Starting phenix.real_space_refine on Mon Jul 22 09:32:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxg_16318/07_2024/8bxg_16318_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxg_16318/07_2024/8bxg_16318.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxg_16318/07_2024/8bxg_16318.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxg_16318/07_2024/8bxg_16318.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxg_16318/07_2024/8bxg_16318_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxg_16318/07_2024/8bxg_16318_trim.cif" } resolution = 3.16 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= 1.000 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: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 4 5.49 5 S 54 5.16 5 C 5547 2.51 5 N 1426 2.21 5 O 1472 1.98 5 H 8796 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 217": "OE1" <-> "OE2" Residue "A PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 2": "OD1" <-> "OD2" Residue "B PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 264": "OD1" <-> "OD2" Residue "B GLU 542": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 17301 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 8584 Classifications: {'peptide': 547} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 18, 'TRANS': 528} Chain breaks: 1 Chain: "B" Number of atoms: 8567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 8567 Classifications: {'peptide': 546} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 18, 'TRANS': 527} Chain breaks: 1 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' K': 1, 'PGW': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 2} Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' K': 1, 'PGW': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 2} Time building chain proxies: 8.77, per 1000 atoms: 0.51 Number of scatterers: 17301 At special positions: 0 Unit cell: (92.6978, 73.7595, 111.636, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 2 19.00 S 54 16.00 P 4 15.00 O 1472 8.00 N 1426 7.00 C 5547 6.00 H 8796 1.00 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: 14.51 Conformation dependent library (CDL) restraints added in 2.1 seconds 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1990 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 2 sheets defined 78.8% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 2 through 26 removed outlier: 5.714A pdb=" N VAL A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Proline residue: A 21 - end of helix Processing helix chain 'A' and resid 29 through 42 Processing helix chain 'A' and resid 52 through 72 Processing helix chain 'A' and resid 75 through 82 Processing helix chain 'A' and resid 82 through 97 removed outlier: 4.647A pdb=" N ALA A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 109 Processing helix chain 'A' and resid 112 through 123 removed outlier: 3.843A pdb=" N GLU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A 117 " --> pdb=" O GLN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 136 removed outlier: 3.534A pdb=" N GLU A 136 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 171 Proline residue: A 161 - end of helix removed outlier: 3.765A pdb=" N ILE A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Proline residue: A 167 - end of helix removed outlier: 3.824A pdb=" N ALA A 170 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 185 through 200 removed outlier: 4.043A pdb=" N LEU A 198 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 199 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 217 through 238 Processing helix chain 'A' and resid 240 through 255 removed outlier: 4.046A pdb=" N GLY A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 245 " --> pdb=" O MET A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 284 Proline residue: A 267 - end of helix removed outlier: 4.637A pdb=" N GLY A 270 " --> pdb=" O GLU A 266 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LEU A 271 " --> pdb=" O PRO A 267 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 292 removed outlier: 3.767A pdb=" N LEU A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 316 removed outlier: 3.741A pdb=" N LEU A 299 " --> pdb=" O ARG A 295 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLY A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARG A 316 " --> pdb=" O TRP A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 337 through 350 removed outlier: 3.861A pdb=" N VAL A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 370 removed outlier: 3.781A pdb=" N LYS A 358 " --> pdb=" O PRO A 354 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 385 removed outlier: 3.642A pdb=" N LEU A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 421 removed outlier: 3.630A pdb=" N SER A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 440 removed outlier: 3.672A pdb=" N ARG A 439 " --> pdb=" O GLU A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 460 Processing helix chain 'A' and resid 473 through 488 Processing helix chain 'A' and resid 499 through 510 Processing helix chain 'A' and resid 519 through 534 Processing helix chain 'A' and resid 536 through 560 removed outlier: 3.775A pdb=" N GLU A 542 " --> pdb=" O TYR A 538 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 27 removed outlier: 3.789A pdb=" N VAL B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Proline residue: B 21 - end of helix Processing helix chain 'B' and resid 31 through 42 removed outlier: 3.845A pdb=" N LEU B 35 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 74 removed outlier: 3.574A pdb=" N LEU B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 82 removed outlier: 4.297A pdb=" N LYS B 81 " --> pdb=" O GLN B 77 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 82 " --> pdb=" O ARG B 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 77 through 82' Processing helix chain 'B' and resid 89 through 108 removed outlier: 3.846A pdb=" N GLN B 93 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 99 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B 100 " --> pdb=" O ILE B 96 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 103 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B 108 " --> pdb=" O PHE B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 123 removed outlier: 3.977A pdb=" N LEU B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET B 120 " --> pdb=" O GLU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 138 Processing helix chain 'B' and resid 142 through 158 Processing helix chain 'B' and resid 159 through 165 Processing helix chain 'B' and resid 165 through 172 Processing helix chain 'B' and resid 176 through 202 Processing helix chain 'B' and resid 203 through 213 removed outlier: 3.807A pdb=" N SER B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 237 removed outlier: 3.643A pdb=" N VAL B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 removed outlier: 3.835A pdb=" N LEU B 247 " --> pdb=" O MET B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 266 Processing helix chain 'B' and resid 268 through 284 removed outlier: 3.984A pdb=" N PHE B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 292 Processing helix chain 'B' and resid 293 through 314 removed outlier: 3.876A pdb=" N VAL B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU B 299 " --> pdb=" O ARG B 295 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 319 Processing helix chain 'B' and resid 321 through 331 removed outlier: 4.411A pdb=" N ARG B 326 " --> pdb=" O ASN B 322 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TRP B 327 " --> pdb=" O LYS B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.925A pdb=" N VAL B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 370 Processing helix chain 'B' and resid 370 through 384 removed outlier: 3.930A pdb=" N LEU B 374 " --> pdb=" O ALA B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 422 removed outlier: 3.592A pdb=" N ILE B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU B 417 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B 418 " --> pdb=" O THR B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 440 removed outlier: 3.552A pdb=" N ARG B 439 " --> pdb=" O GLU B 436 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LYS B 440 " --> pdb=" O THR B 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 436 through 440' Processing helix chain 'B' and resid 452 through 456 removed outlier: 3.611A pdb=" N LEU B 456 " --> pdb=" O MET B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 464 Processing helix chain 'B' and resid 473 through 488 removed outlier: 3.742A pdb=" N MET B 483 " --> pdb=" O GLN B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 510 removed outlier: 3.911A pdb=" N ARG B 505 " --> pdb=" O ASP B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 534 Processing helix chain 'B' and resid 536 through 560 removed outlier: 3.519A pdb=" N ALA B 544 " --> pdb=" O ALA B 540 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP B 545 " --> pdb=" O ARG B 541 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL B 546 " --> pdb=" O GLU B 542 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE B 547 " --> pdb=" O ARG B 543 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 445 through 447 removed outlier: 6.659A pdb=" N ILE A 403 " --> pdb=" O ILE A 468 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU A 467 " --> pdb=" O ILE A 494 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ARG A 496 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASN A 469 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA A 495 " --> pdb=" O GLU A 515 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 424 through 428 removed outlier: 6.518A pdb=" N VAL B 402 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N LEU B 428 " --> pdb=" O VAL B 402 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE B 404 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B 466 " --> pdb=" O ARG B 401 " (cutoff:3.500A) 558 hydrogen bonds defined for protein. 1644 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.96 Time building geometry restraints manager: 15.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8790 1.03 - 1.23: 31 1.23 - 1.42: 3393 1.42 - 1.62: 5127 1.62 - 1.81: 106 Bond restraints: 17447 Sorted by residual: bond pdb=" CG PRO B 205 " pdb=" CD PRO B 205 " ideal model delta sigma weight residual 1.503 1.444 0.059 3.40e-02 8.65e+02 2.97e+00 bond pdb=" CB PRO B 317 " pdb=" CG PRO B 317 " ideal model delta sigma weight residual 1.492 1.557 -0.065 5.00e-02 4.00e+02 1.70e+00 bond pdb=" CB PRO B 205 " pdb=" CG PRO B 205 " ideal model delta sigma weight residual 1.492 1.556 -0.064 5.00e-02 4.00e+02 1.64e+00 bond pdb=" C4 AMP A 602 " pdb=" C5 AMP A 602 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.60e+00 bond pdb=" C4 AMP B 602 " pdb=" C5 AMP B 602 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.49e+00 ... (remaining 17442 not shown) Histogram of bond angle deviations from ideal: 97.94 - 105.68: 167 105.68 - 113.41: 21154 113.41 - 121.15: 7144 121.15 - 128.88: 3121 128.88 - 136.62: 48 Bond angle restraints: 31634 Sorted by residual: angle pdb=" CA PRO B 205 " pdb=" N PRO B 205 " pdb=" CD PRO B 205 " ideal model delta sigma weight residual 112.00 105.41 6.59 1.40e+00 5.10e-01 2.22e+01 angle pdb=" CA PRO B 317 " pdb=" N PRO B 317 " pdb=" CD PRO B 317 " ideal model delta sigma weight residual 112.00 106.38 5.62 1.40e+00 5.10e-01 1.61e+01 angle pdb=" N PRO B 205 " pdb=" CD PRO B 205 " pdb=" CG PRO B 205 " ideal model delta sigma weight residual 103.20 97.94 5.26 1.50e+00 4.44e-01 1.23e+01 angle pdb=" N GLY A 98 " pdb=" CA GLY A 98 " pdb=" C GLY A 98 " ideal model delta sigma weight residual 113.18 107.58 5.60 2.37e+00 1.78e-01 5.59e+00 angle pdb=" CB MET B 106 " pdb=" CG MET B 106 " pdb=" SD MET B 106 " ideal model delta sigma weight residual 112.70 119.76 -7.06 3.00e+00 1.11e-01 5.53e+00 ... (remaining 31629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.50: 7647 34.50 - 69.01: 410 69.01 - 103.51: 24 103.51 - 138.01: 1 138.01 - 172.52: 6 Dihedral angle restraints: 8088 sinusoidal: 4519 harmonic: 3569 Sorted by residual: dihedral pdb=" C5' AMP B 602 " pdb=" O5' AMP B 602 " pdb=" P AMP B 602 " pdb=" O3P AMP B 602 " ideal model delta sinusoidal sigma weight residual -60.00 65.59 -125.59 1 2.00e+01 2.50e-03 3.80e+01 dihedral pdb=" C03 PGW B 603 " pdb=" C01 PGW B 603 " pdb=" C02 PGW B 603 " pdb=" O03 PGW B 603 " ideal model delta sinusoidal sigma weight residual 295.35 122.83 172.52 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O01 PGW B 603 " pdb=" C01 PGW B 603 " pdb=" C02 PGW B 603 " pdb=" O03 PGW B 603 " ideal model delta sinusoidal sigma weight residual 59.30 -112.75 172.05 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 8085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 991 0.028 - 0.056: 253 0.056 - 0.084: 95 0.084 - 0.113: 46 0.113 - 0.141: 6 Chirality restraints: 1391 Sorted by residual: chirality pdb=" CA ILE A 494 " pdb=" N ILE A 494 " pdb=" C ILE A 494 " pdb=" CB ILE A 494 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA VAL A 426 " pdb=" N VAL A 426 " pdb=" C VAL A 426 " pdb=" CB VAL A 426 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA ILE B 494 " pdb=" N ILE B 494 " pdb=" C ILE B 494 " pdb=" CB ILE B 494 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.69e-01 ... (remaining 1388 not shown) Planarity restraints: 2501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 316 " 0.068 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO B 317 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO B 317 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 317 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 204 " 0.057 5.00e-02 4.00e+02 8.25e-02 1.09e+01 pdb=" N PRO B 205 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO B 205 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 205 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 160 " 0.046 5.00e-02 4.00e+02 6.87e-02 7.56e+00 pdb=" N PRO A 161 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " 0.038 5.00e-02 4.00e+02 ... (remaining 2498 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.31: 3705 2.31 - 3.01: 47171 3.01 - 3.72: 60982 3.72 - 4.43: 91969 4.43 - 5.14: 144625 Nonbonded interactions: 348452 Sorted by model distance: nonbonded pdb=" HB2 GLN A 492 " pdb="HE21 GLN A 492 " model vdw 1.598 2.270 nonbonded pdb="HH22 ARG B 295 " pdb=" OE2 GLU B 355 " model vdw 1.679 1.850 nonbonded pdb=" OD1 ASP A 285 " pdb=" H GLY A 287 " model vdw 1.695 1.850 nonbonded pdb=" O VAL A 202 " pdb=" HG1 THR A 203 " model vdw 1.703 1.850 nonbonded pdb=" OE1 GLU A 436 " pdb=" H GLU A 436 " model vdw 1.745 1.850 ... (remaining 348447 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 385 or resid 400 through 560 or resid 601 throug \ h 603)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 0.140 Extract box with map and model: 0.630 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 60.830 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 0.065 8651 Z= 0.198 Angle : 0.536 7.057 11691 Z= 0.276 Chirality : 0.034 0.141 1391 Planarity : 0.005 0.100 1447 Dihedral : 19.913 172.517 3200 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.12 % Allowed : 26.93 % Favored : 72.96 % 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: 1.42 (0.28), residues: 1085 helix: 2.00 (0.19), residues: 811 sheet: -1.24 (0.69), residues: 60 loop : -2.71 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 80 HIS 0.003 0.001 HIS B 434 PHE 0.009 0.001 PHE A 154 TYR 0.007 0.001 TYR B 503 ARG 0.002 0.000 ARG A 541 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 1.415 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 130 average time/residue: 0.3388 time to fit residues: 66.7251 Evaluate side-chains 128 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.0278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8651 Z= 0.232 Angle : 0.530 7.415 11691 Z= 0.267 Chirality : 0.034 0.141 1391 Planarity : 0.004 0.070 1447 Dihedral : 14.542 171.847 1281 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 1.38 % Allowed : 26.58 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.28), residues: 1085 helix: 1.94 (0.19), residues: 809 sheet: -1.18 (0.70), residues: 60 loop : -2.68 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 44 HIS 0.002 0.001 HIS A 502 PHE 0.008 0.001 PHE A 154 TYR 0.007 0.001 TYR B 503 ARG 0.003 0.000 ARG B 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 434 HIS cc_start: 0.5699 (OUTLIER) cc_final: 0.5292 (m-70) outliers start: 12 outliers final: 5 residues processed: 136 average time/residue: 0.3407 time to fit residues: 70.2340 Evaluate side-chains 133 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 127 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 444 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.0363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8651 Z= 0.216 Angle : 0.522 7.136 11691 Z= 0.262 Chirality : 0.034 0.140 1391 Planarity : 0.004 0.064 1447 Dihedral : 14.032 173.885 1281 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 1.61 % Allowed : 26.58 % 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: 1.29 (0.27), residues: 1085 helix: 1.89 (0.19), residues: 809 sheet: -1.14 (0.69), residues: 60 loop : -2.67 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 44 HIS 0.005 0.001 HIS A 430 PHE 0.008 0.001 PHE A 154 TYR 0.007 0.001 TYR B 503 ARG 0.003 0.000 ARG B 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 132 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 HIS cc_start: 0.5804 (OUTLIER) cc_final: 0.5398 (m-70) REVERT: A 507 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8310 (mmm160) outliers start: 14 outliers final: 11 residues processed: 140 average time/residue: 0.3409 time to fit residues: 72.2830 Evaluate side-chains 142 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 455 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.0485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8651 Z= 0.233 Angle : 0.528 7.402 11691 Z= 0.266 Chirality : 0.034 0.141 1391 Planarity : 0.004 0.059 1447 Dihedral : 13.816 174.438 1281 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.30 % Allowed : 26.01 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.27), residues: 1085 helix: 1.84 (0.19), residues: 809 sheet: -1.18 (0.69), residues: 60 loop : -2.72 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 44 HIS 0.004 0.001 HIS A 430 PHE 0.008 0.001 PHE A 154 TYR 0.008 0.001 TYR A 538 ARG 0.003 0.000 ARG B 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 HIS cc_start: 0.5878 (OUTLIER) cc_final: 0.5469 (m-70) REVERT: A 507 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8308 (mmm160) REVERT: B 412 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8599 (mt0) outliers start: 20 outliers final: 15 residues processed: 145 average time/residue: 0.3547 time to fit residues: 78.5342 Evaluate side-chains 149 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 412 GLN Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 455 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 0 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.0623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8651 Z= 0.281 Angle : 0.549 7.938 11691 Z= 0.280 Chirality : 0.035 0.139 1391 Planarity : 0.004 0.056 1447 Dihedral : 13.447 175.703 1281 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 2.99 % Allowed : 25.43 % Favored : 71.58 % 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: 0.99 (0.27), residues: 1085 helix: 1.68 (0.19), residues: 809 sheet: -1.27 (0.68), residues: 60 loop : -2.82 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 44 HIS 0.004 0.001 HIS A 430 PHE 0.010 0.001 PHE B 303 TYR 0.008 0.001 TYR A 201 ARG 0.003 0.000 ARG B 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 507 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8329 (mmm160) REVERT: B 135 ASN cc_start: 0.8909 (m-40) cc_final: 0.8638 (m-40) REVERT: B 412 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8601 (mt0) outliers start: 26 outliers final: 22 residues processed: 150 average time/residue: 0.3462 time to fit residues: 77.8916 Evaluate side-chains 153 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 412 GLN Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 455 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.0030 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 overall best weight: 1.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.0561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8651 Z= 0.167 Angle : 0.513 6.952 11691 Z= 0.255 Chirality : 0.034 0.141 1391 Planarity : 0.004 0.053 1447 Dihedral : 13.183 174.876 1281 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.42 % Allowed : 25.78 % 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: 1.28 (0.27), residues: 1085 helix: 1.90 (0.19), residues: 809 sheet: -1.24 (0.68), residues: 60 loop : -2.73 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 44 HIS 0.004 0.001 HIS A 430 PHE 0.009 0.001 PHE A 154 TYR 0.007 0.001 TYR B 503 ARG 0.002 0.000 ARG B 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 HIS cc_start: 0.5764 (OUTLIER) cc_final: 0.5355 (m-70) REVERT: A 507 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8301 (mmm160) REVERT: B 412 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8585 (mt0) outliers start: 21 outliers final: 15 residues processed: 153 average time/residue: 0.3295 time to fit residues: 76.4747 Evaluate side-chains 151 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 412 GLN Chi-restraints excluded: chain B residue 455 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.0633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8651 Z= 0.238 Angle : 0.531 7.433 11691 Z= 0.267 Chirality : 0.034 0.140 1391 Planarity : 0.004 0.052 1447 Dihedral : 13.141 175.283 1281 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 2.76 % Allowed : 25.66 % Favored : 71.58 % 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: 1.13 (0.27), residues: 1085 helix: 1.79 (0.19), residues: 809 sheet: -1.30 (0.67), residues: 60 loop : -2.78 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 44 HIS 0.004 0.001 HIS A 430 PHE 0.008 0.001 PHE B 303 TYR 0.007 0.001 TYR A 201 ARG 0.003 0.000 ARG B 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 507 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8322 (mmm160) REVERT: B 412 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8592 (mt0) outliers start: 24 outliers final: 19 residues processed: 150 average time/residue: 0.3435 time to fit residues: 76.9248 Evaluate side-chains 152 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 412 GLN Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 560 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.0582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8651 Z= 0.153 Angle : 0.507 6.619 11691 Z= 0.251 Chirality : 0.034 0.141 1391 Planarity : 0.004 0.050 1447 Dihedral : 12.991 174.699 1281 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.65 % Allowed : 25.55 % 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: 1.35 (0.27), residues: 1085 helix: 1.98 (0.19), residues: 807 sheet: -1.27 (0.68), residues: 60 loop : -2.74 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 44 HIS 0.004 0.001 HIS A 430 PHE 0.009 0.001 PHE A 154 TYR 0.008 0.001 TYR B 503 ARG 0.002 0.000 ARG B 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 HIS cc_start: 0.5778 (OUTLIER) cc_final: 0.5399 (m-70) REVERT: A 507 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8300 (mmm160) REVERT: B 412 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8576 (mt0) outliers start: 23 outliers final: 20 residues processed: 152 average time/residue: 0.3294 time to fit residues: 75.9527 Evaluate side-chains 157 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 134 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 412 GLN Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 560 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 58 optimal weight: 0.1980 chunk 42 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.0615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8651 Z= 0.135 Angle : 0.496 6.357 11691 Z= 0.243 Chirality : 0.034 0.141 1391 Planarity : 0.004 0.049 1447 Dihedral : 12.798 174.350 1281 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.07 % Allowed : 26.24 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.28), residues: 1085 helix: 2.11 (0.19), residues: 809 sheet: -1.24 (0.68), residues: 60 loop : -2.63 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 44 HIS 0.004 0.001 HIS A 430 PHE 0.010 0.001 PHE A 154 TYR 0.007 0.001 TYR B 503 ARG 0.002 0.000 ARG B 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 412 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8566 (mt0) outliers start: 18 outliers final: 13 residues processed: 155 average time/residue: 0.3361 time to fit residues: 78.7971 Evaluate side-chains 151 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 137 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 412 GLN Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 560 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.0654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8651 Z= 0.166 Angle : 0.510 8.643 11691 Z= 0.251 Chirality : 0.034 0.140 1391 Planarity : 0.004 0.049 1447 Dihedral : 12.613 174.250 1281 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 1.96 % Allowed : 26.58 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.28), residues: 1085 helix: 2.07 (0.19), residues: 810 sheet: -1.20 (0.68), residues: 60 loop : -2.64 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 44 HIS 0.005 0.001 HIS A 430 PHE 0.008 0.001 PHE A 154 TYR 0.007 0.001 TYR B 503 ARG 0.002 0.000 ARG B 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 HIS cc_start: 0.5790 (OUTLIER) cc_final: 0.5446 (m-70) REVERT: B 184 SER cc_start: 0.8556 (t) cc_final: 0.7912 (m) REVERT: B 412 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8570 (mt0) outliers start: 17 outliers final: 14 residues processed: 145 average time/residue: 0.3328 time to fit residues: 74.1691 Evaluate side-chains 147 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 412 GLN Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 560 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.0040 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.127524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109534 restraints weight = 37148.820| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.02 r_work: 0.3240 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.0665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8651 Z= 0.160 Angle : 0.505 7.105 11691 Z= 0.249 Chirality : 0.034 0.140 1391 Planarity : 0.004 0.049 1447 Dihedral : 12.499 174.061 1281 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 1.73 % Allowed : 26.81 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.28), residues: 1085 helix: 2.08 (0.19), residues: 810 sheet: -1.17 (0.68), residues: 60 loop : -2.61 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 44 HIS 0.005 0.001 HIS A 430 PHE 0.008 0.001 PHE A 154 TYR 0.008 0.001 TYR B 503 ARG 0.002 0.000 ARG B 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3885.58 seconds wall clock time: 68 minutes 12.96 seconds (4092.96 seconds total)