Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 15:34:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xha_33192/04_2023/7xha_33192_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xha_33192/04_2023/7xha_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_33192/04_2023/7xha_33192.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xha_33192/04_2023/7xha_33192.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xha_33192/04_2023/7xha_33192_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xha_33192/04_2023/7xha_33192_updated.pdb" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 5.77, 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: 3.81 Conformation dependent library (CDL) restraints added in 1.5 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: 1.10 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: 2.94 Time building geometry restraints manager: 4.20 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: 2.670 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: 7.760 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 28.680 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.370 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 252 average time/residue: 0.2622 time to fit residues: 89.2162 Evaluate side-chains 163 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 161 time to evaluate : 1.198 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2471 time to fit residues: 2.3291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 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 157 ASN A 198 GLN ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 GLN A 430 GLN A 457 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1978 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= 0.166 Angle : 0.584 11.481 13873 Z= 0.298 Chirality : 0.042 0.169 1583 Planarity : 0.004 0.051 1773 Dihedral : 6.211 114.411 1395 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 1.20 % 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: -1.32 (0.22), residues: 1256 helix: -0.05 (0.18), residues: 787 sheet: -1.56 (0.57), residues: 82 loop : -2.32 (0.29), residues: 387 *********************** 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 204 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 191 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 196 average time/residue: 0.2410 time to fit residues: 65.5928 Evaluate side-chains 176 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 168 time to evaluate : 1.212 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1080 time to fit residues: 3.2735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 0.0270 chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 0.0000 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 101 optimal weight: 0.3980 chunk 112 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.6846 ------------------------------------------------------------------------------- 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 460 ASN Y 7 ASN ** Y 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 10274 Z= 0.222 Angle : 0.572 9.599 13873 Z= 0.294 Chirality : 0.042 0.150 1583 Planarity : 0.004 0.047 1773 Dihedral : 6.016 112.774 1395 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 2.13 % 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: -0.60 (0.23), residues: 1256 helix: 0.63 (0.18), residues: 793 sheet: -1.56 (0.51), residues: 96 loop : -2.28 (0.30), residues: 367 *********************** 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 : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 9 residues processed: 186 average time/residue: 0.2417 time to fit residues: 63.0052 Evaluate side-chains 170 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 161 time to evaluate : 1.214 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0992 time to fit residues: 3.3369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 114 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 chunk 108 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 100 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2784 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= 0.202 Angle : 0.561 11.162 13873 Z= 0.285 Chirality : 0.041 0.149 1583 Planarity : 0.004 0.046 1773 Dihedral : 5.823 109.840 1395 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 0.93 % 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: -0.23 (0.24), residues: 1256 helix: 0.94 (0.18), residues: 793 sheet: -1.76 (0.49), residues: 103 loop : -2.07 (0.31), residues: 360 *********************** 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 178 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 168 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 172 average time/residue: 0.2611 time to fit residues: 61.7379 Evaluate side-chains 159 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 154 time to evaluate : 1.085 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0976 time to fit residues: 2.4107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 83 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 108 optimal weight: 0.0000 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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** ** Y 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2959 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= 0.186 Angle : 0.547 10.752 13873 Z= 0.277 Chirality : 0.041 0.150 1583 Planarity : 0.003 0.046 1773 Dihedral : 5.742 110.881 1395 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 1.02 % 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: 0.03 (0.24), residues: 1256 helix: 1.12 (0.19), residues: 793 sheet: -1.71 (0.49), residues: 103 loop : -1.90 (0.32), residues: 360 *********************** 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 176 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 165 time to evaluate : 1.195 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 169 average time/residue: 0.2377 time to fit residues: 56.8284 Evaluate side-chains 162 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 157 time to evaluate : 1.246 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1111 time to fit residues: 2.7646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.0980 chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 424 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3133 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= 0.200 Angle : 0.550 10.379 13873 Z= 0.279 Chirality : 0.041 0.156 1583 Planarity : 0.003 0.047 1773 Dihedral : 5.719 112.109 1395 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 0.93 % 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: 0.16 (0.24), residues: 1256 helix: 1.20 (0.19), residues: 792 sheet: -1.62 (0.51), residues: 94 loop : -1.79 (0.32), residues: 370 *********************** 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 174 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 164 time to evaluate : 1.112 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 169 average time/residue: 0.2415 time to fit residues: 57.4701 Evaluate side-chains 163 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 160 time to evaluate : 1.169 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1038 time to fit residues: 2.2178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 101 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 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** Y 424 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 10274 Z= 0.225 Angle : 0.575 10.407 13873 Z= 0.290 Chirality : 0.041 0.163 1583 Planarity : 0.004 0.047 1773 Dihedral : 5.762 113.042 1395 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 0.74 % 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: 0.21 (0.24), residues: 1256 helix: 1.23 (0.19), residues: 791 sheet: -1.58 (0.52), residues: 94 loop : -1.76 (0.33), residues: 371 *********************** 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 172 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 164 time to evaluate : 1.218 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 166 average time/residue: 0.2361 time to fit residues: 55.2284 Evaluate side-chains 160 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 157 time to evaluate : 1.089 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1071 time to fit residues: 2.1071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 94 optimal weight: 0.0970 chunk 109 optimal weight: 0.7980 chunk 115 optimal weight: 0.0980 chunk 105 optimal weight: 0.8980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 424 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3336 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= 0.166 Angle : 0.550 10.524 13873 Z= 0.277 Chirality : 0.040 0.165 1583 Planarity : 0.003 0.046 1773 Dihedral : 5.576 110.795 1395 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 0.56 % 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: 0.40 (0.24), residues: 1256 helix: 1.37 (0.19), residues: 791 sheet: -1.42 (0.53), residues: 94 loop : -1.68 (0.33), residues: 371 *********************** 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 180 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 174 time to evaluate : 1.223 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 176 average time/residue: 0.2446 time to fit residues: 62.0449 Evaluate side-chains 165 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 163 time to evaluate : 1.151 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1076 time to fit residues: 2.0183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 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 236 GLN Y 424 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3401 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= 0.245 Angle : 0.595 10.494 13873 Z= 0.301 Chirality : 0.042 0.174 1583 Planarity : 0.004 0.046 1773 Dihedral : 5.720 113.462 1395 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.24), residues: 1256 helix: 1.27 (0.19), residues: 791 sheet: -1.45 (0.53), residues: 94 loop : -1.71 (0.33), residues: 371 *********************** 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 174 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 167 time to evaluate : 1.245 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 171 average time/residue: 0.2343 time to fit residues: 56.5564 Evaluate side-chains 163 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 160 time to evaluate : 1.136 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1153 time to fit residues: 2.1863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 chunk 99 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 0.1980 chunk 78 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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** ** 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: 0.7611 moved from start: 0.3483 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 : 0.585 10.592 13873 Z= 0.294 Chirality : 0.041 0.174 1583 Planarity : 0.003 0.046 1773 Dihedral : 5.629 111.883 1395 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.24), residues: 1256 helix: 1.34 (0.19), residues: 789 sheet: -1.39 (0.53), residues: 94 loop : -1.62 (0.33), residues: 373 ********************** 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 169 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 164 time to evaluate : 1.266 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 166 average time/residue: 0.2354 time to fit residues: 55.8401 Evaluate side-chains 163 residues out of total 1079 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 159 time to evaluate : 1.236 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1023 time to fit residues: 2.5352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.4980 chunk 91 optimal weight: 0.0470 chunk 14 optimal weight: 0.2980 chunk 27 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.4078 ------------------------------------------------------------------------------- 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 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 424 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.191116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.151079 restraints weight = 12720.858| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.19 r_work: 0.3586 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3580 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= 0.178 Angle : 0.570 10.719 13873 Z= 0.287 Chirality : 0.041 0.176 1583 Planarity : 0.003 0.046 1773 Dihedral : 5.529 111.228 1395 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 0.09 % 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: 0.52 (0.25), residues: 1256 helix: 1.41 (0.19), residues: 790 sheet: -1.15 (0.53), residues: 92 loop : -1.54 (0.33), residues: 374 =============================================================================== Job complete usr+sys time: 2338.75 seconds wall clock time: 43 minutes 0.86 seconds (2580.86 seconds total)