Starting phenix.real_space_refine on Sun Mar 17 10:09:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxg_16318/03_2024/8bxg_16318_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxg_16318/03_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_16318/03_2024/8bxg_16318.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxg_16318/03_2024/8bxg_16318.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxg_16318/03_2024/8bxg_16318_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxg_16318/03_2024/8bxg_16318_trim_updated.pdb" } 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 7.99, per 1000 atoms: 0.46 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: 11.73 Conformation dependent library (CDL) restraints added in 1.8 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... running ksdssp... Secondary structure from input PDB file: 57 helices and 2 sheets defined 69.3% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'A' and resid 3 through 25 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 30 through 41 Processing helix chain 'A' and resid 53 through 73 removed outlier: 3.733A pdb=" N GLU A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 81 Processing helix chain 'A' and resid 83 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 102 through 108 Processing helix chain 'A' and resid 113 through 122 removed outlier: 4.080A pdb=" N LEU A 117 " --> pdb=" O GLN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 137 removed outlier: 3.534A pdb=" N GLU A 136 " --> pdb=" O GLN A 132 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 164 Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 166 through 170 removed outlier: 3.824A pdb=" N ALA A 170 " --> pdb=" O ILE A 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 166 through 170' Processing helix chain 'A' and resid 179 through 182 No H-bonds generated for 'chain 'A' and resid 179 through 182' Processing helix chain 'A' and resid 186 through 196 Processing helix chain 'A' and resid 204 through 213 removed outlier: 4.003A pdb=" N SER A 213 " --> pdb=" O PHE A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 237 Processing helix chain 'A' and resid 241 through 254 removed outlier: 3.597A pdb=" N ALA A 245 " --> pdb=" O MET A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 283 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 287 through 291 Processing helix chain 'A' and resid 294 through 314 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) Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 354 through 369 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 371 through 383 removed outlier: 3.559A pdb=" N GLN A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 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 435 through 439 removed outlier: 3.672A pdb=" N ARG A 439 " --> pdb=" O GLU A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 459 Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 500 through 509 Processing helix chain 'A' and resid 520 through 533 Processing helix chain 'A' and resid 537 through 559 removed outlier: 3.775A pdb=" N GLU A 542 " --> pdb=" O TYR A 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 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 32 through 41 Processing helix chain 'B' and resid 52 through 73 Processing helix chain 'B' and resid 78 through 81 No H-bonds generated for 'chain 'B' and resid 78 through 81' Processing helix chain 'B' and resid 90 through 108 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 114 through 122 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 127 through 137 Processing helix chain 'B' and resid 143 through 164 removed outlier: 3.570A pdb=" N ALA B 159 " --> pdb=" O GLN B 155 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Proline residue: B 161 - end of helix Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 177 through 201 Processing helix chain 'B' and resid 204 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 218 through 236 Processing helix chain 'B' and resid 242 through 254 removed outlier: 3.835A pdb=" N LEU B 247 " --> pdb=" O MET B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 283 Proline residue: B 267 - end of helix removed outlier: 4.733A pdb=" N GLY B 270 " --> pdb=" O GLU B 266 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) 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 288 through 291 No H-bonds generated for 'chain 'B' and resid 288 through 291' Processing helix chain 'B' and resid 294 through 318 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) removed outlier: 3.578A pdb=" N ALA B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ARG B 316 " --> pdb=" O TRP B 312 " (cutoff:3.500A) Proline residue: B 317 - end of helix Processing helix chain 'B' and resid 325 through 332 removed outlier: 3.742A pdb=" N LEU B 332 " --> pdb=" O PHE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 354 through 369 Processing helix chain 'B' and resid 371 through 383 Processing helix chain 'B' and resid 409 through 421 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 435 through 438 No H-bonds generated for 'chain 'B' and resid 435 through 438' Processing helix chain 'B' and resid 453 through 455 No H-bonds generated for 'chain 'B' and resid 453 through 455' Processing helix chain 'B' and resid 461 through 463 No H-bonds generated for 'chain 'B' and resid 461 through 463' Processing helix chain 'B' and resid 474 through 487 removed outlier: 3.742A pdb=" N MET B 483 " --> pdb=" O GLN B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 509 removed outlier: 3.911A pdb=" N ARG B 505 " --> pdb=" O ASP B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 533 Processing helix chain 'B' and resid 537 through 559 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) Processing sheet with id= A, first strand: chain 'A' and resid 466 through 469 removed outlier: 6.601A pdb=" N VAL A 426 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 424 through 428 removed outlier: 6.477A pdb=" N VAL B 466 " --> pdb=" O ILE B 403 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ALA B 405 " --> pdb=" O VAL B 466 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE B 468 " --> pdb=" O ALA B 405 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLN B 492 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ASN B 469 " --> pdb=" O GLN B 492 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE B 494 " --> pdb=" O ASN B 469 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1353 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: 5.76 Time building geometry restraints manager: 12.30 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: 3798 2.31 - 3.01: 47262 3.01 - 3.72: 61025 3.72 - 4.43: 92170 4.43 - 5.14: 144627 Nonbonded interactions: 348882 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 348877 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: 0.770 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: 0.240 Extract box with map and model: 3.800 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 56.970 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.580 ------------------------------------------------------------------------------- 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= 0.201 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 : 1.434 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 130 average time/residue: 0.3347 time to fit residues: 66.3402 Evaluate side-chains 128 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.267 ------------------------------------------------------------------------------- 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: 0.6980 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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: 0.8082 moved from start: 0.0408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8651 Z= 0.281 Angle : 0.545 7.751 11691 Z= 0.279 Chirality : 0.035 0.141 1391 Planarity : 0.004 0.063 1447 Dihedral : 14.616 171.961 1281 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 1.15 % Allowed : 27.04 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.27), residues: 1085 helix: 1.67 (0.19), residues: 813 sheet: -1.19 (0.69), residues: 60 loop : -2.90 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 44 HIS 0.002 0.001 HIS A 502 PHE 0.009 0.001 PHE A 328 TYR 0.008 0.001 TYR A 201 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 137 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 127 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 132 average time/residue: 0.3482 time to fit residues: 69.7703 Evaluate side-chains 130 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 125 time to evaluate : 1.255 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 106 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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: 0.8068 moved from start: 0.0472 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= 0.203 Angle : 0.512 7.035 11691 Z= 0.257 Chirality : 0.034 0.142 1391 Planarity : 0.004 0.054 1447 Dihedral : 14.088 173.520 1281 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.38 % Allowed : 26.47 % Favored : 72.15 % 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: 1.03 (0.27), residues: 1085 helix: 1.69 (0.19), residues: 806 sheet: -1.07 (0.69), residues: 60 loop : -2.69 (0.42), residues: 219 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 A 503 ARG 0.002 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 144 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 132 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 434 HIS cc_start: 0.5719 (OUTLIER) cc_final: 0.5288 (m-70) REVERT: A 507 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8303 (mmm160) REVERT: B 184 SER cc_start: 0.8570 (t) cc_final: 0.7940 (m) outliers start: 12 outliers final: 9 residues processed: 140 average time/residue: 0.3320 time to fit residues: 70.4347 Evaluate side-chains 140 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.2980 chunk 73 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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: 0.8079 moved from start: 0.0640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8651 Z= 0.229 Angle : 0.520 7.315 11691 Z= 0.260 Chirality : 0.034 0.141 1391 Planarity : 0.004 0.050 1447 Dihedral : 13.810 174.252 1281 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.65 % Allowed : 24.97 % Favored : 72.38 % 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: 0.90 (0.27), residues: 1085 helix: 1.60 (0.19), residues: 805 sheet: -1.11 (0.69), residues: 60 loop : -2.77 (0.42), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 44 HIS 0.003 0.001 HIS A 430 PHE 0.008 0.001 PHE A 328 TYR 0.007 0.001 TYR A 201 ARG 0.002 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 152 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 434 HIS cc_start: 0.5728 (OUTLIER) cc_final: 0.5346 (m-70) REVERT: A 507 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8307 (mmm160) REVERT: B 184 SER cc_start: 0.8580 (t) cc_final: 0.7957 (m) REVERT: B 412 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8515 (mt0) outliers start: 23 outliers final: 16 residues processed: 143 average time/residue: 0.3371 time to fit residues: 72.2947 Evaluate side-chains 146 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 1.174 ------------------------------------------------------------------------------- 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 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 178 MET Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 412 GLN Chi-restraints excluded: chain B residue 560 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 0 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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: 0.8104 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8651 Z= 0.301 Angle : 0.551 8.074 11691 Z= 0.280 Chirality : 0.035 0.139 1391 Planarity : 0.004 0.049 1447 Dihedral : 13.571 175.483 1281 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.88 % Allowed : 24.97 % Favored : 72.15 % 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: 0.60 (0.27), residues: 1085 helix: 1.37 (0.19), residues: 804 sheet: -1.20 (0.68), residues: 60 loop : -2.81 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 44 HIS 0.004 0.001 HIS A 430 PHE 0.011 0.001 PHE B 303 TYR 0.008 0.002 TYR A 201 ARG 0.009 0.000 ARG B 216 *********************** 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 155 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 350 ASN cc_start: 0.8048 (t0) cc_final: 0.7781 (t0) REVERT: A 507 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8317 (mmm160) REVERT: B 412 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8527 (mt0) outliers start: 25 outliers final: 19 residues processed: 146 average time/residue: 0.3428 time to fit residues: 75.0764 Evaluate side-chains 149 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 128 time to evaluate : 1.245 ------------------------------------------------------------------------------- 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 184 SER 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 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 444 LYS Chi-restraints excluded: chain B residue 481 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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: 0.8092 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8651 Z= 0.236 Angle : 0.532 7.542 11691 Z= 0.266 Chirality : 0.034 0.140 1391 Planarity : 0.004 0.049 1447 Dihedral : 13.316 175.198 1281 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 2.88 % Allowed : 24.97 % Favored : 72.15 % 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: 0.72 (0.27), residues: 1085 helix: 1.47 (0.19), residues: 800 sheet: -1.28 (0.67), residues: 60 loop : -2.70 (0.41), residues: 225 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 328 TYR 0.007 0.001 TYR A 503 ARG 0.003 0.000 ARG B 216 *********************** 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 156 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 350 ASN cc_start: 0.8110 (t0) cc_final: 0.7837 (t0) REVERT: A 434 HIS cc_start: 0.5769 (OUTLIER) cc_final: 0.5340 (m-70) REVERT: A 507 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8309 (mmm160) REVERT: B 135 ASN cc_start: 0.8921 (m-40) cc_final: 0.8647 (m-40) REVERT: B 412 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8534 (mt0) outliers start: 25 outliers final: 20 residues processed: 148 average time/residue: 0.3380 time to fit residues: 75.8241 Evaluate side-chains 152 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE 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 196 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 272 LEU 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=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: 4.9990 chunk 58 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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: 0.8101 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8651 Z= 0.268 Angle : 0.543 7.805 11691 Z= 0.272 Chirality : 0.035 0.140 1391 Planarity : 0.004 0.048 1447 Dihedral : 13.250 175.326 1281 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 3.11 % Allowed : 24.97 % Favored : 71.92 % 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: 0.59 (0.27), residues: 1085 helix: 1.42 (0.19), residues: 793 sheet: -1.34 (0.67), residues: 60 loop : -2.78 (0.39), residues: 232 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 0.009 0.001 PHE A 328 TYR 0.008 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 158 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 131 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 434 HIS cc_start: 0.5796 (OUTLIER) cc_final: 0.5315 (m-70) REVERT: A 507 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8315 (mmm160) REVERT: B 135 ASN cc_start: 0.8949 (m-40) cc_final: 0.8692 (m-40) REVERT: B 412 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8542 (mt0) outliers start: 27 outliers final: 22 residues processed: 151 average time/residue: 0.3386 time to fit residues: 76.7367 Evaluate side-chains 154 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE 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 331 LEU 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.4980 chunk 81 optimal weight: 0.0040 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- 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: 0.8066 moved from start: 0.0879 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= 0.154 Angle : 0.505 6.715 11691 Z= 0.248 Chirality : 0.034 0.140 1391 Planarity : 0.004 0.047 1447 Dihedral : 13.034 174.698 1281 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 2.53 % Allowed : 25.55 % Favored : 71.92 % 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: 0.98 (0.27), residues: 1085 helix: 1.71 (0.19), residues: 794 sheet: -1.22 (0.68), residues: 60 loop : -2.68 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 44 HIS 0.003 0.001 HIS A 430 PHE 0.010 0.001 PHE A 154 TYR 0.007 0.001 TYR B 538 ARG 0.002 0.000 ARG B 216 *********************** 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: 22 poor density : 136 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 HIS cc_start: 0.5713 (OUTLIER) cc_final: 0.5340 (m-70) REVERT: A 507 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8290 (mmm160) outliers start: 22 outliers final: 17 residues processed: 150 average time/residue: 0.3259 time to fit residues: 74.3991 Evaluate side-chains 154 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 1.325 ------------------------------------------------------------------------------- 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 282 MET Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 184 SER 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 272 LEU 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 433 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 76 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8651 Z= 0.197 Angle : 0.519 6.971 11691 Z= 0.256 Chirality : 0.034 0.141 1391 Planarity : 0.004 0.047 1447 Dihedral : 12.973 174.834 1281 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.53 % Allowed : 25.78 % 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: 0.92 (0.27), residues: 1085 helix: 1.67 (0.19), residues: 795 sheet: -1.24 (0.68), residues: 60 loop : -2.73 (0.40), residues: 230 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 0.009 0.001 PHE A 154 TYR 0.007 0.001 TYR B 538 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 155 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 HIS cc_start: 0.5768 (OUTLIER) cc_final: 0.5351 (m-70) REVERT: A 507 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8296 (mmm160) outliers start: 22 outliers final: 19 residues processed: 150 average time/residue: 0.3299 time to fit residues: 74.9575 Evaluate side-chains 153 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 132 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE 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 331 LEU 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 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 433 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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: 0.8085 moved from start: 0.0952 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= 0.226 Angle : 0.529 8.103 11691 Z= 0.262 Chirality : 0.034 0.137 1391 Planarity : 0.004 0.048 1447 Dihedral : 12.826 174.803 1281 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.53 % Allowed : 25.78 % 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: 0.82 (0.27), residues: 1085 helix: 1.60 (0.19), residues: 794 sheet: -1.30 (0.68), residues: 60 loop : -2.76 (0.39), residues: 231 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 0.009 0.001 PHE A 328 TYR 0.008 0.001 TYR A 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 154 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 HIS cc_start: 0.5777 (OUTLIER) cc_final: 0.5406 (m-70) REVERT: A 507 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8300 (mmm160) outliers start: 22 outliers final: 19 residues processed: 148 average time/residue: 0.3575 time to fit residues: 81.0379 Evaluate side-chains 153 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 132 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE 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 331 LEU 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 142 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 VAL 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 367 SER Chi-restraints excluded: chain B residue 433 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.126092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108375 restraints weight = 37153.500| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.93 r_work: 0.3218 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.0942 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= 0.161 Angle : 0.506 7.551 11691 Z= 0.248 Chirality : 0.034 0.140 1391 Planarity : 0.004 0.048 1447 Dihedral : 12.639 174.262 1281 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % 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: 1.02 (0.27), residues: 1085 helix: 1.75 (0.19), residues: 794 sheet: -1.23 (0.68), residues: 60 loop : -2.69 (0.40), residues: 231 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 0.007 0.001 TYR B 538 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: 3793.85 seconds wall clock time: 67 minutes 21.16 seconds (4041.16 seconds total)