Starting phenix.real_space_refine on Fri Feb 16 05:15:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5n_29750/02_2024/8g5n_29750_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5n_29750/02_2024/8g5n_29750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5n_29750/02_2024/8g5n_29750.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5n_29750/02_2024/8g5n_29750.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5n_29750/02_2024/8g5n_29750_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5n_29750/02_2024/8g5n_29750_neut.pdb" } resolution = 2.73 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 38 5.49 5 S 79 5.16 5 C 9099 2.51 5 N 2536 2.21 5 O 2733 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 124": "OE1" <-> "OE2" Residue "A GLU 458": "OE1" <-> "OE2" Residue "A GLU 616": "OE1" <-> "OE2" Residue "A TYR 1108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1207": "OE1" <-> "OE2" Residue "A GLU 1225": "OE1" <-> "OE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B GLU 394": "OE1" <-> "OE2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "B GLU 419": "OE1" <-> "OE2" Residue "C TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 325": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14485 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 919, 7217 Classifications: {'peptide': 919} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 61, 'TRANS': 857} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 3247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3247 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 18, 'TRANS': 388} Chain breaks: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3224 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "R" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 370 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 7, 'rna3p_pyr': 5} Link IDs: {'rna2p': 5, 'rna3p': 11} Chain: "T" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 427 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Time building chain proxies: 8.22, per 1000 atoms: 0.57 Number of scatterers: 14485 At special positions: 0 Unit cell: (105.677, 104.851, 146.131, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 79 16.00 P 38 15.00 O 2733 8.00 N 2536 7.00 C 9099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.94 Conformation dependent library (CDL) restraints added in 2.5 seconds 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3226 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 11 sheets defined 37.9% alpha, 11.4% beta 16 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 4.76 Creating SS restraints... Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.811A pdb=" N LYS A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 159 Proline residue: A 149 - end of helix removed outlier: 3.984A pdb=" N ALA A 153 " --> pdb=" O PRO A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 276 removed outlier: 3.610A pdb=" N ASP A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 305 through 313 removed outlier: 3.502A pdb=" N LEU A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 388 through 418 Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 431 removed outlier: 3.996A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 471 removed outlier: 3.539A pdb=" N CYS A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 475 Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.571A pdb=" N LYS A 480 " --> pdb=" O GLU A 477 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A 481 " --> pdb=" O ARG A 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 477 through 481' Processing helix chain 'A' and resid 536 through 541 Processing helix chain 'A' and resid 561 through 565 Processing helix chain 'A' and resid 570 through 577 Processing helix chain 'A' and resid 760 through 764 removed outlier: 3.917A pdb=" N SER A 764 " --> pdb=" O ASN A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 775 removed outlier: 3.784A pdb=" N GLU A 775 " --> pdb=" O PRO A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 803 WARNING: missing atoms! removed outlier: 5.065A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 809 Processing helix chain 'A' and resid 817 through 821 Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 916 through 923 Processing helix chain 'A' and resid 935 through 940 Processing helix chain 'A' and resid 945 through 955 removed outlier: 3.520A pdb=" N TYR A 955 " --> pdb=" O TYR A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 970 Processing helix chain 'A' and resid 982 through 987 Processing helix chain 'A' and resid 1058 through 1066 Processing helix chain 'A' and resid 1080 through 1084 removed outlier: 3.565A pdb=" N GLU A1084 " --> pdb=" O ARG A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1123 removed outlier: 3.776A pdb=" N ARG A1096 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1167 Processing helix chain 'A' and resid 1202 through 1206 Processing helix chain 'A' and resid 1216 through 1221 removed outlier: 3.715A pdb=" N TYR A1221 " --> pdb=" O LEU A1218 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 119 Processing helix chain 'B' and resid 174 through 178 removed outlier: 4.207A pdb=" N THR B 177 " --> pdb=" O VAL B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 197 removed outlier: 3.717A pdb=" N ALA B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ASN B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 201 Processing helix chain 'B' and resid 247 through 265 Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 342 through 354 removed outlier: 3.561A pdb=" N LEU B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 397 removed outlier: 3.971A pdb=" N GLN B 397 " --> pdb=" O GLU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 408 removed outlier: 3.979A pdb=" N LEU B 402 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ASN B 404 " --> pdb=" O GLN B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 435 Processing helix chain 'B' and resid 444 through 448 removed outlier: 3.913A pdb=" N LEU B 448 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 484 removed outlier: 3.505A pdb=" N PHE B 474 " --> pdb=" O LYS B 470 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 75 Processing helix chain 'C' and resid 76 through 78 No H-bonds generated for 'chain 'C' and resid 76 through 78' Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 120 through 123 Processing helix chain 'C' and resid 185 through 200 removed outlier: 4.338A pdb=" N VAL C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ASN C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP C 198 " --> pdb=" O VAL C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 266 removed outlier: 4.077A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 307 through 314 removed outlier: 4.548A pdb=" N LEU C 311 " --> pdb=" O GLY C 307 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N MET C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 395 through 409 removed outlier: 3.544A pdb=" N ASN C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 removed outlier: 4.022A pdb=" N LEU C 418 " --> pdb=" O PRO C 415 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU C 419 " --> pdb=" O GLY C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 415 through 419' Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 444 through 451 removed outlier: 3.724A pdb=" N LEU C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 484 removed outlier: 3.848A pdb=" N PHE C 474 " --> pdb=" O LYS C 470 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 187 removed outlier: 3.843A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 213 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 198 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 215 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU A 195 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 435 through 436 removed outlier: 3.684A pdb=" N VAL A 814 " --> pdb=" O ALA A 839 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1127 through 1133 removed outlier: 6.891A pdb=" N GLY A1127 " --> pdb=" O ARG A1142 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ARG A1142 " --> pdb=" O GLY A1127 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N PHE A1129 " --> pdb=" O LEU A1140 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU A1140 " --> pdb=" O PHE A1129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.723A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN B 305 " --> pdb=" O LYS B 285 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 133 through 134 removed outlier: 3.909A pdb=" N LYS B 180 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AA7, first strand: chain 'B' and resid 413 through 414 removed outlier: 7.350A pdb=" N TRP B 414 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS B 382 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N VAL B 441 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA B 384 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL B 443 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASP B 386 " --> pdb=" O VAL B 443 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 125 through 127 removed outlier: 5.977A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 133 through 134 Processing sheet with id=AB1, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AB2, first strand: chain 'C' and resid 413 through 414 removed outlier: 7.538A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) 515 hydrogen bonds defined for protein. 1434 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 4.99 Time building geometry restraints manager: 6.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3790 1.33 - 1.46: 3172 1.46 - 1.58: 7760 1.58 - 1.70: 77 1.70 - 1.82: 125 Bond restraints: 14924 Sorted by residual: bond pdb=" C3' G R 20 " pdb=" C2' G R 20 " ideal model delta sigma weight residual 1.525 1.622 -0.097 1.50e-02 4.44e+03 4.17e+01 bond pdb=" C3' C R 16 " pdb=" C2' C R 16 " ideal model delta sigma weight residual 1.523 1.450 0.073 1.50e-02 4.44e+03 2.34e+01 bond pdb=" CG PRO A 772 " pdb=" CD PRO A 772 " ideal model delta sigma weight residual 1.503 1.382 0.121 3.40e-02 8.65e+02 1.27e+01 bond pdb=" N VAL A 229 " pdb=" CA VAL A 229 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.30e-02 5.92e+03 1.05e+01 bond pdb=" N ILE A 342 " pdb=" CA ILE A 342 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.19e-02 7.06e+03 1.03e+01 ... (remaining 14919 not shown) Histogram of bond angle deviations from ideal: 93.74 - 101.83: 64 101.83 - 109.92: 2560 109.92 - 118.01: 9005 118.01 - 126.10: 8342 126.10 - 134.19: 446 Bond angle restraints: 20417 Sorted by residual: angle pdb=" CA PRO A 772 " pdb=" N PRO A 772 " pdb=" CD PRO A 772 " ideal model delta sigma weight residual 112.00 95.28 16.72 1.40e+00 5.10e-01 1.43e+02 angle pdb=" C3' G R 21 " pdb=" O3' G R 21 " pdb=" P G R 22 " ideal model delta sigma weight residual 120.20 107.20 13.00 1.50e+00 4.44e-01 7.51e+01 angle pdb=" C3' U R 9 " pdb=" O3' U R 9 " pdb=" P G R 10 " ideal model delta sigma weight residual 120.20 107.30 12.90 1.50e+00 4.44e-01 7.39e+01 angle pdb=" C3' DT T 9 " pdb=" O3' DT T 9 " pdb=" P DC T 10 " ideal model delta sigma weight residual 120.20 108.61 11.59 1.50e+00 4.44e-01 5.97e+01 angle pdb=" C3' C R 18 " pdb=" O3' C R 18 " pdb=" P G R 19 " ideal model delta sigma weight residual 120.20 108.68 11.52 1.50e+00 4.44e-01 5.89e+01 ... (remaining 20412 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 7625 17.89 - 35.78: 867 35.78 - 53.66: 278 53.66 - 71.55: 91 71.55 - 89.44: 20 Dihedral angle restraints: 8881 sinusoidal: 3881 harmonic: 5000 Sorted by residual: dihedral pdb=" CD ARG C 325 " pdb=" NE ARG C 325 " pdb=" CZ ARG C 325 " pdb=" NH1 ARG C 325 " ideal model delta sinusoidal sigma weight residual 0.00 -64.03 64.03 1 1.00e+01 1.00e-02 5.40e+01 dihedral pdb=" C5' G R 20 " pdb=" C4' G R 20 " pdb=" C3' G R 20 " pdb=" O3' G R 20 " ideal model delta sinusoidal sigma weight residual 147.00 103.33 43.67 1 8.00e+00 1.56e-02 4.15e+01 dihedral pdb=" CD ARG C 344 " pdb=" NE ARG C 344 " pdb=" CZ ARG C 344 " pdb=" NH1 ARG C 344 " ideal model delta sinusoidal sigma weight residual 0.00 48.96 -48.96 1 1.00e+01 1.00e-02 3.30e+01 ... (remaining 8878 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 2141 0.127 - 0.255: 55 0.255 - 0.382: 2 0.382 - 0.510: 29 0.510 - 0.637: 8 Chirality restraints: 2235 Sorted by residual: chirality pdb=" P DT T 5 " pdb=" OP1 DT T 5 " pdb=" OP2 DT T 5 " pdb=" O5' DT T 5 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" P G R 6 " pdb=" OP1 G R 6 " pdb=" OP2 G R 6 " pdb=" O5' G R 6 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.07e+00 chirality pdb=" P DA T 6 " pdb=" OP1 DA T 6 " pdb=" OP2 DA T 6 " pdb=" O5' DA T 6 " both_signs ideal model delta sigma weight residual True 2.35 -2.90 -0.55 2.00e-01 2.50e+01 7.61e+00 ... (remaining 2232 not shown) Planarity restraints: 2486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 325 " 0.988 9.50e-02 1.11e+02 4.43e-01 1.19e+02 pdb=" NE ARG C 325 " -0.059 2.00e-02 2.50e+03 pdb=" CZ ARG C 325 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG C 325 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 325 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 344 " -0.815 9.50e-02 1.11e+02 3.66e-01 8.12e+01 pdb=" NE ARG C 344 " 0.049 2.00e-02 2.50e+03 pdb=" CZ ARG C 344 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG C 344 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 344 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 597 " 0.616 9.50e-02 1.11e+02 2.76e-01 4.66e+01 pdb=" NE ARG A 597 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG A 597 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 597 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 597 " 0.020 2.00e-02 2.50e+03 ... (remaining 2483 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 78 2.48 - 3.08: 10403 3.08 - 3.69: 22516 3.69 - 4.29: 31284 4.29 - 4.90: 51146 Nonbonded interactions: 115427 Sorted by model distance: nonbonded pdb=" OG SER A 237 " pdb=" OG SER A 240 " model vdw 1.871 2.440 nonbonded pdb=" O TYR A 282 " pdb=" OH TYR A 434 " model vdw 2.055 2.440 nonbonded pdb=" OG1 THR A 885 " pdb=" O ASP A1186 " model vdw 2.113 2.440 nonbonded pdb=" O THR A 210 " pdb=" OG SER A 225 " model vdw 2.119 2.440 nonbonded pdb=" O CYS A 224 " pdb=" OG SER A 225 " model vdw 2.123 2.440 ... (remaining 115422 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 'B' and (resid 66 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB )) or resid 108 through 146 or (resid 147 and (name N o \ r name CA or name C or name O or name CB )) or resid 148 through 170 or (resid 1 \ 71 through 176 and (name N or name CA or name C or name O or name CB )) or resid \ 177 through 222 or (resid 223 and (name N or name CA or name C or name O or nam \ e CB )) or resid 224 or (resid 225 and (name N or name CA or name C or name O or \ name CB )) or resid 226 through 283 or (resid 284 and (name N or name CA or nam \ e C or name O or name CB )) or resid 285 through 355 or resid 368 through 485)) selection = (chain 'C' and (resid 66 or (resid 67 through 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 74 or (resid 75 and (name N or nam \ e CA or name C or name O or name CB )) or resid 76 through 137 or (resid 138 and \ (name N or name CA or name C or name O or name CB )) or resid 139 through 145 o \ r (resid 146 through 147 and (name N or name CA or name C or name O or name CB ) \ ) or resid 148 through 160 or resid 170 through 485)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.400 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: 0.010 Extract box with map and model: 7.420 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 43.720 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 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:11.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5953 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 : 0.006 0.129 14924 Z= 0.371 Angle : 1.004 16.720 20417 Z= 0.601 Chirality : 0.079 0.637 2235 Planarity : 0.016 0.443 2486 Dihedral : 17.819 89.437 5655 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 1.85 % Allowed : 24.35 % Favored : 73.80 % 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: -0.17 (0.21), residues: 1712 helix: 1.43 (0.23), residues: 588 sheet: 1.07 (0.36), residues: 215 loop : -1.54 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 255 HIS 0.005 0.001 HIS C 258 PHE 0.025 0.001 PHE A 539 TYR 0.010 0.001 TYR C 315 ARG 0.007 0.000 ARG A 866 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 214 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.7260 (mmm) cc_final: 0.6974 (mmm) REVERT: B 465 MET cc_start: 0.7255 (mmm) cc_final: 0.7000 (mmm) outliers start: 27 outliers final: 12 residues processed: 236 average time/residue: 1.0075 time to fit residues: 267.4845 Evaluate side-chains 190 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 178 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 413 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.5980 chunk 131 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 45 optimal weight: 0.1980 chunk 88 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 158 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 468 ASN ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 GLN A 843 GLN A 879 GLN A 976 GLN A1214 GLN B 158 GLN B 454 HIS C 85 GLN C 109 ASN C 279 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6049 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14924 Z= 0.253 Angle : 0.695 11.206 20417 Z= 0.345 Chirality : 0.044 0.279 2235 Planarity : 0.005 0.068 2486 Dihedral : 15.363 88.486 2397 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 4.46 % Allowed : 22.29 % Favored : 73.25 % 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: -0.31 (0.21), residues: 1712 helix: 1.31 (0.22), residues: 612 sheet: 1.04 (0.37), residues: 209 loop : -1.69 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 607 HIS 0.003 0.001 HIS B 323 PHE 0.019 0.002 PHE A 610 TYR 0.010 0.001 TYR B 290 ARG 0.008 0.001 ARG C 325 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 197 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 793 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: A 821 LEU cc_start: 0.6731 (OUTLIER) cc_final: 0.6508 (mm) REVERT: B 405 GLU cc_start: 0.7479 (tp30) cc_final: 0.7234 (tp30) REVERT: B 446 THR cc_start: 0.7574 (OUTLIER) cc_final: 0.7364 (m) REVERT: B 465 MET cc_start: 0.7129 (mmm) cc_final: 0.6794 (mmm) outliers start: 65 outliers final: 21 residues processed: 242 average time/residue: 0.9348 time to fit residues: 255.5306 Evaluate side-chains 190 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 158 optimal weight: 10.0000 chunk 171 optimal weight: 20.0000 chunk 140 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 126 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 740 ASN B 96 HIS C 132 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6088 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14924 Z= 0.247 Angle : 0.671 11.393 20417 Z= 0.334 Chirality : 0.044 0.210 2235 Planarity : 0.005 0.066 2486 Dihedral : 15.076 86.324 2386 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 5.28 % Allowed : 22.91 % Favored : 71.81 % 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: -0.47 (0.21), residues: 1712 helix: 1.12 (0.22), residues: 613 sheet: 1.04 (0.37), residues: 207 loop : -1.77 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 607 HIS 0.004 0.001 HIS A 613 PHE 0.027 0.002 PHE A 610 TYR 0.025 0.002 TYR B 206 ARG 0.005 0.001 ARG C 325 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 183 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7445 (tt) REVERT: A 544 MET cc_start: 0.7219 (mpp) cc_final: 0.6896 (mpt) REVERT: A 597 ARG cc_start: 0.8017 (tmm160) cc_final: 0.7795 (tmm-80) REVERT: A 793 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: A 821 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6529 (mm) REVERT: B 405 GLU cc_start: 0.7497 (tp30) cc_final: 0.7214 (tp30) REVERT: B 465 MET cc_start: 0.7071 (mmm) cc_final: 0.6714 (mmm) outliers start: 77 outliers final: 36 residues processed: 241 average time/residue: 0.9582 time to fit residues: 260.8537 Evaluate side-chains 208 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 169 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 106 optimal weight: 0.6980 chunk 158 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 140 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN A 613 HIS A 975 GLN C 133 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6079 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14924 Z= 0.207 Angle : 0.663 11.179 20417 Z= 0.325 Chirality : 0.043 0.199 2235 Planarity : 0.005 0.062 2486 Dihedral : 14.954 86.750 2384 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 4.94 % Allowed : 25.10 % Favored : 69.96 % 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: -0.48 (0.21), residues: 1712 helix: 1.10 (0.22), residues: 613 sheet: 1.13 (0.36), residues: 205 loop : -1.79 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 607 HIS 0.004 0.001 HIS A 613 PHE 0.039 0.001 PHE A 610 TYR 0.017 0.001 TYR A 178 ARG 0.006 0.000 ARG A 866 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 189 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 ARG cc_start: 0.8085 (tmm160) cc_final: 0.7810 (tmm-80) REVERT: A 967 MET cc_start: 0.6853 (mmt) cc_final: 0.6472 (mmt) REVERT: B 405 GLU cc_start: 0.7558 (tp30) cc_final: 0.7238 (tp30) REVERT: B 465 MET cc_start: 0.7128 (mmm) cc_final: 0.6788 (mmm) outliers start: 72 outliers final: 38 residues processed: 236 average time/residue: 0.9427 time to fit residues: 252.8683 Evaluate side-chains 210 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 172 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 125 optimal weight: 0.0980 chunk 69 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 150 optimal weight: 4.9990 chunk 42 optimal weight: 0.0270 chunk 56 optimal weight: 0.0980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 HIS ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6021 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14924 Z= 0.171 Angle : 0.651 10.729 20417 Z= 0.317 Chirality : 0.042 0.173 2235 Planarity : 0.005 0.054 2486 Dihedral : 14.725 86.796 2383 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 4.80 % Allowed : 24.62 % Favored : 70.58 % 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: -0.37 (0.21), residues: 1712 helix: 1.31 (0.22), residues: 600 sheet: 1.21 (0.36), residues: 205 loop : -1.78 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 607 HIS 0.006 0.001 HIS A 613 PHE 0.033 0.001 PHE A 610 TYR 0.026 0.001 TYR B 206 ARG 0.006 0.000 ARG A 866 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 182 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.7144 (mpp) cc_final: 0.6792 (mpt) REVERT: A 597 ARG cc_start: 0.7978 (tmm160) cc_final: 0.7721 (tmm-80) REVERT: A 821 LEU cc_start: 0.6625 (OUTLIER) cc_final: 0.6379 (mm) REVERT: A 967 MET cc_start: 0.6855 (mmt) cc_final: 0.6450 (mmt) REVERT: A 1163 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.7603 (tpt) REVERT: B 465 MET cc_start: 0.7218 (mmm) cc_final: 0.6860 (mmm) outliers start: 70 outliers final: 35 residues processed: 230 average time/residue: 1.0039 time to fit residues: 259.5261 Evaluate side-chains 202 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 165 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 77 HIS Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 41 optimal weight: 0.0060 chunk 168 optimal weight: 20.0000 chunk 139 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 13 optimal weight: 0.4980 chunk 55 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 162 optimal weight: 0.3980 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 HIS ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6103 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14924 Z= 0.246 Angle : 0.674 10.392 20417 Z= 0.332 Chirality : 0.043 0.196 2235 Planarity : 0.005 0.058 2486 Dihedral : 14.695 86.304 2383 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.35 % Favored : 91.59 % Rotamer: Outliers : 4.94 % Allowed : 25.38 % Favored : 69.68 % 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: -0.56 (0.21), residues: 1712 helix: 1.13 (0.22), residues: 607 sheet: 0.97 (0.36), residues: 215 loop : -1.90 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 607 HIS 0.016 0.001 HIS C 77 PHE 0.034 0.002 PHE A 610 TYR 0.013 0.001 TYR A 178 ARG 0.008 0.000 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 181 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.7296 (mpp) cc_final: 0.7032 (mpt) REVERT: A 585 TRP cc_start: 0.6825 (t-100) cc_final: 0.6317 (t-100) REVERT: A 597 ARG cc_start: 0.8125 (tmm160) cc_final: 0.7793 (ttp80) REVERT: A 779 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7866 (tm) REVERT: A 793 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7232 (mp0) REVERT: A 821 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6488 (mm) REVERT: A 910 MET cc_start: 0.6600 (mpt) cc_final: 0.6322 (mpt) REVERT: A 967 MET cc_start: 0.6746 (mmt) cc_final: 0.6320 (mmt) REVERT: B 419 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7482 (tp30) REVERT: B 465 MET cc_start: 0.7107 (mmm) cc_final: 0.6787 (mmm) REVERT: C 72 ILE cc_start: 0.5315 (pp) cc_final: 0.5024 (pp) outliers start: 72 outliers final: 45 residues processed: 230 average time/residue: 0.9091 time to fit residues: 237.9395 Evaluate side-chains 214 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 166 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 596 MET Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 77 HIS Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 122 optimal weight: 0.1980 chunk 141 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 167 optimal weight: 20.0000 chunk 104 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6094 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14924 Z= 0.225 Angle : 0.688 10.421 20417 Z= 0.335 Chirality : 0.044 0.343 2235 Planarity : 0.005 0.058 2486 Dihedral : 14.665 85.917 2383 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.53 % Favored : 91.41 % Rotamer: Outliers : 5.08 % Allowed : 25.51 % Favored : 69.41 % 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: -0.58 (0.21), residues: 1712 helix: 1.09 (0.22), residues: 605 sheet: 1.02 (0.36), residues: 208 loop : -1.89 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 607 HIS 0.004 0.001 HIS B 77 PHE 0.032 0.001 PHE A 610 TYR 0.027 0.001 TYR B 206 ARG 0.009 0.000 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 181 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 TRP cc_start: 0.6730 (t-100) cc_final: 0.6239 (t-100) REVERT: A 597 ARG cc_start: 0.8158 (tmm160) cc_final: 0.7872 (ttp80) REVERT: A 779 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7871 (tm) REVERT: A 793 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7294 (mp0) REVERT: A 821 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6512 (mm) REVERT: A 967 MET cc_start: 0.6709 (mmt) cc_final: 0.6262 (mmt) REVERT: B 405 GLU cc_start: 0.7666 (tp30) cc_final: 0.7405 (tp30) REVERT: B 465 MET cc_start: 0.7105 (mmm) cc_final: 0.6747 (mmm) outliers start: 74 outliers final: 46 residues processed: 234 average time/residue: 0.9306 time to fit residues: 247.2341 Evaluate side-chains 216 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 167 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 77 HIS Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 106 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN B 226 ASN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14924 Z= 0.245 Angle : 0.715 11.953 20417 Z= 0.349 Chirality : 0.044 0.259 2235 Planarity : 0.005 0.059 2486 Dihedral : 14.653 85.512 2383 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.23 % Favored : 90.71 % Rotamer: Outliers : 4.66 % Allowed : 26.54 % Favored : 68.79 % 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: -0.64 (0.21), residues: 1712 helix: 1.00 (0.22), residues: 610 sheet: 1.09 (0.37), residues: 205 loop : -1.93 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 607 HIS 0.005 0.001 HIS B 77 PHE 0.032 0.002 PHE A 610 TYR 0.012 0.001 TYR A 178 ARG 0.009 0.000 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 174 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7444 (ttt180) REVERT: A 544 MET cc_start: 0.7254 (mpp) cc_final: 0.6959 (mpp) REVERT: A 585 TRP cc_start: 0.6721 (t-100) cc_final: 0.6284 (t-100) REVERT: A 597 ARG cc_start: 0.8184 (tmm160) cc_final: 0.7888 (ttp80) REVERT: A 779 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7902 (tm) REVERT: A 793 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: A 821 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6465 (mm) REVERT: A 967 MET cc_start: 0.6732 (mmt) cc_final: 0.6287 (mmt) REVERT: B 405 GLU cc_start: 0.7580 (tp30) cc_final: 0.7300 (tp30) REVERT: B 465 MET cc_start: 0.7099 (mmm) cc_final: 0.6740 (mmm) REVERT: C 72 ILE cc_start: 0.5527 (pp) cc_final: 0.5195 (pp) outliers start: 68 outliers final: 47 residues processed: 222 average time/residue: 0.9083 time to fit residues: 229.9657 Evaluate side-chains 219 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 168 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1143 GLU Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 77 HIS Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.6980 chunk 160 optimal weight: 0.0000 chunk 94 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 122 optimal weight: 0.0070 chunk 47 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 147 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 165 optimal weight: 20.0000 overall best weight: 0.5406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6044 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14924 Z= 0.187 Angle : 0.699 12.199 20417 Z= 0.338 Chirality : 0.042 0.176 2235 Planarity : 0.005 0.056 2486 Dihedral : 14.555 85.100 2383 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.35 % Favored : 91.59 % Rotamer: Outliers : 3.64 % Allowed : 28.26 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.21), residues: 1712 helix: 1.20 (0.22), residues: 604 sheet: 1.07 (0.36), residues: 210 loop : -1.88 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 345 HIS 0.009 0.001 HIS A 613 PHE 0.033 0.001 PHE A 389 TYR 0.024 0.001 TYR B 206 ARG 0.009 0.000 ARG A1071 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 186 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7462 (tt) REVERT: A 585 TRP cc_start: 0.6663 (t-100) cc_final: 0.6184 (t-100) REVERT: A 597 ARG cc_start: 0.8133 (tmm160) cc_final: 0.7855 (ttp80) REVERT: A 779 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7848 (tm) REVERT: A 793 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: A 821 LEU cc_start: 0.6695 (OUTLIER) cc_final: 0.6449 (mm) REVERT: A 967 MET cc_start: 0.6764 (mmt) cc_final: 0.6331 (mmt) REVERT: B 405 GLU cc_start: 0.7518 (tp30) cc_final: 0.7210 (tp30) REVERT: B 465 MET cc_start: 0.7299 (mmm) cc_final: 0.7016 (mmm) REVERT: C 72 ILE cc_start: 0.5400 (pp) cc_final: 0.5101 (pp) outliers start: 53 outliers final: 37 residues processed: 220 average time/residue: 0.9014 time to fit residues: 225.5675 Evaluate side-chains 213 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 172 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 173 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 138 optimal weight: 0.0000 chunk 14 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS B 84 GLN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6123 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14924 Z= 0.263 Angle : 0.743 11.707 20417 Z= 0.360 Chirality : 0.044 0.189 2235 Planarity : 0.005 0.060 2486 Dihedral : 14.583 84.472 2383 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.58 % Favored : 90.36 % Rotamer: Outliers : 3.50 % Allowed : 29.15 % Favored : 67.35 % 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: -0.68 (0.21), residues: 1712 helix: 1.06 (0.22), residues: 605 sheet: 0.98 (0.37), residues: 206 loop : -1.98 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 345 HIS 0.005 0.001 HIS B 77 PHE 0.040 0.002 PHE A 389 TYR 0.013 0.001 TYR A 178 ARG 0.010 0.001 ARG A1071 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 181 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 597 ARG cc_start: 0.8205 (tmm160) cc_final: 0.7925 (tmm-80) REVERT: A 793 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7322 (mp0) REVERT: A 821 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6463 (mm) REVERT: A 967 MET cc_start: 0.6735 (mmt) cc_final: 0.6273 (mmt) REVERT: B 405 GLU cc_start: 0.7598 (tp30) cc_final: 0.7290 (tp30) REVERT: B 465 MET cc_start: 0.7217 (mmm) cc_final: 0.6924 (mmm) REVERT: B 466 MET cc_start: 0.7661 (ttt) cc_final: 0.7416 (ttt) REVERT: C 72 ILE cc_start: 0.5558 (pp) cc_final: 0.5256 (pp) outliers start: 51 outliers final: 37 residues processed: 214 average time/residue: 0.9452 time to fit residues: 229.1562 Evaluate side-chains 213 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 174 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 793 GLU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 141 optimal weight: 50.0000 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.185813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.137510 restraints weight = 26694.771| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 4.39 r_work: 0.3863 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14924 Z= 0.208 Angle : 0.728 11.670 20417 Z= 0.356 Chirality : 0.043 0.183 2235 Planarity : 0.005 0.066 2486 Dihedral : 14.551 84.137 2383 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.05 % Favored : 90.89 % Rotamer: Outliers : 3.16 % Allowed : 29.42 % Favored : 67.42 % 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: -0.62 (0.21), residues: 1712 helix: 1.12 (0.22), residues: 603 sheet: 0.96 (0.37), residues: 206 loop : -1.93 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP B 241 HIS 0.006 0.001 HIS A 613 PHE 0.045 0.001 PHE A 389 TYR 0.035 0.001 TYR B 206 ARG 0.015 0.000 ARG B 257 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5259.08 seconds wall clock time: 94 minutes 13.22 seconds (5653.22 seconds total)