Starting phenix.real_space_refine on Thu Mar 14 23:29:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xha_33192/03_2024/7xha_33192_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xha_33192/03_2024/7xha_33192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xha_33192/03_2024/7xha_33192.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xha_33192/03_2024/7xha_33192.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xha_33192/03_2024/7xha_33192_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xha_33192/03_2024/7xha_33192_updated.pdb" } resolution = 3.35 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= 0.001 sd= 0.077 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: 8 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 46 5.16 5 Be 1 3.05 5 C 6455 2.51 5 N 1724 2.21 5 O 1870 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 14": "NH1" <-> "NH2" Residue "A ARG 30": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A ARG 489": "NH1" <-> "NH2" Residue "A ARG 576": "NH1" <-> "NH2" Residue "A ARG 645": "NH1" <-> "NH2" Residue "A ARG 741": "NH1" <-> "NH2" Residue "A ARG 750": "NH1" <-> "NH2" Residue "Y ARG 3": "NH1" <-> "NH2" Residue "Y ARG 107": "NH1" <-> "NH2" Residue "Y ARG 213": "NH1" <-> "NH2" Residue "Y ARG 252": "NH1" <-> "NH2" Residue "Y ARG 423": "NH1" <-> "NH2" Residue "Y ARG 426": "NH1" <-> "NH2" Residue "E ARG 3": "NH1" <-> "NH2" 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: 10102 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 765, 6107 Classifications: {'peptide': 765} Link IDs: {'PTRANS': 15, 'TRANS': 749} Chain: "Y" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3183 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 20, 'TRANS': 385} Chain breaks: 2 Chain: "E" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 480 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "B" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 300 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.73, per 1000 atoms: 0.57 Number of scatterers: 10102 At special positions: 0 Unit cell: (100.225, 110.775, 125.545, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 46 16.00 P 2 15.00 Mg 1 11.99 F 3 9.00 O 1870 8.00 N 1724 7.00 C 6455 6.00 Be 1 4.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.06 Conformation dependent library (CDL) restraints added in 1.6 seconds 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2360 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 7 sheets defined 58.5% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'A' and resid 16 through 32 removed outlier: 4.833A pdb=" N GLY A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ASP A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 52 removed outlier: 3.823A pdb=" N THR A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE A 46 " --> pdb=" O LYS A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 77 removed outlier: 3.721A pdb=" N LEU A 62 " --> pdb=" O ASP A 59 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL A 63 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE A 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 69 " --> pdb=" O PHE A 66 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER A 73 " --> pdb=" O ARG A 70 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR A 77 " --> pdb=" O ARG A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 93 Processing helix chain 'A' and resid 108 through 118 Proline residue: A 113 - end of helix removed outlier: 3.963A pdb=" N LEU A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 148 Processing helix chain 'A' and resid 161 through 169 Processing helix chain 'A' and resid 177 through 187 Processing helix chain 'A' and resid 209 through 212 No H-bonds generated for 'chain 'A' and resid 209 through 212' Processing helix chain 'A' and resid 232 through 243 removed outlier: 3.729A pdb=" N GLN A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 272 Processing helix chain 'A' and resid 284 through 298 Processing helix chain 'A' and resid 302 through 305 No H-bonds generated for 'chain 'A' and resid 302 through 305' Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 378 through 384 Processing helix chain 'A' and resid 411 through 426 Processing helix chain 'A' and resid 440 through 452 removed outlier: 3.989A pdb=" N ASN A 451 " --> pdb=" O LYS A 447 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 472 Processing helix chain 'A' and resid 516 through 526 removed outlier: 4.141A pdb=" N LEU A 522 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG A 523 " --> pdb=" O ASP A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 549 Processing helix chain 'A' and resid 552 through 561 removed outlier: 5.072A pdb=" N ASP A 559 " --> pdb=" O MET A 555 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ARG A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N PHE A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 618 removed outlier: 4.788A pdb=" N GLU A 579 " --> pdb=" O SER A 575 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLN A 598 " --> pdb=" O LYS A 594 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR A 599 " --> pdb=" O GLN A 595 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL A 602 " --> pdb=" O GLN A 598 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU A 603 " --> pdb=" O TYR A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 642 Processing helix chain 'A' and resid 654 through 664 Processing helix chain 'A' and resid 681 through 703 Processing helix chain 'A' and resid 707 through 736 Processing helix chain 'A' and resid 739 through 744 removed outlier: 3.688A pdb=" N ALA A 742 " --> pdb=" O HIS A 739 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR A 743 " --> pdb=" O LEU A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 777 Processing helix chain 'Y' and resid 4 through 10 removed outlier: 3.852A pdb=" N ARG Y 10 " --> pdb=" O SER Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 12 through 32 Processing helix chain 'Y' and resid 43 through 46 No H-bonds generated for 'chain 'Y' and resid 43 through 46' Processing helix chain 'Y' and resid 75 through 87 Processing helix chain 'Y' and resid 93 through 100 Processing helix chain 'Y' and resid 105 through 135 removed outlier: 3.879A pdb=" N LEU Y 126 " --> pdb=" O PHE Y 122 " (cutoff:3.500A) Processing helix chain 'Y' and resid 147 through 173 Processing helix chain 'Y' and resid 178 through 187 Processing helix chain 'Y' and resid 191 through 201 Processing helix chain 'Y' and resid 217 through 235 Processing helix chain 'Y' and resid 272 through 290 Proline residue: Y 284 - end of helix Processing helix chain 'Y' and resid 295 through 303 Processing helix chain 'Y' and resid 309 through 330 removed outlier: 3.936A pdb=" N ILE Y 314 " --> pdb=" O VAL Y 310 " (cutoff:3.500A) Processing helix chain 'Y' and resid 333 through 343 Processing helix chain 'Y' and resid 355 through 389 removed outlier: 4.290A pdb=" N ARG Y 366 " --> pdb=" O ARG Y 362 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU Y 369 " --> pdb=" O TYR Y 365 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL Y 370 " --> pdb=" O ARG Y 366 " (cutoff:3.500A) Proline residue: Y 382 - end of helix Processing helix chain 'Y' and resid 400 through 421 Processing helix chain 'E' and resid 3 through 16 removed outlier: 4.187A pdb=" N LYS E 16 " --> pdb=" O VAL E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 57 Processing helix chain 'B' and resid 3 through 21 removed outlier: 3.630A pdb=" N ILE B 7 " --> pdb=" O LYS B 3 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA B 14 " --> pdb=" O ALA B 10 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 97 through 99 Processing sheet with id= B, first strand: chain 'A' and resid 366 through 370 removed outlier: 7.074A pdb=" N HIS A 125 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ASP A 207 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL A 127 " --> pdb=" O ASP A 207 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR A 174 " --> pdb=" O GLY A 153 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 250 through 252 removed outlier: 3.662A pdb=" N GLN A 260 " --> pdb=" O THR A 251 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 306 through 309 Processing sheet with id= E, first strand: chain 'A' and resid 534 through 537 removed outlier: 3.584A pdb=" N ILE A 482 " --> pdb=" O GLN A 457 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 220 through 225 removed outlier: 3.530A pdb=" N ILE A 223 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N GLY A 225 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N THR A 351 " --> pdb=" O GLY A 225 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'Y' and resid 238 through 241 542 hydrogen bonds defined for protein. 1587 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: 2.96 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1683 1.27 - 1.40: 2470 1.40 - 1.54: 5838 1.54 - 1.67: 192 1.67 - 1.81: 91 Bond restraints: 10274 Sorted by residual: bond pdb=" C TYR B 52 " pdb=" O TYR B 52 " ideal model delta sigma weight residual 1.236 1.132 0.104 1.21e-02 6.83e+03 7.38e+01 bond pdb=" CA SER A 224 " pdb=" C SER A 224 " ideal model delta sigma weight residual 1.522 1.425 0.097 1.20e-02 6.94e+03 6.59e+01 bond pdb=" CA ARG A 525 " pdb=" C ARG A 525 " ideal model delta sigma weight residual 1.524 1.417 0.107 1.32e-02 5.74e+03 6.57e+01 bond pdb=" C SER A 224 " pdb=" O SER A 224 " ideal model delta sigma weight residual 1.235 1.145 0.090 1.30e-02 5.92e+03 4.82e+01 bond pdb=" CA TYR A 234 " pdb=" C TYR A 234 " ideal model delta sigma weight residual 1.524 1.441 0.082 1.27e-02 6.20e+03 4.19e+01 ... (remaining 10269 not shown) Histogram of bond angle deviations from ideal: 96.94 - 104.76: 154 104.76 - 112.58: 5118 112.58 - 120.39: 4862 120.39 - 128.21: 3683 128.21 - 136.02: 56 Bond angle restraints: 13873 Sorted by residual: angle pdb=" N ARG A 525 " pdb=" CA ARG A 525 " pdb=" C ARG A 525 " ideal model delta sigma weight residual 111.69 103.92 7.77 1.23e+00 6.61e-01 3.99e+01 angle pdb=" C THR A 394 " pdb=" N ASN A 395 " pdb=" CA ASN A 395 " ideal model delta sigma weight residual 121.54 133.43 -11.89 1.91e+00 2.74e-01 3.88e+01 angle pdb=" N LYS A 106 " pdb=" CA LYS A 106 " pdb=" C LYS A 106 " ideal model delta sigma weight residual 113.15 120.56 -7.41 1.19e+00 7.06e-01 3.87e+01 angle pdb=" N GLU A 216 " pdb=" CA GLU A 216 " pdb=" C GLU A 216 " ideal model delta sigma weight residual 113.02 119.92 -6.90 1.20e+00 6.94e-01 3.30e+01 angle pdb=" N GLN Y 201 " pdb=" CA GLN Y 201 " pdb=" C GLN Y 201 " ideal model delta sigma weight residual 111.36 105.20 6.16 1.09e+00 8.42e-01 3.19e+01 ... (remaining 13868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.23: 6087 30.23 - 60.46: 99 60.46 - 90.69: 10 90.69 - 120.92: 1 120.92 - 151.14: 1 Dihedral angle restraints: 6198 sinusoidal: 2527 harmonic: 3671 Sorted by residual: dihedral pdb=" N LEU A 233 " pdb=" C LEU A 233 " pdb=" CA LEU A 233 " pdb=" CB LEU A 233 " ideal model delta harmonic sigma weight residual 122.80 141.34 -18.54 0 2.50e+00 1.60e-01 5.50e+01 dihedral pdb=" C LEU A 233 " pdb=" N LEU A 233 " pdb=" CA LEU A 233 " pdb=" CB LEU A 233 " ideal model delta harmonic sigma weight residual -122.60 -140.90 18.30 0 2.50e+00 1.60e-01 5.36e+01 dihedral pdb=" O1B ADP A1003 " pdb=" O3A ADP A1003 " pdb=" PB ADP A1003 " pdb=" PA ADP A1003 " ideal model delta sinusoidal sigma weight residual 300.00 148.85 151.14 1 2.00e+01 2.50e-03 4.50e+01 ... (remaining 6195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 1536 0.154 - 0.308: 34 0.308 - 0.462: 10 0.462 - 0.616: 2 0.616 - 0.770: 1 Chirality restraints: 1583 Sorted by residual: chirality pdb=" CA LEU A 233 " pdb=" N LEU A 233 " pdb=" C LEU A 233 " pdb=" CB LEU A 233 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" CA SER B 54 " pdb=" N SER B 54 " pdb=" C SER B 54 " pdb=" CB SER B 54 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.47e+00 chirality pdb=" CA ASN A 238 " pdb=" N ASN A 238 " pdb=" C ASN A 238 " pdb=" CB ASN A 238 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.73e+00 ... (remaining 1580 not shown) Planarity restraints: 1773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 232 " 0.036 2.00e-02 2.50e+03 6.90e-02 4.76e+01 pdb=" C LYS A 232 " -0.119 2.00e-02 2.50e+03 pdb=" O LYS A 232 " 0.043 2.00e-02 2.50e+03 pdb=" N LEU A 233 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 524 " -0.020 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C GLY A 524 " 0.067 2.00e-02 2.50e+03 pdb=" O GLY A 524 " -0.025 2.00e-02 2.50e+03 pdb=" N ARG A 525 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 215 " 0.017 2.00e-02 2.50e+03 3.46e-02 1.19e+01 pdb=" C ASP A 215 " -0.060 2.00e-02 2.50e+03 pdb=" O ASP A 215 " 0.023 2.00e-02 2.50e+03 pdb=" N GLU A 216 " 0.020 2.00e-02 2.50e+03 ... (remaining 1770 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 29 2.47 - 3.08: 6458 3.08 - 3.68: 15090 3.68 - 4.29: 21867 4.29 - 4.90: 36338 Nonbonded interactions: 79782 Sorted by model distance: nonbonded pdb=" OD1 ASN A 238 " pdb=" NE2 HIS A 297 " model vdw 1.860 2.520 nonbonded pdb=" O TYR Y 199 " pdb=" O GLN Y 202 " model vdw 1.937 3.040 nonbonded pdb=" O GLN A 521 " pdb=" NH1 ARG A 525 " model vdw 2.236 2.520 nonbonded pdb=" CD1 ILE Y 14 " pdb=" CD1 LEU Y 420 " model vdw 2.291 3.880 nonbonded pdb=" O2' ADP A1003 " pdb=" O3' ADP A1003 " model vdw 2.300 2.432 ... (remaining 79777 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.270 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 29.240 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 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 : 0.008 0.107 10274 Z= 0.532 Angle : 1.063 18.342 13873 Z= 0.591 Chirality : 0.073 0.770 1583 Planarity : 0.008 0.069 1773 Dihedral : 11.409 151.144 3838 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.70 % Favored : 95.22 % Rotamer: Outliers : 0.28 % Allowed : 3.06 % Favored : 96.66 % Cbeta Deviations : 0.34 % 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: -3.53 (0.19), residues: 1256 helix: -1.93 (0.14), residues: 803 sheet: -1.82 (0.59), residues: 78 loop : -3.00 (0.26), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP Y 299 HIS 0.008 0.002 HIS A 202 PHE 0.043 0.003 PHE A 48 TYR 0.034 0.003 TYR B 53 ARG 0.008 0.001 ARG A 593 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 250 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ASP cc_start: 0.7630 (m-30) cc_final: 0.7354 (m-30) REVERT: A 469 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7056 (mp10) REVERT: A 707 GLN cc_start: 0.8082 (mm110) cc_final: 0.7850 (mt0) REVERT: A 731 MET cc_start: 0.8572 (tpt) cc_final: 0.8214 (tpt) REVERT: A 762 HIS cc_start: 0.7385 (m-70) cc_final: 0.7123 (m-70) REVERT: A 769 ASP cc_start: 0.7801 (m-30) cc_final: 0.7349 (m-30) REVERT: Y 302 ARG cc_start: 0.7969 (mtp180) cc_final: 0.7575 (mtm-85) REVERT: E 44 PHE cc_start: 0.8796 (m-80) cc_final: 0.8386 (m-80) REVERT: B 50 TYR cc_start: 0.7555 (p90) cc_final: 0.7223 (p90) outliers start: 3 outliers final: 2 residues processed: 252 average time/residue: 0.2493 time to fit residues: 85.0805 Evaluate side-chains 165 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 162 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain Y residue 212 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 63 optimal weight: 7.9990 chunk 50 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 0.0070 chunk 59 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 113 optimal weight: 0.0010 overall best weight: 0.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 198 GLN ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 GLN A 430 GLN ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN A 529 GLN A 622 ASN A 733 GLN ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 7 ASN Y 169 GLN ** Y 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 308 HIS Y 419 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10274 Z= 0.164 Angle : 0.578 11.370 13873 Z= 0.294 Chirality : 0.041 0.168 1583 Planarity : 0.004 0.052 1773 Dihedral : 6.647 113.081 1404 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.30 % Allowed : 10.57 % Favored : 88.14 % 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: -1.23 (0.23), residues: 1256 helix: 0.01 (0.18), residues: 788 sheet: -1.43 (0.57), residues: 80 loop : -2.27 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Y 98 HIS 0.003 0.001 HIS A 297 PHE 0.021 0.001 PHE A 703 TYR 0.010 0.001 TYR A 234 ARG 0.006 0.001 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 194 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8003 (mtmm) REVERT: A 194 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7558 (pm20) REVERT: A 331 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7232 (mm-30) REVERT: A 460 ASN cc_start: 0.7459 (m-40) cc_final: 0.7183 (m110) REVERT: E 44 PHE cc_start: 0.8773 (m-80) cc_final: 0.8498 (m-80) outliers start: 14 outliers final: 8 residues processed: 201 average time/residue: 0.2433 time to fit residues: 67.2445 Evaluate side-chains 180 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 170 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 23 LEU Chi-restraints excluded: chain Y residue 219 LEU Chi-restraints excluded: chain Y residue 421 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 0.0030 chunk 35 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 122 optimal weight: 8.9990 chunk 101 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 GLN Y 7 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10274 Z= 0.229 Angle : 0.575 9.498 13873 Z= 0.295 Chirality : 0.042 0.149 1583 Planarity : 0.004 0.047 1773 Dihedral : 6.210 114.594 1399 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.13 % Allowed : 11.40 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.23), residues: 1256 helix: 0.62 (0.18), residues: 793 sheet: -1.56 (0.53), residues: 91 loop : -2.27 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 165 HIS 0.003 0.001 HIS A 297 PHE 0.021 0.001 PHE A 703 TYR 0.015 0.002 TYR Y 245 ARG 0.004 0.000 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 171 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8177 (mtmm) REVERT: A 331 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7387 (mm-30) REVERT: A 460 ASN cc_start: 0.7515 (m-40) cc_final: 0.7009 (m110) REVERT: A 657 LEU cc_start: 0.8191 (tp) cc_final: 0.7969 (tt) REVERT: Y 10 ARG cc_start: 0.7393 (mmt180) cc_final: 0.6516 (tpp80) REVERT: Y 429 ILE cc_start: 0.7305 (OUTLIER) cc_final: 0.6904 (pp) REVERT: E 44 PHE cc_start: 0.8781 (m-80) cc_final: 0.8517 (m-80) outliers start: 23 outliers final: 12 residues processed: 186 average time/residue: 0.2419 time to fit residues: 63.1287 Evaluate side-chains 175 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 161 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain Y residue 23 LEU Chi-restraints excluded: chain Y residue 151 LEU Chi-restraints excluded: chain Y residue 401 SER Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain Y residue 429 ILE Chi-restraints excluded: chain E residue 19 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 76 optimal weight: 0.0980 chunk 114 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 108 optimal weight: 0.0970 chunk 32 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 GLN ** Y 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10274 Z= 0.170 Angle : 0.539 11.501 13873 Z= 0.274 Chirality : 0.040 0.147 1583 Planarity : 0.003 0.046 1773 Dihedral : 5.937 111.593 1399 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.76 % Allowed : 12.60 % Favored : 85.63 % 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: -0.11 (0.24), residues: 1256 helix: 1.01 (0.19), residues: 792 sheet: -1.67 (0.52), residues: 96 loop : -1.97 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 165 HIS 0.002 0.000 HIS A 297 PHE 0.022 0.001 PHE A 703 TYR 0.009 0.001 TYR Y 245 ARG 0.003 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 171 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8153 (mtmm) REVERT: A 500 LYS cc_start: 0.8174 (ptpp) cc_final: 0.7872 (mtpt) REVERT: A 705 LYS cc_start: 0.8367 (ptmt) cc_final: 0.8105 (tttt) REVERT: A 731 MET cc_start: 0.8544 (tpt) cc_final: 0.8013 (tpt) REVERT: Y 10 ARG cc_start: 0.7390 (mmt180) cc_final: 0.6523 (tpp80) REVERT: E 44 PHE cc_start: 0.8697 (m-80) cc_final: 0.8496 (m-80) outliers start: 19 outliers final: 13 residues processed: 181 average time/residue: 0.2517 time to fit residues: 62.5841 Evaluate side-chains 174 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 160 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain Y residue 23 LEU Chi-restraints excluded: chain Y residue 219 LEU Chi-restraints excluded: chain Y residue 401 SER Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain E residue 19 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 61 optimal weight: 0.1980 chunk 108 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN A 460 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10274 Z= 0.235 Angle : 0.561 10.670 13873 Z= 0.287 Chirality : 0.042 0.152 1583 Planarity : 0.004 0.046 1773 Dihedral : 6.005 113.947 1399 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.22 % Allowed : 13.16 % Favored : 84.62 % 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: -0.02 (0.24), residues: 1256 helix: 1.09 (0.19), residues: 791 sheet: -1.71 (0.49), residues: 103 loop : -1.93 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Y 165 HIS 0.003 0.000 HIS A 297 PHE 0.025 0.001 PHE E 43 TYR 0.013 0.001 TYR Y 245 ARG 0.004 0.000 ARG A 624 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 165 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 THR cc_start: 0.8966 (p) cc_final: 0.8683 (p) REVERT: A 500 LYS cc_start: 0.8191 (ptpp) cc_final: 0.7881 (mtpt) REVERT: A 705 LYS cc_start: 0.8383 (ptmt) cc_final: 0.8041 (tttp) REVERT: Y 10 ARG cc_start: 0.7532 (mmt180) cc_final: 0.6620 (tpp80) REVERT: Y 429 ILE cc_start: 0.7246 (OUTLIER) cc_final: 0.6871 (pp) REVERT: E 44 PHE cc_start: 0.8756 (m-80) cc_final: 0.8518 (m-80) outliers start: 24 outliers final: 15 residues processed: 176 average time/residue: 0.2375 time to fit residues: 58.0554 Evaluate side-chains 175 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 159 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain Y residue 23 LEU Chi-restraints excluded: chain Y residue 163 LEU Chi-restraints excluded: chain Y residue 401 SER Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain Y residue 429 ILE Chi-restraints excluded: chain E residue 19 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 424 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10274 Z= 0.238 Angle : 0.571 10.695 13873 Z= 0.290 Chirality : 0.042 0.154 1583 Planarity : 0.004 0.046 1773 Dihedral : 5.966 111.838 1399 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.59 % Allowed : 13.53 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.24), residues: 1256 helix: 1.13 (0.18), residues: 791 sheet: -1.68 (0.49), residues: 101 loop : -1.86 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Y 165 HIS 0.003 0.001 HIS A 297 PHE 0.029 0.001 PHE A 703 TYR 0.013 0.001 TYR Y 245 ARG 0.004 0.000 ARG A 624 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 169 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 THR cc_start: 0.8991 (p) cc_final: 0.8714 (p) REVERT: A 500 LYS cc_start: 0.8201 (ptpp) cc_final: 0.7903 (mtpt) REVERT: A 705 LYS cc_start: 0.8394 (ptmt) cc_final: 0.8045 (tttp) REVERT: Y 10 ARG cc_start: 0.7558 (mmt180) cc_final: 0.6600 (tpp80) REVERT: Y 429 ILE cc_start: 0.7271 (OUTLIER) cc_final: 0.6887 (pp) REVERT: E 44 PHE cc_start: 0.8798 (m-80) cc_final: 0.8560 (m-80) outliers start: 28 outliers final: 18 residues processed: 182 average time/residue: 0.2281 time to fit residues: 58.0471 Evaluate side-chains 183 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 164 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain Y residue 23 LEU Chi-restraints excluded: chain Y residue 151 LEU Chi-restraints excluded: chain Y residue 163 LEU Chi-restraints excluded: chain Y residue 401 SER Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain Y residue 429 ILE Chi-restraints excluded: chain E residue 19 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 73 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 424 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10274 Z= 0.201 Angle : 0.557 9.923 13873 Z= 0.282 Chirality : 0.041 0.150 1583 Planarity : 0.003 0.046 1773 Dihedral : 5.869 110.967 1399 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.22 % Allowed : 13.90 % Favored : 83.87 % 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: 0.20 (0.24), residues: 1256 helix: 1.22 (0.18), residues: 792 sheet: -1.58 (0.50), residues: 101 loop : -1.75 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Y 165 HIS 0.002 0.000 HIS A 297 PHE 0.029 0.001 PHE A 703 TYR 0.010 0.001 TYR Y 233 ARG 0.004 0.000 ARG A 624 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 175 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 THR cc_start: 0.9005 (p) cc_final: 0.8716 (p) REVERT: A 500 LYS cc_start: 0.8182 (ptpp) cc_final: 0.7896 (mtpt) REVERT: A 705 LYS cc_start: 0.8337 (ptmt) cc_final: 0.8019 (tttp) REVERT: A 731 MET cc_start: 0.8584 (tpt) cc_final: 0.8011 (tpt) REVERT: A 770 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7947 (tm-30) REVERT: Y 10 ARG cc_start: 0.7477 (mmt180) cc_final: 0.6491 (tpp80) REVERT: Y 429 ILE cc_start: 0.7223 (OUTLIER) cc_final: 0.6828 (pp) REVERT: E 44 PHE cc_start: 0.8735 (m-80) cc_final: 0.8493 (m-80) outliers start: 24 outliers final: 20 residues processed: 186 average time/residue: 0.2238 time to fit residues: 57.9603 Evaluate side-chains 189 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 168 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain Y residue 23 LEU Chi-restraints excluded: chain Y residue 151 LEU Chi-restraints excluded: chain Y residue 163 LEU Chi-restraints excluded: chain Y residue 401 SER Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain Y residue 429 ILE Chi-restraints excluded: chain E residue 19 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 0.6980 chunk 36 optimal weight: 0.0050 chunk 23 optimal weight: 0.0170 chunk 76 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 11 optimal weight: 0.4980 chunk 94 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 overall best weight: 0.3432 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 424 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10274 Z= 0.162 Angle : 0.551 11.434 13873 Z= 0.276 Chirality : 0.040 0.149 1583 Planarity : 0.003 0.046 1773 Dihedral : 5.715 109.679 1399 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.95 % Allowed : 14.92 % Favored : 83.13 % 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: 0.42 (0.24), residues: 1256 helix: 1.37 (0.19), residues: 792 sheet: -1.46 (0.52), residues: 94 loop : -1.64 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Y 165 HIS 0.001 0.000 HIS A 464 PHE 0.031 0.001 PHE A 703 TYR 0.009 0.001 TYR Y 326 ARG 0.003 0.000 ARG A 624 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 172 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 THR cc_start: 0.8979 (p) cc_final: 0.8635 (p) REVERT: A 705 LYS cc_start: 0.8297 (ptmt) cc_final: 0.7991 (tttp) REVERT: Y 10 ARG cc_start: 0.7537 (mmt180) cc_final: 0.6547 (tpp80) REVERT: Y 254 PRO cc_start: 0.7984 (Cg_endo) cc_final: 0.7626 (Cg_exo) REVERT: Y 429 ILE cc_start: 0.7219 (OUTLIER) cc_final: 0.6883 (pp) REVERT: E 44 PHE cc_start: 0.8704 (m-80) cc_final: 0.8491 (m-80) outliers start: 21 outliers final: 15 residues processed: 182 average time/residue: 0.2282 time to fit residues: 58.0601 Evaluate side-chains 178 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 162 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain Y residue 23 LEU Chi-restraints excluded: chain Y residue 151 LEU Chi-restraints excluded: chain Y residue 401 SER Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain Y residue 429 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 73 optimal weight: 0.0870 chunk 118 optimal weight: 0.4980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN ** Y 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 236 GLN Y 424 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10274 Z= 0.198 Angle : 0.562 9.804 13873 Z= 0.283 Chirality : 0.041 0.152 1583 Planarity : 0.003 0.046 1773 Dihedral : 5.738 111.438 1399 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.67 % Allowed : 15.94 % Favored : 82.39 % 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: 0.46 (0.24), residues: 1256 helix: 1.40 (0.19), residues: 788 sheet: -1.42 (0.53), residues: 94 loop : -1.58 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Y 165 HIS 0.002 0.000 HIS A 297 PHE 0.030 0.001 PHE A 703 TYR 0.010 0.001 TYR Y 326 ARG 0.005 0.000 ARG A 624 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 168 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 THR cc_start: 0.8977 (p) cc_final: 0.8644 (p) REVERT: A 705 LYS cc_start: 0.8282 (ptmt) cc_final: 0.7968 (tttp) REVERT: A 708 MET cc_start: 0.8050 (tpt) cc_final: 0.7789 (tpt) REVERT: Y 10 ARG cc_start: 0.7563 (mmt180) cc_final: 0.6578 (tpp80) REVERT: Y 254 PRO cc_start: 0.7953 (Cg_endo) cc_final: 0.7597 (Cg_exo) REVERT: Y 429 ILE cc_start: 0.7197 (OUTLIER) cc_final: 0.6837 (pp) REVERT: E 44 PHE cc_start: 0.8727 (m-80) cc_final: 0.8507 (m-80) outliers start: 18 outliers final: 14 residues processed: 175 average time/residue: 0.2226 time to fit residues: 54.8519 Evaluate side-chains 179 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 164 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain Y residue 23 LEU Chi-restraints excluded: chain Y residue 401 SER Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain Y residue 429 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10274 Z= 0.228 Angle : 0.581 9.702 13873 Z= 0.293 Chirality : 0.042 0.175 1583 Planarity : 0.003 0.046 1773 Dihedral : 5.836 113.223 1399 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.67 % Allowed : 16.50 % Favored : 81.84 % 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: 0.41 (0.24), residues: 1256 helix: 1.36 (0.19), residues: 788 sheet: -1.43 (0.53), residues: 94 loop : -1.61 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP Y 165 HIS 0.003 0.001 HIS A 297 PHE 0.023 0.001 PHE A 703 TYR 0.011 0.001 TYR Y 233 ARG 0.004 0.000 ARG A 624 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 166 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 THR cc_start: 0.8987 (p) cc_final: 0.8686 (p) REVERT: A 705 LYS cc_start: 0.8305 (ptmt) cc_final: 0.8031 (tttp) REVERT: A 708 MET cc_start: 0.8031 (tpt) cc_final: 0.7682 (tpt) REVERT: Y 10 ARG cc_start: 0.7545 (mmt180) cc_final: 0.6541 (tpp80) REVERT: Y 254 PRO cc_start: 0.7947 (Cg_endo) cc_final: 0.7605 (Cg_exo) REVERT: Y 429 ILE cc_start: 0.7313 (OUTLIER) cc_final: 0.6938 (pp) REVERT: E 44 PHE cc_start: 0.8755 (m-80) cc_final: 0.8508 (m-80) outliers start: 18 outliers final: 15 residues processed: 174 average time/residue: 0.2311 time to fit residues: 56.0863 Evaluate side-chains 181 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 165 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain Y residue 23 LEU Chi-restraints excluded: chain Y residue 401 SER Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain Y residue 429 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.1980 chunk 91 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 99 optimal weight: 0.3980 chunk 41 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 87 optimal weight: 9.9990 chunk 5 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.180573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.139880 restraints weight = 12793.856| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.20 r_work: 0.3505 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10274 Z= 0.195 Angle : 0.571 9.870 13873 Z= 0.287 Chirality : 0.041 0.173 1583 Planarity : 0.003 0.046 1773 Dihedral : 5.738 111.206 1399 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.58 % Allowed : 16.68 % Favored : 81.74 % 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: 0.49 (0.25), residues: 1256 helix: 1.43 (0.19), residues: 789 sheet: -1.43 (0.52), residues: 94 loop : -1.58 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP Y 165 HIS 0.002 0.000 HIS A 297 PHE 0.022 0.001 PHE A 703 TYR 0.010 0.001 TYR Y 233 ARG 0.004 0.000 ARG A 624 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2381.13 seconds wall clock time: 43 minutes 35.60 seconds (2615.60 seconds total)