360 " pdb=" C VAL A 360 " pdb=" CB VAL A 360 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.45e-01 ... (remaining 2150 not shown) Planarity restraints: 2379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 708 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.11e+00 pdb=" C SER A 708 " -0.025 2.00e-02 2.50e+03 pdb=" O SER A 708 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN A 709 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 20 " -0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO B 21 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 21 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 21 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 424 " -0.022 5.00e-02 4.00e+02 3.38e-02 1.82e+00 pdb=" N PRO A 425 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 425 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 425 " -0.019 5.00e-02 4.00e+02 ... (remaining 2376 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 12 2.48 - 3.08: 9503 3.08 - 3.69: 19739 3.69 - 4.29: 31430 4.29 - 4.90: 49906 Nonbonded interactions: 110590 Sorted by model distance: nonbonded pdb=" OD2 ASP A 753 " pdb="MG MG A1101 " model vdw 1.873 2.170 nonbonded pdb=" OD2 ASP A 549 " pdb="MG MG A1102 " model vdw 1.986 2.170 nonbonded pdb=" O TYR A 550 " pdb="MG MG A1101 " model vdw 2.023 2.170 nonbonded pdb=" OD1 ASP A 549 " pdb="MG MG A1101 " model vdw 2.032 2.170 nonbonded pdb=" O HOH A1201 " pdb=" O HOH A1202 " model vdw 2.233 3.040 ... (remaining 110585 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.170 Process input model: 46.560 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.051 14324 Z= 0.575 Angle : 0.681 6.417 19477 Z= 0.434 Chirality : 0.054 0.176 2153 Planarity : 0.003 0.035 2379 Dihedral : 12.043 119.119 5439 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.51 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.19), residues: 1632 helix: -0.07 (0.19), residues: 566 sheet: 0.81 (0.26), residues: 357 loop : -0.11 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 8 HIS 0.001 0.000 HIS A 185 PHE 0.001 0.000 PHE A 548 TYR 0.001 0.000 TYR A 300 ARG 0.001 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 1.640 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: A 709 ASN cc_start: 0.7833 (m-40) cc_final: 0.7455 (p0) REVERT: A 733 VAL cc_start: 0.8096 (t) cc_final: 0.7855 (m) REVERT: A 738 PRO cc_start: 0.6644 (Cg_endo) cc_final: 0.6016 (Cg_exo) REVERT: A 815 SER cc_start: 0.8260 (m) cc_final: 0.8040 (p) REVERT: A 908 MET cc_start: 0.7463 (mtm) cc_final: 0.6959 (mmm) REVERT: A 976 THR cc_start: 0.8480 (m) cc_final: 0.8274 (p) REVERT: B 1 MET cc_start: -0.1770 (mmm) cc_final: -0.2356 (mmm) REVERT: B 43 SER cc_start: 0.6533 (m) cc_final: 0.6304 (p) REVERT: C 95 MET cc_start: 0.2033 (ttm) cc_final: 0.0520 (ttm) REVERT: C 97 GLU cc_start: 0.6778 (tt0) cc_final: 0.6527 (tt0) REVERT: C 138 MET cc_start: 0.7000 (ttp) cc_final: 0.6608 (ttp) REVERT: C 195 ILE cc_start: 0.7588 (mt) cc_final: 0.7205 (pt) REVERT: C 317 LYS cc_start: 0.8993 (mttt) cc_final: 0.8631 (mmtm) REVERT: C 347 LYS cc_start: 0.6623 (tttp) cc_final: 0.5974 (mtmt) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.3632 time to fit residues: 178.3687 Evaluate side-chains 191 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 128 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 chunk 148 optimal weight: 9.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 551 ASN A 797 ASN A 839 HIS A 915 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14324 Z= 0.200 Angle : 0.587 11.444 19477 Z= 0.315 Chirality : 0.043 0.168 2153 Planarity : 0.004 0.041 2379 Dihedral : 12.826 114.774 2114 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.21 % Favored : 97.73 % Rotamer: Outliers : 1.12 % Allowed : 6.67 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.20), residues: 1632 helix: 0.99 (0.21), residues: 572 sheet: 0.69 (0.26), residues: 383 loop : -0.20 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 470 HIS 0.005 0.001 HIS A 839 PHE 0.029 0.002 PHE A 175 TYR 0.015 0.002 TYR C 89 ARG 0.003 0.001 ARG A 894 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 209 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 CYS cc_start: 0.8633 (m) cc_final: 0.8426 (m) REVERT: A 711 MET cc_start: 0.7075 (ppp) cc_final: 0.6838 (ppp) REVERT: A 788 LYS cc_start: 0.8641 (mptt) cc_final: 0.8409 (mmtm) REVERT: A 908 MET cc_start: 0.7242 (mtm) cc_final: 0.6882 (mmm) REVERT: B 1 MET cc_start: -0.2208 (mmm) cc_final: -0.2613 (mmm) REVERT: B 43 SER cc_start: 0.6635 (m) cc_final: 0.6321 (p) REVERT: C 152 PHE cc_start: 0.4207 (m-10) cc_final: 0.3976 (m-10) REVERT: C 317 LYS cc_start: 0.8947 (mttt) cc_final: 0.8744 (mmtm) REVERT: C 347 LYS cc_start: 0.6559 (tttp) cc_final: 0.5959 (mtmm) outliers start: 17 outliers final: 8 residues processed: 218 average time/residue: 0.2681 time to fit residues: 85.2220 Evaluate side-chains 167 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 159 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 226 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 132 optimal weight: 0.7980 chunk 147 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN A 825 ASN A 915 ASN C 134 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 14324 Z= 0.373 Angle : 0.680 12.607 19477 Z= 0.359 Chirality : 0.046 0.235 2153 Planarity : 0.005 0.067 2379 Dihedral : 13.315 111.543 2114 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.31 % Favored : 96.63 % Rotamer: Outliers : 2.38 % Allowed : 8.38 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.20), residues: 1632 helix: 0.70 (0.21), residues: 591 sheet: 0.38 (0.26), residues: 384 loop : -0.74 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 470 HIS 0.007 0.002 HIS A 36 PHE 0.022 0.002 PHE A 838 TYR 0.031 0.003 TYR A 37 ARG 0.005 0.001 ARG A 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 178 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8486 (p) REVERT: A 407 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7431 (mtm180) REVERT: A 428 ILE cc_start: 0.7668 (OUTLIER) cc_final: 0.7440 (tp) REVERT: A 604 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8560 (ttm170) REVERT: A 788 LYS cc_start: 0.8617 (mptt) cc_final: 0.8192 (mmtt) REVERT: A 908 MET cc_start: 0.7445 (mtm) cc_final: 0.6986 (mmm) REVERT: B 1 MET cc_start: -0.2238 (mmm) cc_final: -0.2668 (mmm) REVERT: B 43 SER cc_start: 0.6822 (m) cc_final: 0.6455 (p) REVERT: C 347 LYS cc_start: 0.6799 (tttp) cc_final: 0.6025 (ptpt) REVERT: C 384 VAL cc_start: 0.7072 (t) cc_final: 0.6395 (m) outliers start: 36 outliers final: 20 residues processed: 197 average time/residue: 0.2676 time to fit residues: 76.8958 Evaluate side-chains 172 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 148 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 407 ARG Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 309 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 40.0000 chunk 112 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 71 optimal weight: 0.0980 chunk 100 optimal weight: 40.0000 chunk 149 optimal weight: 6.9990 chunk 158 optimal weight: 7.9990 chunk 78 optimal weight: 0.5980 chunk 141 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 225 GLN A 915 ASN A 917 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14324 Z= 0.189 Angle : 0.535 8.825 19477 Z= 0.287 Chirality : 0.042 0.234 2153 Planarity : 0.004 0.045 2379 Dihedral : 12.759 102.884 2114 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.12 % Favored : 96.81 % Rotamer: Outliers : 2.11 % Allowed : 9.77 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.20), residues: 1632 helix: 1.11 (0.21), residues: 588 sheet: 0.34 (0.26), residues: 377 loop : -0.68 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 470 HIS 0.003 0.001 HIS A 36 PHE 0.022 0.001 PHE A 838 TYR 0.012 0.001 TYR A 637 ARG 0.003 0.000 ARG A 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 166 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7245 (ttt) cc_final: 0.6606 (ttt) REVERT: A 261 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8523 (p) REVERT: A 711 MET cc_start: 0.7008 (ppp) cc_final: 0.6504 (ppp) REVERT: A 734 LYS cc_start: 0.8219 (tptt) cc_final: 0.8019 (tptm) REVERT: A 788 LYS cc_start: 0.8631 (mptt) cc_final: 0.8204 (mmtt) REVERT: A 908 MET cc_start: 0.7298 (mtm) cc_final: 0.6892 (mmm) REVERT: B 1 MET cc_start: -0.2205 (mmm) cc_final: -0.2660 (mmm) REVERT: B 43 SER cc_start: 0.6697 (m) cc_final: 0.6257 (p) REVERT: C 347 LYS cc_start: 0.6791 (tttp) cc_final: 0.5933 (ptpp) REVERT: C 384 VAL cc_start: 0.6938 (t) cc_final: 0.6316 (m) outliers start: 32 outliers final: 18 residues processed: 178 average time/residue: 0.2134 time to fit residues: 57.4036 Evaluate side-chains 164 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 226 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 118 optimal weight: 0.0770 chunk 65 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 142 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 915 ASN B 147 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14324 Z= 0.246 Angle : 0.557 6.648 19477 Z= 0.297 Chirality : 0.043 0.229 2153 Planarity : 0.004 0.044 2379 Dihedral : 12.742 98.082 2114 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.68 % Favored : 96.26 % Rotamer: Outliers : 2.24 % Allowed : 10.50 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.20), residues: 1632 helix: 1.07 (0.21), residues: 597 sheet: 0.17 (0.26), residues: 387 loop : -0.76 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 470 HIS 0.005 0.001 HIS A 36 PHE 0.022 0.002 PHE A 838 TYR 0.017 0.002 TYR A 37 ARG 0.003 0.000 ARG A 727 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 148 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8760 (mp10) REVERT: A 261 THR cc_start: 0.8799 (OUTLIER) cc_final: 0.8518 (p) REVERT: A 428 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7313 (tp) REVERT: A 777 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8088 (mt) REVERT: A 788 LYS cc_start: 0.8675 (mptt) cc_final: 0.8242 (mmtt) REVERT: A 908 MET cc_start: 0.7245 (mtm) cc_final: 0.6818 (mmm) REVERT: B 1 MET cc_start: -0.2256 (mmm) cc_final: -0.2762 (mmm) REVERT: B 43 SER cc_start: 0.6755 (m) cc_final: 0.6342 (p) REVERT: C 87 PHE cc_start: 0.7402 (m-10) cc_final: 0.6920 (m-10) REVERT: C 347 LYS cc_start: 0.6708 (tttp) cc_final: 0.5971 (ptpt) REVERT: C 384 VAL cc_start: 0.6956 (t) cc_final: 0.6321 (m) outliers start: 34 outliers final: 21 residues processed: 167 average time/residue: 0.2623 time to fit residues: 65.1842 Evaluate side-chains 165 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 226 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 1.9990 chunk 142 optimal weight: 40.0000 chunk 31 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 52 optimal weight: 0.0670 chunk 83 optimal weight: 3.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 252 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14324 Z= 0.242 Angle : 0.548 6.351 19477 Z= 0.293 Chirality : 0.043 0.270 2153 Planarity : 0.004 0.043 2379 Dihedral : 12.661 95.788 2114 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.31 % Favored : 96.63 % Rotamer: Outliers : 2.38 % Allowed : 10.23 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.20), residues: 1632 helix: 1.12 (0.22), residues: 596 sheet: 0.04 (0.26), residues: 387 loop : -0.80 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 470 HIS 0.004 0.001 HIS A 36 PHE 0.032 0.002 PHE A 175 TYR 0.015 0.002 TYR A 37 ARG 0.003 0.000 ARG A 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 143 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7288 (ttt) cc_final: 0.6508 (ttt) REVERT: A 261 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8501 (p) REVERT: A 428 ILE cc_start: 0.7625 (OUTLIER) cc_final: 0.7344 (tp) REVERT: A 566 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8437 (pm20) REVERT: A 788 LYS cc_start: 0.8678 (mptt) cc_final: 0.8271 (mmtt) REVERT: A 908 MET cc_start: 0.7114 (mtm) cc_final: 0.6783 (mmm) REVERT: B 1 MET cc_start: -0.2242 (mmm) cc_final: -0.2774 (mmm) REVERT: B 23 MET cc_start: -0.0268 (mmm) cc_final: -0.0675 (mmt) REVERT: C 87 PHE cc_start: 0.7417 (m-10) cc_final: 0.6859 (m-10) REVERT: C 252 HIS cc_start: 0.4967 (OUTLIER) cc_final: 0.4721 (t-170) REVERT: C 347 LYS cc_start: 0.6671 (tttp) cc_final: 0.5931 (ptpt) REVERT: C 384 VAL cc_start: 0.6994 (t) cc_final: 0.6363 (m) outliers start: 36 outliers final: 25 residues processed: 163 average time/residue: 0.2658 time to fit residues: 64.1674 Evaluate side-chains 167 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 138 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 252 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 3.9990 chunk 17 optimal weight: 0.0570 chunk 90 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 88 optimal weight: 0.0170 chunk 158 optimal weight: 0.6980 chunk 98 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 ASN C 318 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14324 Z= 0.288 Angle : 0.586 15.531 19477 Z= 0.309 Chirality : 0.044 0.282 2153 Planarity : 0.004 0.044 2379 Dihedral : 12.725 93.584 2114 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.11 % Favored : 95.83 % Rotamer: Outliers : 2.31 % Allowed : 10.03 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.20), residues: 1632 helix: 1.02 (0.22), residues: 595 sheet: -0.07 (0.26), residues: 387 loop : -0.90 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 470 HIS 0.015 0.002 HIS C 252 PHE 0.029 0.002 PHE A 175 TYR 0.020 0.002 TYR B 121 ARG 0.005 0.000 ARG C 255 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 143 time to evaluate : 2.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8567 (p) REVERT: A 428 ILE cc_start: 0.7665 (OUTLIER) cc_final: 0.7388 (tp) REVERT: A 566 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8426 (pm20) REVERT: A 788 LYS cc_start: 0.8658 (mptt) cc_final: 0.8238 (mmtt) REVERT: A 908 MET cc_start: 0.7104 (mtm) cc_final: 0.6749 (mmm) REVERT: B 1 MET cc_start: -0.2008 (mmm) cc_final: -0.2590 (mmm) REVERT: C 87 PHE cc_start: 0.7408 (m-10) cc_final: 0.6822 (m-10) REVERT: C 347 LYS cc_start: 0.6692 (tttp) cc_final: 0.5967 (ptpt) REVERT: C 384 VAL cc_start: 0.6973 (t) cc_final: 0.6341 (m) outliers start: 35 outliers final: 26 residues processed: 159 average time/residue: 0.2718 time to fit residues: 64.1601 Evaluate side-chains 162 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 318 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 100 optimal weight: 0.0030 chunk 107 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 896 HIS A 915 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14324 Z= 0.165 Angle : 0.526 15.103 19477 Z= 0.279 Chirality : 0.042 0.245 2153 Planarity : 0.004 0.043 2379 Dihedral : 12.439 91.207 2114 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.62 % Favored : 96.32 % Rotamer: Outliers : 2.11 % Allowed : 10.43 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.21), residues: 1632 helix: 1.30 (0.22), residues: 589 sheet: 0.01 (0.26), residues: 387 loop : -0.79 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 470 HIS 0.002 0.001 HIS A 36 PHE 0.023 0.001 PHE A 838 TYR 0.015 0.001 TYR A 749 ARG 0.005 0.000 ARG A 636 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 144 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8524 (p) REVERT: A 428 ILE cc_start: 0.7604 (OUTLIER) cc_final: 0.7313 (tp) REVERT: A 788 LYS cc_start: 0.8625 (mptt) cc_final: 0.8153 (mmtt) REVERT: A 908 MET cc_start: 0.7033 (mtm) cc_final: 0.6770 (mmm) REVERT: B 1 MET cc_start: -0.2036 (mmm) cc_final: -0.2619 (mmm) REVERT: C 87 PHE cc_start: 0.7391 (m-10) cc_final: 0.6851 (m-10) REVERT: C 89 TYR cc_start: 0.3746 (t80) cc_final: 0.3471 (t80) REVERT: C 347 LYS cc_start: 0.6664 (tttp) cc_final: 0.5953 (ptpt) REVERT: C 384 VAL cc_start: 0.6989 (t) cc_final: 0.6395 (m) outliers start: 32 outliers final: 23 residues processed: 159 average time/residue: 0.2656 time to fit residues: 62.7624 Evaluate side-chains 165 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 226 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 6.9990 chunk 151 optimal weight: 20.0000 chunk 138 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 chunk 88 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 133 optimal weight: 40.0000 chunk 139 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 ASN B 181 HIS C 393 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 14324 Z= 0.490 Angle : 0.714 14.089 19477 Z= 0.376 Chirality : 0.048 0.357 2153 Planarity : 0.005 0.055 2379 Dihedral : 13.270 97.010 2114 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.78 % Favored : 95.16 % Rotamer: Outliers : 2.05 % Allowed : 10.83 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.20), residues: 1632 helix: 0.63 (0.21), residues: 590 sheet: -0.26 (0.26), residues: 388 loop : -1.18 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 470 HIS 0.005 0.002 HIS A 265 PHE 0.023 0.002 PHE A 838 TYR 0.042 0.003 TYR B 121 ARG 0.010 0.001 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 147 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7430 (ttt) cc_final: 0.6984 (ttt) REVERT: A 428 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7536 (tp) REVERT: A 566 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8468 (pm20) REVERT: A 788 LYS cc_start: 0.8715 (mptt) cc_final: 0.8357 (mmtt) REVERT: A 908 MET cc_start: 0.7235 (mtm) cc_final: 0.6781 (mmm) REVERT: B 1 MET cc_start: -0.2012 (mmm) cc_final: -0.2642 (mmm) REVERT: C 87 PHE cc_start: 0.7297 (m-10) cc_final: 0.6713 (m-10) REVERT: C 89 TYR cc_start: 0.3903 (t80) cc_final: 0.3231 (t80) REVERT: C 95 MET cc_start: 0.3438 (ttm) cc_final: 0.2936 (ttm) REVERT: C 347 LYS cc_start: 0.6716 (tttp) cc_final: 0.6010 (ptpt) outliers start: 31 outliers final: 25 residues processed: 161 average time/residue: 0.2482 time to fit residues: 58.1252 Evaluate side-chains 167 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 140 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 179 PHE Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 226 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 108 optimal weight: 0.0170 chunk 163 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 130 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 79 optimal weight: 0.4980 overall best weight: 0.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.5544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14324 Z= 0.187 Angle : 0.555 15.120 19477 Z= 0.295 Chirality : 0.043 0.267 2153 Planarity : 0.004 0.046 2379 Dihedral : 12.570 91.217 2114 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.62 % Favored : 96.32 % Rotamer: Outliers : 1.58 % Allowed : 11.62 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.21), residues: 1632 helix: 1.13 (0.22), residues: 586 sheet: -0.11 (0.27), residues: 372 loop : -0.95 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 137 HIS 0.005 0.001 HIS B 181 PHE 0.023 0.001 PHE A 838 TYR 0.018 0.001 TYR B 121 ARG 0.011 0.000 ARG C 186 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 146 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7297 (ttt) cc_final: 0.6855 (ttt) REVERT: A 261 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8399 (p) REVERT: A 428 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7365 (tp) REVERT: A 788 LYS cc_start: 0.8709 (mptt) cc_final: 0.8361 (mmtt) REVERT: A 908 MET cc_start: 0.7093 (mtm) cc_final: 0.6794 (mmm) REVERT: B 1 MET cc_start: -0.2129 (mmm) cc_final: -0.2690 (mmm) REVERT: C 87 PHE cc_start: 0.7256 (m-10) cc_final: 0.6691 (m-10) REVERT: C 89 TYR cc_start: 0.3792 (t80) cc_final: 0.3139 (t80) REVERT: C 95 MET cc_start: 0.3433 (ttm) cc_final: 0.2900 (ttm) REVERT: C 347 LYS cc_start: 0.6668 (tttp) cc_final: 0.6049 (pttt) REVERT: C 384 VAL cc_start: 0.6965 (t) cc_final: 0.6368 (m) outliers start: 24 outliers final: 18 residues processed: 158 average time/residue: 0.2942 time to fit residues: 68.4615 Evaluate side-chains 160 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 140 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 226 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 4.9990 chunk 138 optimal weight: 40.0000 chunk 39 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 133 optimal weight: 30.0000 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 ASN C 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.230024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.179579 restraints weight = 16947.085| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 2.24 r_work: 0.3526 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.5619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14324 Z= 0.236 Angle : 0.569 14.469 19477 Z= 0.302 Chirality : 0.043 0.222 2153 Planarity : 0.004 0.046 2379 Dihedral : 12.637 89.851 2114 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.80 % Favored : 96.14 % Rotamer: Outliers : 1.72 % Allowed : 11.68 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.21), residues: 1632 helix: 1.18 (0.22), residues: 587 sheet: -0.19 (0.26), residues: 387 loop : -0.92 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 470 HIS 0.005 0.001 HIS B 181 PHE 0.024 0.001 PHE A 838 TYR 0.018 0.002 TYR B 121 ARG 0.010 0.000 ARG C 186 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3019.70 seconds wall clock time: 59 minutes 24.22 seconds (3564.22 seconds total)