Starting phenix.real_space_refine on Tue Apr 9 09:39:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9p_36114/04_2024/8j9p_36114.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9p_36114/04_2024/8j9p_36114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9p_36114/04_2024/8j9p_36114.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9p_36114/04_2024/8j9p_36114.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9p_36114/04_2024/8j9p_36114.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9p_36114/04_2024/8j9p_36114.pdb" } resolution = 3.4 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= -0.000 sd= 0.016 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 83 5.49 5 Mg 2 5.21 5 S 44 5.16 5 C 10089 2.51 5 N 2705 2.21 5 O 3090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 309": "OD1" <-> "OD2" Residue "A TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 369": "OE1" <-> "OE2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "B ASP 14": "OD1" <-> "OD2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B ASP 100": "OD1" <-> "OD2" Residue "B TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 334": "OE1" <-> "OE2" Residue "C GLU 369": "OE1" <-> "OE2" Residue "D PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 13": "OE1" <-> "OE2" Residue "D ASP 100": "OD1" <-> "OD2" Residue "D GLU 111": "OE1" <-> "OE2" Residue "D PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 16013 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3618 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 25, 'TRANS': 422} Chain breaks: 1 Chain: "B" Number of atoms: 3529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3529 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 407} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 422 Classifications: {'DNA': 13, 'RNA': 8} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 20} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "F" Number of atoms: 432 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 21, 432 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "C" Number of atoms: 3646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3646 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 25, 'TRANS': 425} Chain breaks: 1 Chain: "D" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3531 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 14, 'TRANS': 407} Chain: "G" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 422 Classifications: {'DNA': 13, 'RNA': 8} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 20} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "H" Number of atoms: 411 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.85, per 1000 atoms: 0.49 Number of scatterers: 16013 At special positions: 0 Unit cell: (113.4, 168, 137.55, 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 44 16.00 P 83 15.00 Mg 2 11.99 O 3090 8.00 N 2705 7.00 C 10089 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: 6.27 Conformation dependent library (CDL) restraints added in 2.4 seconds 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3310 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 23 sheets defined 34.9% alpha, 14.3% beta 26 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 5.18 Creating SS restraints... Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 22 through 30 Processing helix chain 'A' and resid 46 through 61 removed outlier: 3.978A pdb=" N GLN A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 102 through 107 removed outlier: 3.583A pdb=" N ASN A 107 " --> pdb=" O TYR A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 132 removed outlier: 3.548A pdb=" N PHE A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 214 removed outlier: 3.670A pdb=" N LYS A 211 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 248 through 264 removed outlier: 3.547A pdb=" N ALA A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.501A pdb=" N TYR A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 375 Processing helix chain 'A' and resid 451 through 462 Processing helix chain 'A' and resid 477 through 492 removed outlier: 3.606A pdb=" N ARG A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU A 488 " --> pdb=" O ASN A 484 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 507 removed outlier: 4.006A pdb=" N TYR A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 29 Processing helix chain 'B' and resid 44 through 56 removed outlier: 3.578A pdb=" N THR B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 89 removed outlier: 3.647A pdb=" N HIS B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN B 89 " --> pdb=" O LYS B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 139 Processing helix chain 'B' and resid 151 through 156 removed outlier: 3.945A pdb=" N GLN B 155 " --> pdb=" O ASN B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 203 removed outlier: 3.582A pdb=" N THR B 202 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 224 removed outlier: 3.548A pdb=" N ASP B 222 " --> pdb=" O TRP B 219 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE B 223 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 248 Processing helix chain 'B' and resid 257 through 278 Processing helix chain 'B' and resid 300 through 304 removed outlier: 3.668A pdb=" N ASP B 303 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 366 Processing helix chain 'B' and resid 369 through 384 Processing helix chain 'C' and resid 15 through 17 No H-bonds generated for 'chain 'C' and resid 15 through 17' Processing helix chain 'C' and resid 22 through 30 Processing helix chain 'C' and resid 46 through 60 Processing helix chain 'C' and resid 77 through 82 Processing helix chain 'C' and resid 100 through 108 removed outlier: 3.759A pdb=" N TYR C 104 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N PHE C 106 " --> pdb=" O ARG C 103 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA C 108 " --> pdb=" O LEU C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 132 removed outlier: 3.722A pdb=" N ARG C 113 " --> pdb=" O SER C 109 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE C 121 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 214 Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 248 through 265 removed outlier: 3.522A pdb=" N GLY C 265 " --> pdb=" O TYR C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 351 removed outlier: 4.062A pdb=" N LYS C 336 " --> pdb=" O PRO C 332 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA C 337 " --> pdb=" O LYS C 333 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR C 346 " --> pdb=" O ALA C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 375 removed outlier: 3.620A pdb=" N TRP C 370 " --> pdb=" O ASN C 366 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE C 373 " --> pdb=" O GLU C 369 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN C 374 " --> pdb=" O TRP C 370 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU C 375 " --> pdb=" O ASN C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 462 Processing helix chain 'C' and resid 463 through 465 No H-bonds generated for 'chain 'C' and resid 463 through 465' Processing helix chain 'C' and resid 477 through 493 removed outlier: 4.071A pdb=" N ALA C 483 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN C 484 " --> pdb=" O LEU C 480 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU C 488 " --> pdb=" O ASN C 484 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE C 489 " --> pdb=" O LYS C 485 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER C 493 " --> pdb=" O ILE C 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 removed outlier: 3.699A pdb=" N LEU D 21 " --> pdb=" O PHE D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 52 Processing helix chain 'D' and resid 65 through 69 removed outlier: 3.923A pdb=" N GLY D 68 " --> pdb=" O SER D 65 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASN D 69 " --> pdb=" O THR D 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 65 through 69' Processing helix chain 'D' and resid 71 through 89 removed outlier: 3.845A pdb=" N LEU D 75 " --> pdb=" O ARG D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 115 removed outlier: 3.564A pdb=" N ARG D 114 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU D 115 " --> pdb=" O ILE D 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 111 through 115' Processing helix chain 'D' and resid 123 through 138 removed outlier: 3.511A pdb=" N GLY D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 158 removed outlier: 4.074A pdb=" N SER D 150 " --> pdb=" O ASP D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 248 Processing helix chain 'D' and resid 257 through 277 removed outlier: 3.731A pdb=" N CYS D 261 " --> pdb=" O ARG D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 300 through 304 Processing helix chain 'D' and resid 353 through 366 Processing helix chain 'D' and resid 369 through 385 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6 removed outlier: 5.429A pdb=" N ILE A 443 " --> pdb=" O THR A 389 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THR A 389 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ILE A 445 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR A 387 " --> pdb=" O ILE A 445 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS A 447 " --> pdb=" O GLY A 385 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 384 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N CYS A 279 " --> pdb=" O PHE A 358 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N HIS A 360 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU A 281 " --> pdb=" O HIS A 360 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 13 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 95 removed outlier: 3.634A pdb=" N LYS A 94 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY A 45 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLY A 42 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ILE A 142 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 44 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 284 through 285 removed outlier: 3.766A pdb=" N VAL A 284 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 300 " --> pdb=" O VAL A 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 303 through 306 Processing sheet with id=AA6, first strand: chain 'A' and resid 397 through 398 Processing sheet with id=AA7, first strand: chain 'A' and resid 425 through 426 removed outlier: 3.563A pdb=" N SER A 431 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 63 through 64 removed outlier: 3.842A pdb=" N ALA B 98 " --> pdb=" O ILE B 118 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 175 through 177 Processing sheet with id=AB1, first strand: chain 'B' and resid 175 through 177 Processing sheet with id=AB2, first strand: chain 'B' and resid 207 through 210 Processing sheet with id=AB3, first strand: chain 'B' and resid 390 through 394 Processing sheet with id=AB4, first strand: chain 'C' and resid 5 through 6 removed outlier: 6.875A pdb=" N GLY C 385 " --> pdb=" O ASN C 446 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE C 358 " --> pdb=" O CYS C 279 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 12 through 13 Processing sheet with id=AB6, first strand: chain 'C' and resid 91 through 95 removed outlier: 3.610A pdb=" N LYS C 94 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY C 45 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY C 42 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ILE C 142 " --> pdb=" O GLY C 42 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL C 44 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N TRP C 139 " --> pdb=" O GLN C 222 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU C 224 " --> pdb=" O TRP C 139 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL C 141 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 300 through 306 Processing sheet with id=AB8, first strand: chain 'C' and resid 397 through 398 removed outlier: 4.678A pdb=" N GLU D 169 " --> pdb=" O GLY D 412 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY D 412 " --> pdb=" O GLU D 169 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 425 through 426 Processing sheet with id=AC1, first strand: chain 'D' and resid 63 through 64 Processing sheet with id=AC2, first strand: chain 'D' and resid 214 through 216 Processing sheet with id=AC3, first strand: chain 'D' and resid 283 through 285 Processing sheet with id=AC4, first strand: chain 'D' and resid 311 through 314 Processing sheet with id=AC5, first strand: chain 'D' and resid 390 through 394 517 hydrogen bonds defined for protein. 1443 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 5.33 Time building geometry restraints manager: 6.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4149 1.33 - 1.45: 3466 1.45 - 1.57: 8732 1.57 - 1.69: 162 1.69 - 1.81: 68 Bond restraints: 16577 Sorted by residual: bond pdb=" CB LYS A 59 " pdb=" CG LYS A 59 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.45e+00 bond pdb=" CB LYS A 62 " pdb=" CG LYS A 62 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.55e+00 bond pdb=" CB ARG D 193 " pdb=" CG ARG D 193 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.47e+00 bond pdb=" C TYR D 330 " pdb=" N PRO D 331 " ideal model delta sigma weight residual 1.336 1.350 -0.014 1.20e-02 6.94e+03 1.35e+00 bond pdb=" CG LYS A 62 " pdb=" CD LYS A 62 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.34e+00 ... (remaining 16572 not shown) Histogram of bond angle deviations from ideal: 98.89 - 105.96: 730 105.96 - 113.04: 8811 113.04 - 120.11: 6006 120.11 - 127.19: 6877 127.19 - 134.26: 320 Bond angle restraints: 22744 Sorted by residual: angle pdb=" CB LYS A 59 " pdb=" CG LYS A 59 " pdb=" CD LYS A 59 " ideal model delta sigma weight residual 111.30 120.39 -9.09 2.30e+00 1.89e-01 1.56e+01 angle pdb=" CA LYS A 59 " pdb=" CB LYS A 59 " pdb=" CG LYS A 59 " ideal model delta sigma weight residual 114.10 121.55 -7.45 2.00e+00 2.50e-01 1.39e+01 angle pdb=" CB LYS A 62 " pdb=" CG LYS A 62 " pdb=" CD LYS A 62 " ideal model delta sigma weight residual 111.30 119.84 -8.54 2.30e+00 1.89e-01 1.38e+01 angle pdb=" CA LYS D 59 " pdb=" CB LYS D 59 " pdb=" CG LYS D 59 " ideal model delta sigma weight residual 114.10 121.51 -7.41 2.00e+00 2.50e-01 1.37e+01 angle pdb=" N LEU B 310 " pdb=" CA LEU B 310 " pdb=" C LEU B 310 " ideal model delta sigma weight residual 114.56 110.17 4.39 1.27e+00 6.20e-01 1.19e+01 ... (remaining 22739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.16: 8974 29.16 - 58.31: 783 58.31 - 87.47: 68 87.47 - 116.62: 0 116.62 - 145.78: 6 Dihedral angle restraints: 9831 sinusoidal: 4709 harmonic: 5122 Sorted by residual: dihedral pdb=" CA ARG D 193 " pdb=" C ARG D 193 " pdb=" N LEU D 194 " pdb=" CA LEU D 194 " ideal model delta harmonic sigma weight residual 180.00 -156.35 -23.65 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA ARG B 189 " pdb=" C ARG B 189 " pdb=" N TYR B 190 " pdb=" CA TYR B 190 " ideal model delta harmonic sigma weight residual 180.00 159.46 20.54 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA TYR A 328 " pdb=" C TYR A 328 " pdb=" N HIS A 329 " pdb=" CA HIS A 329 " ideal model delta harmonic sigma weight residual 180.00 -159.63 -20.37 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 9828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2070 0.058 - 0.115: 345 0.115 - 0.173: 35 0.173 - 0.230: 3 0.230 - 0.288: 3 Chirality restraints: 2456 Sorted by residual: chirality pdb=" CG LEU D 227 " pdb=" CB LEU D 227 " pdb=" CD1 LEU D 227 " pdb=" CD2 LEU D 227 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C1' U E 1 " pdb=" O4' U E 1 " pdb=" C2' U E 1 " pdb=" N1 U E 1 " both_signs ideal model delta sigma weight residual False 2.46 2.19 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C1' U E 15 " pdb=" O4' U E 15 " pdb=" C2' U E 15 " pdb=" N1 U E 15 " both_signs ideal model delta sigma weight residual False 2.46 2.22 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 2453 not shown) Planarity restraints: 2595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 318 " -0.039 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO C 319 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 319 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 319 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 193 " 0.153 9.50e-02 1.11e+02 6.91e-02 3.54e+00 pdb=" NE ARG D 193 " -0.004 2.00e-02 2.50e+03 pdb=" CZ ARG D 193 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG D 193 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 193 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC F 4 " 0.001 2.00e-02 2.50e+03 1.25e-02 3.51e+00 pdb=" N1 DC F 4 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DC F 4 " 0.029 2.00e-02 2.50e+03 pdb=" O2 DC F 4 " -0.017 2.00e-02 2.50e+03 pdb=" N3 DC F 4 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DC F 4 " 0.011 2.00e-02 2.50e+03 pdb=" N4 DC F 4 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DC F 4 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DC F 4 " -0.005 2.00e-02 2.50e+03 ... (remaining 2592 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 188 2.60 - 3.17: 13089 3.17 - 3.75: 24642 3.75 - 4.32: 31554 4.32 - 4.90: 51641 Nonbonded interactions: 121114 Sorted by model distance: nonbonded pdb=" OP3 U G 1 " pdb="MG MG G 101 " model vdw 2.020 2.170 nonbonded pdb=" OP1 A G 3 " pdb="MG MG G 101 " model vdw 2.089 2.170 nonbonded pdb=" NE2 GLN A 302 " pdb=" O THR A 479 " model vdw 2.150 2.520 nonbonded pdb=" O4 U E 21 " pdb=" N7 DA F 3 " model vdw 2.154 2.496 nonbonded pdb=" OD1 ASN A 307 " pdb=" N GLY A 308 " model vdw 2.162 2.520 ... (remaining 121109 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 507) selection = (chain 'C' and (resid 1 through 144 or resid 204 through 507)) } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 1 through 421 or (resid 422 and (name N or name CA or name \ C or name O or name CB )))) } ncs_group { reference = chain 'E' selection = (chain 'G' and resid 1 through 21) } ncs_group { reference = (chain 'F' and resid 4 through 23) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.95 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 12.490 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 45.030 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16577 Z= 0.166 Angle : 0.623 9.528 22744 Z= 0.323 Chirality : 0.044 0.288 2456 Planarity : 0.004 0.069 2595 Dihedral : 19.679 145.777 6521 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.26 % Allowed : 32.07 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.20), residues: 1731 helix: 0.74 (0.23), residues: 550 sheet: -0.58 (0.32), residues: 307 loop : -2.56 (0.18), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 20 HIS 0.002 0.001 HIS D 320 PHE 0.016 0.001 PHE D 273 TYR 0.019 0.001 TYR C 104 ARG 0.014 0.000 ARG D 193 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 time to evaluate : 1.825 Fit side-chains REVERT: A 307 ASN cc_start: 0.7561 (t0) cc_final: 0.7329 (t0) REVERT: C 247 LYS cc_start: 0.8419 (mptt) cc_final: 0.7995 (mmtt) REVERT: D 219 TRP cc_start: 0.8151 (m100) cc_final: 0.7476 (m100) outliers start: 4 outliers final: 3 residues processed: 113 average time/residue: 0.2804 time to fit residues: 48.7117 Evaluate side-chains 105 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain B residue 156 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 141 optimal weight: 0.0980 chunk 54 optimal weight: 20.0000 chunk 86 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN A 296 ASN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS C 205 GLN C 295 GLN C 296 ASN ** C 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 405 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16577 Z= 0.187 Angle : 0.575 8.661 22744 Z= 0.297 Chirality : 0.043 0.292 2456 Planarity : 0.004 0.051 2595 Dihedral : 16.923 151.439 2904 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.34 % Allowed : 30.14 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.20), residues: 1731 helix: 0.73 (0.23), residues: 556 sheet: -0.57 (0.31), residues: 326 loop : -2.58 (0.19), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 124 HIS 0.004 0.001 HIS C 207 PHE 0.017 0.001 PHE D 273 TYR 0.017 0.001 TYR D 213 ARG 0.006 0.000 ARG D 193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 103 time to evaluate : 1.714 Fit side-chains revert: symmetry clash REVERT: A 275 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7612 (mtm-85) REVERT: A 307 ASN cc_start: 0.7877 (t0) cc_final: 0.7538 (t0) REVERT: A 373 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.8505 (m-10) REVERT: A 462 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9033 (tt) REVERT: C 111 HIS cc_start: 0.9065 (OUTLIER) cc_final: 0.8763 (p-80) REVERT: C 283 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9091 (mt) REVERT: C 369 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8836 (pt0) REVERT: C 388 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.9035 (mp) REVERT: C 488 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8118 (pm20) REVERT: D 60 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.6997 (t80) REVERT: D 219 TRP cc_start: 0.8133 (m100) cc_final: 0.7394 (m100) REVERT: D 354 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7847 (mmtp) outliers start: 52 outliers final: 22 residues processed: 148 average time/residue: 0.2748 time to fit residues: 61.5519 Evaluate side-chains 127 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 95 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 217 PHE Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 418 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 91 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 chunk 136 optimal weight: 7.9990 chunk 111 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 chunk 164 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 146 optimal weight: 0.0970 chunk 163 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 251 HIS A 296 ASN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS ** C 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16577 Z= 0.161 Angle : 0.564 8.192 22744 Z= 0.289 Chirality : 0.042 0.277 2456 Planarity : 0.003 0.045 2595 Dihedral : 16.798 152.511 2897 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 4.24 % Allowed : 29.11 % Favored : 66.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.20), residues: 1731 helix: 0.77 (0.23), residues: 557 sheet: -0.66 (0.30), residues: 335 loop : -2.56 (0.19), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 124 HIS 0.008 0.001 HIS C 111 PHE 0.013 0.001 PHE D 273 TYR 0.015 0.001 TYR D 213 ARG 0.004 0.000 ARG D 193 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 98 time to evaluate : 1.742 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8294 (OUTLIER) cc_final: 0.5941 (p90) REVERT: A 275 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7554 (mtm-85) REVERT: A 307 ASN cc_start: 0.7986 (t0) cc_final: 0.7617 (t0) REVERT: A 373 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8543 (m-10) REVERT: B 217 PHE cc_start: 0.9123 (OUTLIER) cc_final: 0.8149 (t80) REVERT: B 296 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8058 (tp30) REVERT: C 369 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8823 (pt0) REVERT: C 432 THR cc_start: 0.8069 (OUTLIER) cc_final: 0.7633 (t) REVERT: C 488 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8119 (pm20) REVERT: C 501 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9065 (pp) REVERT: D 60 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.7007 (t80) REVERT: D 219 TRP cc_start: 0.8160 (m100) cc_final: 0.7436 (m100) REVERT: D 354 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7824 (mmtp) outliers start: 66 outliers final: 35 residues processed: 153 average time/residue: 0.2884 time to fit residues: 66.6312 Evaluate side-chains 142 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 96 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 217 PHE Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 418 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 162 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS ** C 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 382 ASN C 430 GLN D 340 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 16577 Z= 0.401 Angle : 0.684 9.826 22744 Z= 0.355 Chirality : 0.047 0.403 2456 Planarity : 0.004 0.043 2595 Dihedral : 17.063 156.145 2897 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.53 % Favored : 90.41 % Rotamer: Outliers : 6.88 % Allowed : 27.89 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.20), residues: 1731 helix: 0.43 (0.21), residues: 560 sheet: -0.73 (0.30), residues: 335 loop : -2.73 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 124 HIS 0.008 0.001 HIS C 67 PHE 0.017 0.002 PHE A 365 TYR 0.030 0.002 TYR D 213 ARG 0.004 0.000 ARG D 193 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 95 time to evaluate : 1.809 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8531 (OUTLIER) cc_final: 0.6388 (p90) REVERT: A 303 MET cc_start: 0.7598 (mmm) cc_final: 0.7375 (mmm) REVERT: A 307 ASN cc_start: 0.8391 (t0) cc_final: 0.7997 (t0) REVERT: A 432 THR cc_start: 0.8143 (OUTLIER) cc_final: 0.7569 (t) REVERT: A 462 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9031 (tt) REVERT: B 181 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.8730 (m-80) REVERT: B 217 PHE cc_start: 0.9254 (OUTLIER) cc_final: 0.8346 (t80) REVERT: C 37 TYR cc_start: 0.8225 (OUTLIER) cc_final: 0.6301 (p90) REVERT: C 111 HIS cc_start: 0.9093 (OUTLIER) cc_final: 0.8781 (p90) REVERT: C 232 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8519 (mmm-85) REVERT: C 283 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9187 (mp) REVERT: C 369 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.8971 (pt0) REVERT: C 388 ILE cc_start: 0.9327 (OUTLIER) cc_final: 0.9096 (mp) REVERT: C 501 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9188 (pp) REVERT: D 219 TRP cc_start: 0.8197 (m100) cc_final: 0.7517 (m100) REVERT: D 354 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7910 (mmtp) REVERT: D 406 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8772 (mmtm) outliers start: 107 outliers final: 61 residues processed: 187 average time/residue: 0.2814 time to fit residues: 79.5512 Evaluate side-chains 166 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 91 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 406 LYS Chi-restraints excluded: chain D residue 418 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 145 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 120 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS ** C 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16577 Z= 0.274 Angle : 0.626 8.801 22744 Z= 0.323 Chirality : 0.045 0.341 2456 Planarity : 0.004 0.044 2595 Dihedral : 17.035 158.319 2897 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 6.43 % Allowed : 28.28 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.20), residues: 1731 helix: 0.51 (0.22), residues: 557 sheet: -0.84 (0.29), residues: 339 loop : -2.72 (0.19), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 124 HIS 0.011 0.001 HIS C 111 PHE 0.014 0.001 PHE D 273 TYR 0.028 0.001 TYR D 213 ARG 0.005 0.000 ARG D 193 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 88 time to evaluate : 1.962 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.6646 (p90) REVERT: A 275 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7649 (mtm-85) REVERT: A 307 ASN cc_start: 0.8447 (t0) cc_final: 0.8046 (t0) REVERT: A 365 PHE cc_start: 0.7373 (OUTLIER) cc_final: 0.7093 (p90) REVERT: A 462 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9019 (tt) REVERT: B 217 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8323 (t80) REVERT: B 296 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7992 (tp30) REVERT: C 37 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.6485 (p90) REVERT: C 111 HIS cc_start: 0.9102 (m90) cc_final: 0.8832 (p-80) REVERT: C 232 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8513 (mmm-85) REVERT: C 283 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9222 (mp) REVERT: C 369 GLU cc_start: 0.9208 (OUTLIER) cc_final: 0.8917 (pt0) REVERT: C 388 ILE cc_start: 0.9304 (OUTLIER) cc_final: 0.9078 (mp) REVERT: C 488 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8172 (pm20) REVERT: C 501 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9181 (pp) REVERT: D 219 TRP cc_start: 0.8137 (m100) cc_final: 0.7435 (m100) REVERT: D 354 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7893 (mmtp) outliers start: 100 outliers final: 68 residues processed: 178 average time/residue: 0.2738 time to fit residues: 74.1113 Evaluate side-chains 171 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 89 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 201 ARG Chi-restraints excluded: chain D residue 217 PHE Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 418 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 58 optimal weight: 9.9990 chunk 157 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 16577 Z= 0.358 Angle : 0.671 9.283 22744 Z= 0.346 Chirality : 0.047 0.373 2456 Planarity : 0.004 0.046 2595 Dihedral : 17.122 160.188 2897 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 7.52 % Allowed : 27.57 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.19), residues: 1731 helix: 0.39 (0.21), residues: 562 sheet: -0.78 (0.30), residues: 324 loop : -2.84 (0.19), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 124 HIS 0.007 0.001 HIS C 207 PHE 0.015 0.002 PHE A 365 TYR 0.032 0.002 TYR D 213 ARG 0.004 0.000 ARG D 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 92 time to evaluate : 2.308 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8523 (OUTLIER) cc_final: 0.6847 (p90) REVERT: A 94 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8644 (ptpp) REVERT: A 275 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.7741 (mtm-85) REVERT: A 307 ASN cc_start: 0.8607 (t0) cc_final: 0.8311 (t0) REVERT: A 365 PHE cc_start: 0.7494 (OUTLIER) cc_final: 0.7049 (p90) REVERT: A 432 THR cc_start: 0.8193 (OUTLIER) cc_final: 0.7619 (t) REVERT: A 462 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9039 (tt) REVERT: B 217 PHE cc_start: 0.9199 (OUTLIER) cc_final: 0.8392 (t80) REVERT: C 37 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.6649 (p90) REVERT: C 232 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8526 (mmm-85) REVERT: C 283 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9257 (mp) REVERT: C 388 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9096 (mp) REVERT: C 501 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9171 (pp) REVERT: D 83 LYS cc_start: 0.8766 (mmtt) cc_final: 0.8536 (mmmt) REVERT: D 219 TRP cc_start: 0.8132 (m100) cc_final: 0.7476 (m100) REVERT: D 354 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7923 (mmtp) REVERT: D 406 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8777 (mmtm) outliers start: 117 outliers final: 83 residues processed: 195 average time/residue: 0.2879 time to fit residues: 83.9704 Evaluate side-chains 183 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 86 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 201 ARG Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 406 LYS Chi-restraints excluded: chain D residue 418 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 168 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN B 370 ASN C 111 HIS ** C 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16577 Z= 0.205 Angle : 0.615 15.014 22744 Z= 0.313 Chirality : 0.045 0.304 2456 Planarity : 0.004 0.045 2595 Dihedral : 17.011 161.510 2897 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 6.36 % Allowed : 28.73 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.20), residues: 1731 helix: 0.61 (0.22), residues: 560 sheet: -0.86 (0.30), residues: 336 loop : -2.70 (0.19), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 124 HIS 0.008 0.001 HIS C 67 PHE 0.012 0.001 PHE A 206 TYR 0.021 0.001 TYR D 213 ARG 0.002 0.000 ARG D 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 95 time to evaluate : 1.802 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.6655 (p90) REVERT: A 94 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8619 (ptpp) REVERT: A 275 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7657 (mtm-85) REVERT: A 307 ASN cc_start: 0.8616 (t0) cc_final: 0.8344 (t0) REVERT: A 365 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.6948 (p90) REVERT: B 44 ASP cc_start: 0.7240 (p0) cc_final: 0.6987 (p0) REVERT: B 217 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.8366 (t80) REVERT: C 37 TYR cc_start: 0.8099 (OUTLIER) cc_final: 0.6436 (p90) REVERT: C 232 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8481 (mmm-85) REVERT: C 388 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.9069 (mp) REVERT: C 488 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8106 (pm20) REVERT: C 501 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9150 (pp) REVERT: D 83 LYS cc_start: 0.8744 (mmtt) cc_final: 0.8516 (mmmt) REVERT: D 201 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8744 (mtt-85) REVERT: D 219 TRP cc_start: 0.8080 (m100) cc_final: 0.7500 (m100) REVERT: D 354 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7849 (mmtp) outliers start: 99 outliers final: 70 residues processed: 182 average time/residue: 0.2889 time to fit residues: 79.3971 Evaluate side-chains 169 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 87 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 201 ARG Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 384 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 69 optimal weight: 3.9990 chunk 104 optimal weight: 0.0030 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 0.2980 chunk 110 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 overall best weight: 1.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN C 111 HIS ** C 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 GLN ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16577 Z= 0.203 Angle : 0.632 18.302 22744 Z= 0.318 Chirality : 0.045 0.301 2456 Planarity : 0.004 0.045 2595 Dihedral : 16.970 161.747 2897 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 6.36 % Allowed : 29.24 % Favored : 64.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.20), residues: 1731 helix: 0.63 (0.22), residues: 563 sheet: -0.88 (0.29), residues: 340 loop : -2.66 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 124 HIS 0.007 0.001 HIS C 67 PHE 0.022 0.001 PHE D 17 TYR 0.020 0.001 TYR D 213 ARG 0.002 0.000 ARG D 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 92 time to evaluate : 1.695 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8436 (OUTLIER) cc_final: 0.6565 (p90) REVERT: A 94 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8570 (ptpp) REVERT: A 275 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7648 (mtm-85) REVERT: A 307 ASN cc_start: 0.8635 (t0) cc_final: 0.8375 (t0) REVERT: A 365 PHE cc_start: 0.7499 (OUTLIER) cc_final: 0.6985 (p90) REVERT: B 44 ASP cc_start: 0.7205 (p0) cc_final: 0.6988 (p0) REVERT: B 217 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.8335 (t80) REVERT: C 37 TYR cc_start: 0.8130 (OUTLIER) cc_final: 0.6417 (p90) REVERT: C 232 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8491 (mmm-85) REVERT: C 388 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.9068 (mp) REVERT: C 488 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8099 (pm20) REVERT: C 501 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9135 (pp) REVERT: D 83 LYS cc_start: 0.8727 (mmtt) cc_final: 0.8491 (mmmt) REVERT: D 201 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8749 (mtt-85) REVERT: D 219 TRP cc_start: 0.8085 (m100) cc_final: 0.7492 (m100) REVERT: D 315 LYS cc_start: 0.9317 (tmtt) cc_final: 0.8843 (mptt) REVERT: D 354 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7852 (mmtp) outliers start: 99 outliers final: 73 residues processed: 179 average time/residue: 0.3018 time to fit residues: 80.1061 Evaluate side-chains 175 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 90 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 201 ARG Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 418 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 167 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 97 optimal weight: 0.0970 chunk 70 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 171 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN C 111 HIS ** C 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16577 Z= 0.179 Angle : 0.616 10.975 22744 Z= 0.310 Chirality : 0.044 0.284 2456 Planarity : 0.004 0.043 2595 Dihedral : 16.899 161.693 2897 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 5.33 % Allowed : 29.88 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.20), residues: 1731 helix: 0.76 (0.22), residues: 561 sheet: -0.73 (0.30), residues: 338 loop : -2.59 (0.19), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 124 HIS 0.006 0.001 HIS C 67 PHE 0.011 0.001 PHE A 206 TYR 0.016 0.001 TYR D 213 ARG 0.002 0.000 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 93 time to evaluate : 1.938 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.6584 (p90) REVERT: A 275 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7620 (mtm-85) REVERT: A 307 ASN cc_start: 0.8666 (t0) cc_final: 0.8416 (t0) REVERT: A 365 PHE cc_start: 0.7404 (OUTLIER) cc_final: 0.6887 (p90) REVERT: B 44 ASP cc_start: 0.7209 (p0) cc_final: 0.6989 (p0) REVERT: B 217 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8232 (t80) REVERT: C 37 TYR cc_start: 0.8092 (OUTLIER) cc_final: 0.6453 (p90) REVERT: C 74 MET cc_start: 0.7623 (tpp) cc_final: 0.7326 (tpp) REVERT: C 232 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8482 (mmm-85) REVERT: C 369 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8747 (pt0) REVERT: C 388 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.9037 (mp) REVERT: C 488 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8116 (pm20) REVERT: C 501 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9126 (pp) REVERT: D 83 LYS cc_start: 0.8728 (mmtt) cc_final: 0.8496 (mmmt) REVERT: D 201 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8761 (mtt-85) REVERT: D 219 TRP cc_start: 0.8104 (m100) cc_final: 0.7474 (m100) REVERT: D 315 LYS cc_start: 0.9390 (tmtt) cc_final: 0.9101 (ptpp) REVERT: D 354 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7841 (mmtp) outliers start: 83 outliers final: 66 residues processed: 165 average time/residue: 0.2856 time to fit residues: 71.1452 Evaluate side-chains 168 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 90 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 201 ARG Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 418 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 104 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN C 111 HIS ** C 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16577 Z= 0.210 Angle : 0.618 10.301 22744 Z= 0.312 Chirality : 0.044 0.304 2456 Planarity : 0.004 0.044 2595 Dihedral : 16.903 161.386 2897 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 5.66 % Allowed : 29.76 % Favored : 64.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.20), residues: 1731 helix: 0.75 (0.22), residues: 563 sheet: -0.70 (0.30), residues: 338 loop : -2.63 (0.19), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 124 HIS 0.006 0.001 HIS C 67 PHE 0.022 0.001 PHE B 255 TYR 0.019 0.001 TYR D 213 ARG 0.003 0.000 ARG D 114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 89 time to evaluate : 1.798 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.6645 (p90) REVERT: A 275 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7621 (mtm-85) REVERT: A 303 MET cc_start: 0.7171 (mmm) cc_final: 0.6875 (mmt) REVERT: A 307 ASN cc_start: 0.8688 (t0) cc_final: 0.8454 (t0) REVERT: A 365 PHE cc_start: 0.7455 (OUTLIER) cc_final: 0.6918 (p90) REVERT: B 44 ASP cc_start: 0.7209 (p0) cc_final: 0.7007 (p0) REVERT: B 217 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8249 (t80) REVERT: C 37 TYR cc_start: 0.8136 (OUTLIER) cc_final: 0.6508 (p90) REVERT: C 74 MET cc_start: 0.7703 (tpp) cc_final: 0.7414 (tpp) REVERT: C 232 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8490 (mmm-85) REVERT: C 369 GLU cc_start: 0.9109 (OUTLIER) cc_final: 0.8783 (pt0) REVERT: C 388 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.9056 (mp) REVERT: C 488 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8120 (pm20) REVERT: C 501 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9146 (pp) REVERT: D 83 LYS cc_start: 0.8751 (mmtt) cc_final: 0.8527 (mmmt) REVERT: D 201 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8775 (mtt-85) REVERT: D 219 TRP cc_start: 0.8130 (m100) cc_final: 0.7458 (m100) REVERT: D 354 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7846 (mmtp) outliers start: 88 outliers final: 73 residues processed: 166 average time/residue: 0.2663 time to fit residues: 67.4803 Evaluate side-chains 173 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 88 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 201 ARG Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 418 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 43 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 21 optimal weight: 0.0570 chunk 39 optimal weight: 2.9990 chunk 143 optimal weight: 0.2980 chunk 60 optimal weight: 0.1980 chunk 147 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN C 111 HIS ** C 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 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 = 0.3690 r_free = 0.3690 target = 0.095922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.073338 restraints weight = 55976.325| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 4.78 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16577 Z= 0.151 Angle : 0.602 10.432 22744 Z= 0.302 Chirality : 0.044 0.255 2456 Planarity : 0.003 0.042 2595 Dihedral : 16.829 160.896 2897 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 4.63 % Allowed : 30.85 % Favored : 64.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.20), residues: 1731 helix: 0.86 (0.22), residues: 562 sheet: -0.53 (0.30), residues: 336 loop : -2.47 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 20 HIS 0.004 0.001 HIS C 67 PHE 0.018 0.001 PHE B 255 TYR 0.011 0.001 TYR A 104 ARG 0.002 0.000 ARG D 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3164.25 seconds wall clock time: 59 minutes 1.50 seconds (3541.50 seconds total)