Starting phenix.real_space_refine on Fri Jun 28 07:11:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z90_39852/06_2024/8z90_39852_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z90_39852/06_2024/8z90_39852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z90_39852/06_2024/8z90_39852.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z90_39852/06_2024/8z90_39852.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z90_39852/06_2024/8z90_39852_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z90_39852/06_2024/8z90_39852_updated.pdb" } resolution = 2.87 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1345 atoms to isotropic. 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 36 5.49 5 S 77 5.16 5 C 8402 2.51 5 N 2345 2.21 5 O 2621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 140": "OD1" <-> "OD2" Residue "A TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 363": "OE1" <-> "OE2" Residue "A ASP 441": "OD1" <-> "OD2" Residue "A PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B GLU 278": "OE1" <-> "OE2" Residue "B GLU 368": "OE1" <-> "OE2" Residue "B GLU 409": "OE1" <-> "OE2" Residue "B ASP 422": "OD1" <-> "OD2" Residue "B PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 500": "OD1" <-> "OD2" Residue "B ASP 575": "OD1" <-> "OD2" Residue "B ASP 606": "OD1" <-> "OD2" Residue "B GLU 689": "OE1" <-> "OE2" Residue "C TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 26": "OE1" <-> "OE2" Residue "C ASP 37": "OD1" <-> "OD2" Residue "C PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 74": "OE1" <-> "OE2" Residue "C ASP 86": "OD1" <-> "OD2" Residue "C PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 13481 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 5014 Classifications: {'peptide': 620} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 588} Chain: "B" Number of atoms: 5710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5710 Classifications: {'peptide': 710} Link IDs: {'PTRANS': 39, 'TRANS': 670} Chain: "C" Number of atoms: 1986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1986 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 16, 'TRANS': 228} Chain: "D" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 388 Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 10, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 14} Chain: "E" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 351 Classifications: {'RNA': 17} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 2, 'rna3p_pyr': 8} Link IDs: {'rna2p': 7, 'rna3p': 9} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.81, per 1000 atoms: 0.58 Number of scatterers: 13481 At special positions: 0 Unit cell: (103.323, 106.018, 137.465, 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 77 16.00 P 36 15.00 O 2621 8.00 N 2345 7.00 C 8402 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: 5.34 Conformation dependent library (CDL) restraints added in 2.5 seconds 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3006 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 65 helices and 16 sheets defined 42.2% alpha, 8.8% beta 8 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 5.71 Creating SS restraints... Processing helix chain 'A' and resid 10 through 18 removed outlier: 4.644A pdb=" N THR A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 24 No H-bonds generated for 'chain 'A' and resid 22 through 24' Processing helix chain 'A' and resid 28 through 46 Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 135 through 153 Processing helix chain 'A' and resid 158 through 166 Processing helix chain 'A' and resid 177 through 185 removed outlier: 3.585A pdb=" N ARG A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 256 Processing helix chain 'A' and resid 271 through 286 removed outlier: 3.803A pdb=" N ILE A 274 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR A 275 " --> pdb=" O SER A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 300 No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 305 through 315 Processing helix chain 'A' and resid 336 through 345 removed outlier: 3.813A pdb=" N ARG A 345 " --> pdb=" O MET A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 380 Processing helix chain 'A' and resid 383 through 400 Processing helix chain 'A' and resid 485 through 492 Processing helix chain 'A' and resid 494 through 516 removed outlier: 3.939A pdb=" N GLN A 500 " --> pdb=" O VAL A 497 " (cutoff:3.500A) Proline residue: A 501 - end of helix removed outlier: 3.505A pdb=" N LEU A 510 " --> pdb=" O GLN A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 556 removed outlier: 3.590A pdb=" N ARG A 545 " --> pdb=" O TYR A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 581 removed outlier: 4.760A pdb=" N ARG A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 598 No H-bonds generated for 'chain 'A' and resid 595 through 598' Processing helix chain 'A' and resid 605 through 616 Processing helix chain 'B' and resid 12 through 19 removed outlier: 4.271A pdb=" N GLU B 17 " --> pdb=" O THR B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 46 removed outlier: 4.080A pdb=" N ARG B 43 " --> pdb=" O GLU B 39 " (cutoff:3.500A) Proline residue: B 44 - end of helix Processing helix chain 'B' and resid 54 through 59 removed outlier: 4.435A pdb=" N ASP B 59 " --> pdb=" O GLN B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 69 No H-bonds generated for 'chain 'B' and resid 67 through 69' Processing helix chain 'B' and resid 81 through 93 Processing helix chain 'B' and resid 96 through 107 Processing helix chain 'B' and resid 110 through 112 No H-bonds generated for 'chain 'B' and resid 110 through 112' Processing helix chain 'B' and resid 115 through 120 removed outlier: 3.579A pdb=" N LYS B 120 " --> pdb=" O GLU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 149 Processing helix chain 'B' and resid 158 through 170 removed outlier: 3.681A pdb=" N MET B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 248 through 267 removed outlier: 4.544A pdb=" N GLY B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N PHE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASN B 267 " --> pdb=" O GLU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 277 No H-bonds generated for 'chain 'B' and resid 275 through 277' Processing helix chain 'B' and resid 279 through 286 removed outlier: 3.606A pdb=" N LYS B 283 " --> pdb=" O GLU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 308 No H-bonds generated for 'chain 'B' and resid 305 through 308' Processing helix chain 'B' and resid 311 through 325 Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 374 through 379 removed outlier: 3.705A pdb=" N VAL B 377 " --> pdb=" O ASP B 374 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG B 378 " --> pdb=" O ASP B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 408 Processing helix chain 'B' and resid 433 through 450 removed outlier: 3.730A pdb=" N VAL B 450 " --> pdb=" O THR B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 485 No H-bonds generated for 'chain 'B' and resid 483 through 485' Processing helix chain 'B' and resid 487 through 489 No H-bonds generated for 'chain 'B' and resid 487 through 489' Processing helix chain 'B' and resid 497 through 513 Processing helix chain 'B' and resid 519 through 536 Processing helix chain 'B' and resid 544 through 551 Processing helix chain 'B' and resid 559 through 561 No H-bonds generated for 'chain 'B' and resid 559 through 561' Processing helix chain 'B' and resid 576 through 583 Processing helix chain 'B' and resid 591 through 594 No H-bonds generated for 'chain 'B' and resid 591 through 594' Processing helix chain 'B' and resid 644 through 661 removed outlier: 4.266A pdb=" N ALA B 647 " --> pdb=" O PRO B 644 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 661 " --> pdb=" O VAL B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 694 Processing helix chain 'B' and resid 699 through 708 removed outlier: 3.601A pdb=" N ARG B 708 " --> pdb=" O ARG B 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 26 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 35 through 41 removed outlier: 3.694A pdb=" N ASN C 39 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE C 41 " --> pdb=" O TYR C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 60 removed outlier: 3.607A pdb=" N LEU C 57 " --> pdb=" O GLN C 54 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N VAL C 58 " --> pdb=" O MET C 55 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR C 59 " --> pdb=" O ARG C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 110 Proline residue: C 104 - end of helix removed outlier: 3.922A pdb=" N TYR C 110 " --> pdb=" O TRP C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 122 removed outlier: 3.594A pdb=" N ASN C 120 " --> pdb=" O LEU C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 135 Processing helix chain 'C' and resid 167 through 175 removed outlier: 3.888A pdb=" N GLN C 173 " --> pdb=" O HIS C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 193 through 203 Proline residue: C 202 - end of helix Processing helix chain 'C' and resid 209 through 220 removed outlier: 3.673A pdb=" N VAL C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N HIS C 214 " --> pdb=" O GLU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 244 No H-bonds generated for 'chain 'C' and resid 241 through 244' Processing sheet with id= A, first strand: chain 'A' and resid 57 through 59 Processing sheet with id= B, first strand: chain 'A' and resid 240 through 242 removed outlier: 6.586A pdb=" N ILE A 414 " --> pdb=" O TRP A 426 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N MET A 428 " --> pdb=" O CYS A 412 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N CYS A 412 " --> pdb=" O MET A 428 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU A 430 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N THR A 410 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 442 through 451 removed outlier: 4.084A pdb=" N LEU A 475 " --> pdb=" O MET A 451 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N SER A 466 " --> pdb=" O CYS A 262 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N CYS A 262 " --> pdb=" O SER A 466 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LYS A 468 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE A 260 " --> pdb=" O LYS A 468 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 527 through 531 Processing sheet with id= E, first strand: chain 'B' and resid 173 through 175 Processing sheet with id= F, first strand: chain 'B' and resid 178 through 180 Processing sheet with id= G, first strand: chain 'B' and resid 188 through 191 removed outlier: 3.948A pdb=" N GLN B 188 " --> pdb=" O VAL B 204 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 226 through 230 Processing sheet with id= I, first strand: chain 'B' and resid 460 through 462 Processing sheet with id= J, first strand: chain 'B' and resid 346 through 348 Processing sheet with id= K, first strand: chain 'B' and resid 353 through 357 removed outlier: 3.972A pdb=" N LEU B 360 " --> pdb=" O LYS B 357 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 467 through 470 Processing sheet with id= M, first strand: chain 'B' and resid 608 through 611 Processing sheet with id= N, first strand: chain 'C' and resid 67 through 69 removed outlier: 3.619A pdb=" N ILE C 67 " --> pdb=" O ALA C 99 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 141 through 143 removed outlier: 3.542A pdb=" N ARG C 142 " --> pdb=" O TYR C 250 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 149 through 154 removed outlier: 3.743A pdb=" N LYS C 151 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 227 " --> pdb=" O LYS C 151 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1170 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 4.35 Time building geometry restraints manager: 5.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4319 1.34 - 1.47: 3350 1.47 - 1.60: 6019 1.60 - 1.72: 37 1.72 - 1.85: 128 Bond restraints: 13853 Sorted by residual: bond pdb=" CB PRO A 55 " pdb=" CG PRO A 55 " ideal model delta sigma weight residual 1.492 1.583 -0.091 5.00e-02 4.00e+02 3.32e+00 bond pdb=" CA ARG B 323 " pdb=" C ARG B 323 " ideal model delta sigma weight residual 1.522 1.500 0.022 1.40e-02 5.10e+03 2.53e+00 bond pdb=" C ARG B 96 " pdb=" N PRO B 97 " ideal model delta sigma weight residual 1.334 1.355 -0.021 1.51e-02 4.39e+03 1.98e+00 bond pdb=" C ILE C 167 " pdb=" N PRO C 168 " ideal model delta sigma weight residual 1.335 1.353 -0.017 1.36e-02 5.41e+03 1.65e+00 bond pdb=" C3' A E 2 " pdb=" O3' A E 2 " ideal model delta sigma weight residual 1.427 1.445 -0.018 1.50e-02 4.44e+03 1.50e+00 ... (remaining 13848 not shown) Histogram of bond angle deviations from ideal: 98.70 - 105.77: 550 105.77 - 112.85: 7350 112.85 - 119.92: 4908 119.92 - 126.99: 5861 126.99 - 134.07: 261 Bond angle restraints: 18930 Sorted by residual: angle pdb=" CA PRO A 55 " pdb=" N PRO A 55 " pdb=" CD PRO A 55 " ideal model delta sigma weight residual 112.00 105.50 6.50 1.40e+00 5.10e-01 2.16e+01 angle pdb=" N SER A 616 " pdb=" CA SER A 616 " pdb=" C SER A 616 " ideal model delta sigma weight residual 114.09 107.18 6.91 1.55e+00 4.16e-01 1.99e+01 angle pdb=" N VAL C 230 " pdb=" CA VAL C 230 " pdb=" C VAL C 230 " ideal model delta sigma weight residual 111.48 107.72 3.76 9.40e-01 1.13e+00 1.60e+01 angle pdb=" N VAL B 669 " pdb=" CA VAL B 669 " pdb=" C VAL B 669 " ideal model delta sigma weight residual 112.83 108.96 3.87 9.90e-01 1.02e+00 1.53e+01 angle pdb=" C THR C 40 " pdb=" N PHE C 41 " pdb=" CA PHE C 41 " ideal model delta sigma weight residual 122.65 116.46 6.19 1.60e+00 3.91e-01 1.50e+01 ... (remaining 18925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.36: 8316 34.36 - 68.71: 181 68.71 - 103.07: 21 103.07 - 137.43: 1 137.43 - 171.79: 2 Dihedral angle restraints: 8521 sinusoidal: 3892 harmonic: 4629 Sorted by residual: dihedral pdb=" CA MET A 538 " pdb=" C MET A 538 " pdb=" N THR A 539 " pdb=" CA THR A 539 " ideal model delta harmonic sigma weight residual -180.00 -152.50 -27.50 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA HIS C 233 " pdb=" C HIS C 233 " pdb=" N THR C 234 " pdb=" CA THR C 234 " ideal model delta harmonic sigma weight residual 180.00 156.09 23.91 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" C4' A E 2 " pdb=" C3' A E 2 " pdb=" O3' A E 2 " pdb=" P C E 3 " ideal model delta sinusoidal sigma weight residual -110.00 61.79 -171.79 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 8518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1561 0.043 - 0.086: 441 0.086 - 0.129: 107 0.129 - 0.172: 12 0.172 - 0.215: 2 Chirality restraints: 2123 Sorted by residual: chirality pdb=" CB VAL A 132 " pdb=" CA VAL A 132 " pdb=" CG1 VAL A 132 " pdb=" CG2 VAL A 132 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C3' A E 2 " pdb=" C4' A E 2 " pdb=" O3' A E 2 " pdb=" C2' A E 2 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.19 2.00e-01 2.50e+01 8.66e-01 chirality pdb=" C3' C E 7 " pdb=" C4' C E 7 " pdb=" O3' C E 7 " pdb=" C2' C E 7 " both_signs ideal model delta sigma weight residual False -2.48 -2.33 -0.15 2.00e-01 2.50e+01 5.59e-01 ... (remaining 2120 not shown) Planarity restraints: 2301 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 54 " -0.067 5.00e-02 4.00e+02 9.89e-02 1.56e+01 pdb=" N PRO A 55 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO A 55 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 55 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 643 " 0.051 5.00e-02 4.00e+02 7.73e-02 9.56e+00 pdb=" N PRO B 644 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 644 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 644 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 96 " -0.046 5.00e-02 4.00e+02 7.00e-02 7.85e+00 pdb=" N PRO B 97 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 97 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 97 " -0.039 5.00e-02 4.00e+02 ... (remaining 2298 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 299 2.67 - 3.23: 13121 3.23 - 3.79: 21904 3.79 - 4.34: 31235 4.34 - 4.90: 49535 Nonbonded interactions: 116094 Sorted by model distance: nonbonded pdb=" OD1 ASN B 306 " pdb=" O2' G2P B 801 " model vdw 2.113 2.440 nonbonded pdb=" OG SER A 318 " pdb=" OE1 GLU A 320 " model vdw 2.138 2.440 nonbonded pdb=" OD2 ASP A 21 " pdb=" OG1 THR A 24 " model vdw 2.157 2.440 nonbonded pdb=" OG1 THR C 229 " pdb=" O VAL C 231 " model vdw 2.188 2.440 nonbonded pdb=" O ALA B 404 " pdb=" OG SER B 407 " model vdw 2.211 2.440 ... (remaining 116089 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 2.300 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 41.620 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 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:11.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 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 0.091 13853 Z= 0.191 Angle : 0.666 7.780 18930 Z= 0.392 Chirality : 0.042 0.215 2123 Planarity : 0.006 0.099 2301 Dihedral : 14.444 171.787 5515 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: -0.73 (0.21), residues: 1569 helix: 0.55 (0.21), residues: 678 sheet: -0.86 (0.38), residues: 180 loop : -1.37 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 13 HIS 0.007 0.001 HIS C 233 PHE 0.034 0.002 PHE C 149 TYR 0.018 0.001 TYR A 96 ARG 0.008 0.001 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 LEU cc_start: 0.9008 (mp) cc_final: 0.8800 (mp) REVERT: B 167 ASP cc_start: 0.7999 (m-30) cc_final: 0.7713 (m-30) REVERT: B 673 GLU cc_start: 0.7688 (mp0) cc_final: 0.7462 (mp0) REVERT: B 701 ARG cc_start: 0.7909 (mmp80) cc_final: 0.7173 (mmp80) REVERT: B 704 ARG cc_start: 0.8443 (ttt90) cc_final: 0.8133 (mtp85) REVERT: C 146 MET cc_start: 0.7917 (mmp) cc_final: 0.7645 (mpm) outliers start: 0 outliers final: 1 residues processed: 261 average time/residue: 1.5008 time to fit residues: 420.9401 Evaluate side-chains 181 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 180 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN A 358 ASN A 535 GLN B 148 GLN B 429 ASN B 650 ASN C 233 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13853 Z= 0.232 Angle : 0.595 8.580 18930 Z= 0.308 Chirality : 0.042 0.215 2123 Planarity : 0.006 0.059 2301 Dihedral : 13.809 168.565 2293 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.70 % Allowed : 9.89 % Favored : 88.41 % 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: -0.63 (0.21), residues: 1569 helix: 0.59 (0.20), residues: 680 sheet: -0.74 (0.38), residues: 181 loop : -1.30 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.005 0.001 HIS C 189 PHE 0.032 0.002 PHE C 41 TYR 0.011 0.001 TYR B 537 ARG 0.015 0.001 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 187 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 VAL cc_start: 0.8471 (p) cc_final: 0.8026 (m) REVERT: A 142 LYS cc_start: 0.8373 (tptt) cc_final: 0.8165 (tptt) REVERT: A 149 LEU cc_start: 0.9096 (mp) cc_final: 0.8870 (mp) REVERT: B 167 ASP cc_start: 0.8124 (m-30) cc_final: 0.7834 (m-30) REVERT: B 588 GLU cc_start: 0.6385 (pm20) cc_final: 0.6107 (pm20) REVERT: B 603 GLN cc_start: 0.7087 (OUTLIER) cc_final: 0.6880 (pt0) REVERT: B 624 TYR cc_start: 0.8730 (m-80) cc_final: 0.8506 (m-80) REVERT: B 673 GLU cc_start: 0.7746 (mp0) cc_final: 0.7533 (mp0) REVERT: B 689 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7345 (mt-10) REVERT: B 701 ARG cc_start: 0.7887 (mmp80) cc_final: 0.7134 (mmp80) REVERT: B 704 ARG cc_start: 0.8526 (ttt90) cc_final: 0.8029 (mtp85) REVERT: C 186 ARG cc_start: 0.8908 (mtm180) cc_final: 0.8357 (mtp180) outliers start: 24 outliers final: 6 residues processed: 200 average time/residue: 1.4921 time to fit residues: 321.6293 Evaluate side-chains 174 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 167 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 603 GLN Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain C residue 181 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 chunk 128 optimal weight: 0.0670 chunk 143 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN C 207 GLN C 233 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13853 Z= 0.161 Angle : 0.532 6.026 18930 Z= 0.275 Chirality : 0.040 0.200 2123 Planarity : 0.005 0.053 2301 Dihedral : 13.663 170.172 2291 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.20 % Allowed : 11.31 % Favored : 87.49 % 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: -0.50 (0.21), residues: 1569 helix: 0.66 (0.21), residues: 685 sheet: -0.57 (0.38), residues: 181 loop : -1.24 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.004 0.001 HIS A 115 PHE 0.026 0.001 PHE C 41 TYR 0.011 0.001 TYR C 250 ARG 0.011 0.001 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 184 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7442 (t0) REVERT: A 92 ARG cc_start: 0.8254 (ttm110) cc_final: 0.8026 (ttm110) REVERT: B 99 MET cc_start: 0.9150 (mmt) cc_final: 0.8858 (mmt) REVERT: B 144 GLU cc_start: 0.7783 (tp30) cc_final: 0.7547 (tm-30) REVERT: B 167 ASP cc_start: 0.8145 (m-30) cc_final: 0.7837 (m-30) REVERT: B 332 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8555 (mtp) REVERT: B 588 GLU cc_start: 0.6447 (pm20) cc_final: 0.6230 (pm20) REVERT: B 624 TYR cc_start: 0.8707 (m-80) cc_final: 0.8484 (m-80) REVERT: B 689 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7319 (mt-10) REVERT: B 701 ARG cc_start: 0.7863 (mmp80) cc_final: 0.7069 (mmp80) REVERT: B 703 LYS cc_start: 0.8661 (pptt) cc_final: 0.8460 (pptt) REVERT: B 704 ARG cc_start: 0.8411 (ttt90) cc_final: 0.8103 (mtp85) REVERT: B 706 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8749 (mm) REVERT: C 113 GLN cc_start: 0.8990 (mt0) cc_final: 0.8760 (mt0) REVERT: C 186 ARG cc_start: 0.8915 (mtm180) cc_final: 0.8439 (mtp180) outliers start: 17 outliers final: 9 residues processed: 196 average time/residue: 1.5121 time to fit residues: 319.3713 Evaluate side-chains 178 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 166 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 181 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 69 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 153 optimal weight: 0.7980 chunk 137 optimal weight: 0.0470 chunk 41 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 GLN A 358 ASN A 473 GLN ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN B 603 GLN ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 ASN C 131 GLN C 233 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13853 Z= 0.158 Angle : 0.520 6.226 18930 Z= 0.268 Chirality : 0.040 0.182 2123 Planarity : 0.005 0.060 2301 Dihedral : 13.600 168.684 2291 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.55 % Allowed : 11.94 % Favored : 86.50 % 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: -0.32 (0.21), residues: 1569 helix: 0.79 (0.21), residues: 684 sheet: -0.40 (0.37), residues: 182 loop : -1.13 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.004 0.001 HIS A 115 PHE 0.025 0.001 PHE C 41 TYR 0.010 0.001 TYR B 533 ARG 0.009 0.001 ARG B 708 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 183 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7445 (t0) REVERT: A 92 ARG cc_start: 0.8336 (ttm110) cc_final: 0.8049 (ttm110) REVERT: A 147 ARG cc_start: 0.8220 (mtm-85) cc_final: 0.7726 (mtm-85) REVERT: B 144 GLU cc_start: 0.7790 (tp30) cc_final: 0.7551 (tm-30) REVERT: B 167 ASP cc_start: 0.8170 (m-30) cc_final: 0.7861 (m-30) REVERT: B 332 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8567 (mtp) REVERT: B 369 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8200 (mtp) REVERT: B 588 GLU cc_start: 0.6341 (pm20) cc_final: 0.6106 (pm20) REVERT: B 689 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7367 (mt-10) REVERT: B 704 ARG cc_start: 0.8494 (ttt90) cc_final: 0.8040 (mtp85) REVERT: C 69 MET cc_start: 0.9254 (ttp) cc_final: 0.8945 (ttp) REVERT: C 186 ARG cc_start: 0.8911 (mtm180) cc_final: 0.8479 (mtp180) outliers start: 22 outliers final: 9 residues processed: 195 average time/residue: 1.5904 time to fit residues: 333.1590 Evaluate side-chains 177 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 165 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain C residue 181 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 90 ASN A 156 ASN ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 GLN C 163 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 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 : 0.005 0.051 13853 Z= 0.358 Angle : 0.620 8.202 18930 Z= 0.319 Chirality : 0.044 0.211 2123 Planarity : 0.005 0.056 2301 Dihedral : 13.739 169.238 2291 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.47 % Allowed : 12.86 % Favored : 84.66 % 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: -0.43 (0.21), residues: 1569 helix: 0.65 (0.20), residues: 688 sheet: -0.49 (0.37), residues: 185 loop : -1.13 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.003 0.001 HIS C 189 PHE 0.030 0.002 PHE C 41 TYR 0.014 0.002 TYR B 115 ARG 0.010 0.001 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 174 time to evaluate : 1.707 Fit side-chains revert: symmetry clash REVERT: A 21 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7601 (t0) REVERT: A 156 ASN cc_start: 0.8475 (t0) cc_final: 0.8163 (t0) REVERT: A 322 LYS cc_start: 0.8706 (ptpt) cc_final: 0.8504 (pttp) REVERT: B 96 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7469 (tmt170) REVERT: B 144 GLU cc_start: 0.7847 (tp30) cc_final: 0.7577 (tm-30) REVERT: B 167 ASP cc_start: 0.8272 (m-30) cc_final: 0.8005 (m-30) REVERT: B 332 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8699 (mtp) REVERT: B 588 GLU cc_start: 0.6450 (pm20) cc_final: 0.6212 (pm20) REVERT: B 686 ARG cc_start: 0.8038 (mmp80) cc_final: 0.7470 (mmp80) REVERT: B 689 GLU cc_start: 0.7718 (mt-10) cc_final: 0.6649 (mt-10) REVERT: B 694 ARG cc_start: 0.9100 (mtp-110) cc_final: 0.8894 (mtp85) REVERT: B 701 ARG cc_start: 0.7860 (mmp80) cc_final: 0.6779 (mmp80) REVERT: B 704 ARG cc_start: 0.8368 (ttt90) cc_final: 0.8135 (mtp85) REVERT: C 69 MET cc_start: 0.9338 (ttp) cc_final: 0.8846 (ptm) outliers start: 35 outliers final: 15 residues processed: 197 average time/residue: 1.5261 time to fit residues: 324.5404 Evaluate side-chains 183 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 165 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 233 HIS Chi-restraints excluded: chain C residue 251 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 0.0970 chunk 30 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 12 optimal weight: 30.0000 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 ASN ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13853 Z= 0.218 Angle : 0.559 9.023 18930 Z= 0.287 Chirality : 0.041 0.201 2123 Planarity : 0.005 0.068 2301 Dihedral : 13.700 168.818 2291 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.12 % Allowed : 14.63 % Favored : 83.25 % 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: -0.28 (0.21), residues: 1569 helix: 0.75 (0.21), residues: 687 sheet: -0.42 (0.38), residues: 175 loop : -1.01 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.003 0.001 HIS A 115 PHE 0.027 0.001 PHE C 41 TYR 0.010 0.001 TYR C 250 ARG 0.015 0.001 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 172 time to evaluate : 1.523 Fit side-chains revert: symmetry clash REVERT: A 21 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7529 (t0) REVERT: A 133 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8482 (mp) REVERT: A 134 ARG cc_start: 0.8764 (mtm110) cc_final: 0.8540 (mtm110) REVERT: A 147 ARG cc_start: 0.8227 (mtm-85) cc_final: 0.7600 (mtm-85) REVERT: A 156 ASN cc_start: 0.8414 (t0) cc_final: 0.8103 (t0) REVERT: B 144 GLU cc_start: 0.7833 (tp30) cc_final: 0.7571 (tm-30) REVERT: B 167 ASP cc_start: 0.8309 (m-30) cc_final: 0.8066 (m-30) REVERT: B 332 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8633 (mtp) REVERT: B 588 GLU cc_start: 0.6419 (pm20) cc_final: 0.6195 (pm20) REVERT: B 686 ARG cc_start: 0.8024 (mmp80) cc_final: 0.7430 (mmp80) REVERT: B 689 GLU cc_start: 0.7705 (mt-10) cc_final: 0.6620 (mt-10) REVERT: B 694 ARG cc_start: 0.9093 (mtp-110) cc_final: 0.8889 (mtp85) REVERT: B 704 ARG cc_start: 0.8494 (ttt90) cc_final: 0.8049 (mtp85) REVERT: C 69 MET cc_start: 0.9328 (ttp) cc_final: 0.8863 (ptm) outliers start: 30 outliers final: 14 residues processed: 190 average time/residue: 1.5097 time to fit residues: 308.9365 Evaluate side-chains 181 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 164 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 233 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 ASN C 131 GLN C 163 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13853 Z= 0.217 Angle : 0.555 9.869 18930 Z= 0.285 Chirality : 0.041 0.177 2123 Planarity : 0.005 0.070 2301 Dihedral : 13.685 168.854 2291 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.84 % Allowed : 14.84 % Favored : 83.32 % 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: -0.24 (0.21), residues: 1569 helix: 0.76 (0.20), residues: 691 sheet: -0.42 (0.39), residues: 175 loop : -0.97 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.003 0.001 HIS C 189 PHE 0.026 0.002 PHE C 41 TYR 0.012 0.001 TYR C 250 ARG 0.017 0.001 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 176 time to evaluate : 1.621 Fit side-chains revert: symmetry clash REVERT: A 21 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7524 (t0) REVERT: A 49 HIS cc_start: 0.8006 (m-70) cc_final: 0.7667 (m-70) REVERT: A 133 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8479 (mp) REVERT: A 147 ARG cc_start: 0.8203 (mtm-85) cc_final: 0.7965 (mtm-85) REVERT: A 156 ASN cc_start: 0.8456 (t0) cc_final: 0.8156 (t0) REVERT: B 167 ASP cc_start: 0.8305 (m-30) cc_final: 0.8050 (m-30) REVERT: B 332 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8603 (mtp) REVERT: B 588 GLU cc_start: 0.6361 (pm20) cc_final: 0.6159 (pm20) REVERT: B 686 ARG cc_start: 0.8027 (mmp80) cc_final: 0.7417 (mmp80) REVERT: B 689 GLU cc_start: 0.7684 (mt-10) cc_final: 0.6535 (mt-10) REVERT: B 704 ARG cc_start: 0.8365 (ttt90) cc_final: 0.8115 (mtp85) REVERT: C 69 MET cc_start: 0.9340 (ttp) cc_final: 0.8967 (ttp) outliers start: 26 outliers final: 13 residues processed: 190 average time/residue: 1.5807 time to fit residues: 322.2336 Evaluate side-chains 181 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 165 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 233 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 146 optimal weight: 0.3980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 GLN ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 ASN C 131 GLN C 233 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13853 Z= 0.238 Angle : 0.578 10.572 18930 Z= 0.296 Chirality : 0.042 0.212 2123 Planarity : 0.005 0.076 2301 Dihedral : 13.704 168.724 2291 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.19 % Allowed : 15.41 % Favored : 82.40 % 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: -0.19 (0.21), residues: 1569 helix: 0.79 (0.20), residues: 691 sheet: -0.37 (0.38), residues: 174 loop : -0.95 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.003 0.001 HIS C 189 PHE 0.026 0.002 PHE C 41 TYR 0.013 0.001 TYR C 250 ARG 0.018 0.001 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 172 time to evaluate : 1.455 Fit side-chains revert: symmetry clash REVERT: A 21 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7529 (t0) REVERT: A 99 LEU cc_start: 0.8050 (tp) cc_final: 0.7614 (tt) REVERT: A 133 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8429 (mp) REVERT: A 156 ASN cc_start: 0.8551 (t0) cc_final: 0.8264 (t0) REVERT: B 167 ASP cc_start: 0.8324 (m-30) cc_final: 0.8034 (m-30) REVERT: B 248 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.7928 (tpt) REVERT: B 332 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8582 (mtp) REVERT: B 686 ARG cc_start: 0.8015 (mmp80) cc_final: 0.7366 (mmp80) REVERT: B 689 GLU cc_start: 0.7694 (mt-10) cc_final: 0.6512 (mt-10) REVERT: B 704 ARG cc_start: 0.8449 (ttt90) cc_final: 0.8143 (mtp85) REVERT: C 69 MET cc_start: 0.9324 (ttp) cc_final: 0.8956 (ttp) REVERT: C 127 ASP cc_start: 0.7493 (t70) cc_final: 0.7234 (t70) outliers start: 31 outliers final: 17 residues processed: 189 average time/residue: 1.5464 time to fit residues: 315.1358 Evaluate side-chains 184 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 163 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 172 ASP Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 703 LYS Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 251 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 0.0170 chunk 142 optimal weight: 0.0030 chunk 146 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 62 optimal weight: 0.4980 chunk 112 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 151 optimal weight: 8.9990 overall best weight: 0.4428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 ASN ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 GLN C 163 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13853 Z= 0.151 Angle : 0.555 11.004 18930 Z= 0.283 Chirality : 0.040 0.176 2123 Planarity : 0.005 0.087 2301 Dihedral : 13.619 168.161 2291 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.20 % Allowed : 16.33 % Favored : 82.47 % 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: -0.01 (0.21), residues: 1569 helix: 0.94 (0.21), residues: 684 sheet: -0.32 (0.38), residues: 176 loop : -0.82 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.006 0.001 HIS A 51 PHE 0.023 0.001 PHE C 41 TYR 0.014 0.001 TYR C 250 ARG 0.023 0.001 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 177 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LEU cc_start: 0.7844 (tp) cc_final: 0.7476 (tt) REVERT: A 133 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8412 (mp) REVERT: A 147 ARG cc_start: 0.8225 (mtm-85) cc_final: 0.7645 (mtm-85) REVERT: A 156 ASN cc_start: 0.8592 (t0) cc_final: 0.8317 (t0) REVERT: A 196 ARG cc_start: 0.7752 (mmm160) cc_final: 0.7456 (mmm160) REVERT: B 167 ASP cc_start: 0.8309 (m-30) cc_final: 0.8043 (m-30) REVERT: B 307 GLU cc_start: 0.8310 (mp0) cc_final: 0.7893 (mp0) REVERT: B 588 GLU cc_start: 0.6292 (pm20) cc_final: 0.6078 (pm20) REVERT: B 686 ARG cc_start: 0.7996 (mmp80) cc_final: 0.7402 (mmp80) REVERT: B 689 GLU cc_start: 0.7667 (mt-10) cc_final: 0.6493 (mt-10) REVERT: C 69 MET cc_start: 0.9289 (ttp) cc_final: 0.8930 (ttp) REVERT: C 127 ASP cc_start: 0.7407 (t70) cc_final: 0.7044 (t70) REVERT: C 131 GLN cc_start: 0.7976 (mt0) cc_final: 0.7759 (mt0) REVERT: C 140 GLU cc_start: 0.7225 (pp20) cc_final: 0.6959 (pp20) outliers start: 17 outliers final: 10 residues processed: 183 average time/residue: 1.5815 time to fit residues: 311.0815 Evaluate side-chains 178 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 167 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 703 LYS Chi-restraints excluded: chain C residue 206 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 158 optimal weight: 10.0000 chunk 145 optimal weight: 0.6980 chunk 126 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13853 Z= 0.173 Angle : 0.559 12.299 18930 Z= 0.284 Chirality : 0.040 0.174 2123 Planarity : 0.005 0.081 2301 Dihedral : 13.612 167.946 2291 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.99 % Allowed : 16.96 % Favored : 82.05 % 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: 0.05 (0.21), residues: 1569 helix: 1.00 (0.21), residues: 683 sheet: -0.33 (0.38), residues: 176 loop : -0.77 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.006 0.001 HIS C 233 PHE 0.023 0.001 PHE C 41 TYR 0.015 0.001 TYR C 250 ARG 0.019 0.001 ARG A 196 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 170 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LEU cc_start: 0.7860 (tp) cc_final: 0.7469 (tt) REVERT: A 120 ASN cc_start: 0.8033 (p0) cc_final: 0.7505 (t0) REVERT: A 147 ARG cc_start: 0.8229 (mtm-85) cc_final: 0.7665 (mtm-85) REVERT: A 156 ASN cc_start: 0.8606 (t0) cc_final: 0.8336 (t0) REVERT: B 167 ASP cc_start: 0.8313 (m-30) cc_final: 0.8025 (m-30) REVERT: B 307 GLU cc_start: 0.8329 (mp0) cc_final: 0.7886 (mp0) REVERT: B 588 GLU cc_start: 0.6171 (pm20) cc_final: 0.5951 (pm20) REVERT: B 686 ARG cc_start: 0.7998 (mmp80) cc_final: 0.7351 (mmp80) REVERT: B 689 GLU cc_start: 0.7655 (mt-10) cc_final: 0.6469 (mt-10) REVERT: C 69 MET cc_start: 0.9295 (ttp) cc_final: 0.8969 (ttp) REVERT: C 140 GLU cc_start: 0.7231 (pp20) cc_final: 0.6957 (pp20) outliers start: 14 outliers final: 13 residues processed: 176 average time/residue: 1.6267 time to fit residues: 307.7332 Evaluate side-chains 175 residues out of total 1415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 162 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 703 LYS Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 251 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 129 optimal weight: 0.2980 chunk 15 optimal weight: 0.3980 chunk 23 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 ASN ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.110773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.086273 restraints weight = 20889.549| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.13 r_work: 0.2934 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13853 Z= 0.167 Angle : 0.557 11.950 18930 Z= 0.284 Chirality : 0.040 0.203 2123 Planarity : 0.005 0.089 2301 Dihedral : 13.598 167.562 2291 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.27 % Allowed : 16.68 % Favored : 82.05 % 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: 0.10 (0.21), residues: 1569 helix: 1.03 (0.21), residues: 683 sheet: -0.32 (0.38), residues: 176 loop : -0.74 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.006 0.001 HIS C 233 PHE 0.023 0.001 PHE C 41 TYR 0.013 0.001 TYR C 250 ARG 0.022 0.001 ARG A 196 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5500.90 seconds wall clock time: 96 minutes 41.87 seconds (5801.87 seconds total)