Starting phenix.real_space_refine on Fri Feb 14 12:33:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xha_33192/02_2025/7xha_33192.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xha_33192/02_2025/7xha_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/cci-nas-00/data/ceres_data/7xha_33192/02_2025/7xha_33192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xha_33192/02_2025/7xha_33192.map" model { file = "/net/cci-nas-00/data/ceres_data/7xha_33192/02_2025/7xha_33192.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xha_33192/02_2025/7xha_33192.cif" } 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. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.17, per 1000 atoms: 0.61 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 - 3.00 Amino acid : True - 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: 2.57 Conformation dependent library (CDL) restraints added in 1.1 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... Secondary structure from input PDB file: 51 helices and 7 sheets defined 64.5% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 15 through 29 Processing helix chain 'A' and resid 30 through 33 Processing helix chain 'A' and resid 37 through 53 removed outlier: 3.523A pdb=" N LEU A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) 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 58 through 60 No H-bonds generated for 'chain 'A' and resid 58 through 60' Processing helix chain 'A' and resid 61 through 78 removed outlier: 4.027A pdb=" N ARG A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 94 Processing helix chain 'A' and resid 107 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 130 through 149 Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 177 through 188 Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 231 through 242 removed outlier: 3.741A pdb=" N VAL A 235 " --> pdb=" O THR A 231 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 283 through 299 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 333 through 341 Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 377 through 385 Processing helix chain 'A' and resid 410 through 427 Processing helix chain 'A' and resid 439 through 451 removed outlier: 3.989A pdb=" N ASN A 451 " --> pdb=" O LYS A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 473 Processing helix chain 'A' and resid 515 through 527 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 543 through 550 Processing helix chain 'A' and resid 551 through 558 Processing helix chain 'A' and resid 559 through 562 removed outlier: 3.750A pdb=" N GLY A 562 " --> pdb=" O ASP A 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 559 through 562' Processing helix chain 'A' and resid 573 through 619 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 623 through 643 Processing helix chain 'A' and resid 653 through 665 Processing helix chain 'A' and resid 680 through 704 Processing helix chain 'A' and resid 706 through 737 removed outlier: 3.876A pdb=" N GLU A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY A 737 " --> pdb=" O GLN A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 745 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 747 through 778 removed outlier: 3.742A pdb=" N ALA A 778 " --> pdb=" O PHE A 774 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 9 Processing helix chain 'Y' and resid 11 through 33 Processing helix chain 'Y' and resid 42 through 47 Processing helix chain 'Y' and resid 74 through 88 Processing helix chain 'Y' and resid 92 through 101 Processing helix chain 'Y' and resid 105 through 136 removed outlier: 3.879A pdb=" N LEU Y 126 " --> pdb=" O PHE Y 122 " (cutoff:3.500A) Processing helix chain 'Y' and resid 146 through 174 Processing helix chain 'Y' and resid 177 through 188 Processing helix chain 'Y' and resid 190 through 202 Processing helix chain 'Y' and resid 216 through 236 Processing helix chain 'Y' and resid 271 through 291 removed outlier: 3.640A pdb=" N ILE Y 275 " --> pdb=" O VAL Y 271 " (cutoff:3.500A) Proline residue: Y 284 - end of helix Processing helix chain 'Y' and resid 294 through 304 Processing helix chain 'Y' and resid 308 through 331 removed outlier: 3.936A pdb=" N ILE Y 314 " --> pdb=" O VAL Y 310 " (cutoff:3.500A) Processing helix chain 'Y' and resid 332 through 344 Processing helix chain 'Y' and resid 354 through 390 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 399 through 422 removed outlier: 4.296A pdb=" N LEU Y 403 " --> pdb=" O GLY Y 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 15 Processing helix chain 'E' and resid 22 through 58 Processing helix chain 'B' and resid 3 through 20 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=AA1, first strand: chain 'A' and resid 98 through 99 Processing sheet with id=AA2, first strand: chain 'A' and resid 152 through 154 removed outlier: 3.755A pdb=" N TYR A 174 " --> pdb=" O GLY A 153 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 327 through 329 removed outlier: 6.250A pdb=" N ILE A 222 " --> pdb=" O TYR B 52 " (cutoff:3.500A) 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=AA4, 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=AA5, first strand: chain 'A' and resid 306 through 309 Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 402 removed outlier: 3.806A pdb=" N THR A 535 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A 507 " --> pdb=" O GLN A 536 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU A 433 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL A 432 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ALA A 483 " --> pdb=" O VAL A 432 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N VAL A 434 " --> pdb=" O ALA A 483 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 482 " --> pdb=" O GLN A 457 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Y' and resid 238 through 241 610 hydrogen bonds defined for protein. 1806 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: 3.08 Time building geometry restraints manager: 2.93 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: 0.00 - 3.67: 13675 3.67 - 7.34: 165 7.34 - 11.01: 27 11.01 - 14.67: 5 14.67 - 18.34: 1 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: 6384 3.08 - 3.68: 15067 3.68 - 4.29: 21692 4.29 - 4.90: 36338 Nonbonded interactions: 79510 Sorted by model distance: nonbonded pdb=" OD1 ASN A 238 " pdb=" NE2 HIS A 297 " model vdw 1.860 3.120 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 3.120 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 79505 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.660 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: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 24.710 Find NCS groups from input model: 0.110 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.830 ------------------------------------------------------------------------------- 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= 0.520 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 to be fit. rotamer outliers: 3 poor density : 250 time to evaluate : 0.905 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: 0.2528 time to fit residues: 85.7733 Evaluate side-chains 165 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 162 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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: 0.7980 chunk 94 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 63 optimal weight: 10.0000 chunk 50 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 113 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 GLN A 430 GLN A 457 GLN A 529 GLN A 536 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 355 ASN Y 419 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.193557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.153355 restraints weight = 12657.280| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.52 r_work: 0.3594 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2018 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= 0.217 Angle : 0.616 11.722 13873 Z= 0.319 Chirality : 0.043 0.215 1583 Planarity : 0.005 0.052 1773 Dihedral : 7.109 131.399 1404 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.85 % Allowed : 9.92 % Favored : 88.23 % 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: -1.26 (0.23), residues: 1256 helix: 0.04 (0.17), residues: 798 sheet: -1.91 (0.52), residues: 96 loop : -2.33 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 98 HIS 0.005 0.001 HIS A 93 PHE 0.025 0.002 PHE A 703 TYR 0.014 0.001 TYR Y 245 ARG 0.007 0.001 ARG A 466 *********************** 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 207 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 HIS cc_start: 0.8594 (t70) cc_final: 0.8375 (t-90) REVERT: A 106 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8403 (mtmm) REVERT: A 189 MET cc_start: 0.8298 (mtp) cc_final: 0.8091 (mtp) REVERT: A 194 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7905 (pm20) REVERT: A 273 PHE cc_start: 0.7987 (m-10) cc_final: 0.7667 (m-80) REVERT: A 331 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7825 (mm-30) REVERT: A 350 MET cc_start: 0.8815 (pmm) cc_final: 0.8497 (ptp) REVERT: A 362 ARG cc_start: 0.8738 (mmm-85) cc_final: 0.8533 (mmm-85) REVERT: A 560 ARG cc_start: 0.7775 (ptt90) cc_final: 0.7559 (ptt90) REVERT: A 707 GLN cc_start: 0.8153 (mm110) cc_final: 0.7893 (mt0) REVERT: A 762 HIS cc_start: 0.7725 (m-70) cc_final: 0.7504 (m-70) REVERT: A 769 ASP cc_start: 0.8248 (m-30) cc_final: 0.7815 (m-30) REVERT: E 44 PHE cc_start: 0.8907 (m-80) cc_final: 0.8528 (m-80) outliers start: 20 outliers final: 12 residues processed: 198 average time/residue: 0.2885 time to fit residues: 78.4380 Evaluate side-chains 179 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU 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 618 ILE 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 32 THR Chi-restraints excluded: chain Y residue 151 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 78 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 0.0570 chunk 6 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 0.0870 chunk 74 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 7 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.193441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.153797 restraints weight = 12911.225| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 2.15 r_work: 0.3610 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2432 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= 0.194 Angle : 0.575 9.459 13873 Z= 0.297 Chirality : 0.042 0.206 1583 Planarity : 0.004 0.047 1773 Dihedral : 6.091 113.527 1399 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.22 % Allowed : 10.94 % Favored : 86.84 % 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: -0.39 (0.24), residues: 1256 helix: 0.78 (0.18), residues: 806 sheet: -1.61 (0.52), residues: 96 loop : -2.22 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 98 HIS 0.004 0.001 HIS A 93 PHE 0.025 0.001 PHE A 703 TYR 0.016 0.001 TYR Y 149 ARG 0.004 0.000 ARG A 403 *********************** 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 202 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8403 (mtmm) REVERT: A 189 MET cc_start: 0.8393 (mtp) cc_final: 0.7974 (mtp) REVERT: A 273 PHE cc_start: 0.8089 (m-10) cc_final: 0.7625 (m-80) REVERT: A 331 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8076 (mm-30) REVERT: A 460 ASN cc_start: 0.7853 (m-40) cc_final: 0.7644 (m110) REVERT: A 500 LYS cc_start: 0.8399 (ptpp) cc_final: 0.8032 (mtpt) REVERT: A 657 LEU cc_start: 0.7941 (tp) cc_final: 0.7680 (tt) REVERT: A 707 GLN cc_start: 0.8284 (mm110) cc_final: 0.7934 (mt0) REVERT: A 762 HIS cc_start: 0.7884 (m-70) cc_final: 0.7586 (m-70) REVERT: Y 429 ILE cc_start: 0.7526 (OUTLIER) cc_final: 0.7093 (pp) outliers start: 24 outliers final: 11 residues processed: 191 average time/residue: 0.2404 time to fit residues: 63.7941 Evaluate side-chains 173 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 224 SER 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 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 421 VAL Chi-restraints excluded: chain Y residue 429 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 7 ASN ** Y 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.181600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.140649 restraints weight = 12816.292| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.39 r_work: 0.3479 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10274 Z= 0.289 Angle : 0.612 11.150 13873 Z= 0.319 Chirality : 0.044 0.216 1583 Planarity : 0.004 0.047 1773 Dihedral : 6.186 115.261 1399 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.32 % Allowed : 12.33 % Favored : 85.36 % 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: -0.15 (0.24), residues: 1256 helix: 1.03 (0.18), residues: 802 sheet: -1.92 (0.49), residues: 101 loop : -2.13 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 165 HIS 0.005 0.001 HIS A 297 PHE 0.033 0.002 PHE A 703 TYR 0.018 0.002 TYR Y 245 ARG 0.005 0.001 ARG Y 362 *********************** 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 to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8431 (mtmm) REVERT: A 189 MET cc_start: 0.8428 (mtp) cc_final: 0.7996 (mtp) REVERT: A 273 PHE cc_start: 0.7953 (m-10) cc_final: 0.7746 (m-10) REVERT: A 331 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7828 (mm-30) REVERT: A 373 THR cc_start: 0.9029 (p) cc_final: 0.8763 (p) REVERT: A 500 LYS cc_start: 0.8341 (ptpp) cc_final: 0.7977 (mtpt) REVERT: A 576 ARG cc_start: 0.7583 (ttm170) cc_final: 0.7046 (mtp-110) REVERT: A 624 ARG cc_start: 0.8031 (ttm170) cc_final: 0.7808 (ttm-80) REVERT: A 707 GLN cc_start: 0.8302 (mm110) cc_final: 0.7938 (mt0) REVERT: A 731 MET cc_start: 0.8689 (tpt) cc_final: 0.8142 (tpt) REVERT: A 762 HIS cc_start: 0.7690 (m-70) cc_final: 0.7372 (m-70) REVERT: Y 10 ARG cc_start: 0.7685 (mmt180) cc_final: 0.6538 (tpp80) REVERT: Y 429 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7098 (pp) outliers start: 25 outliers final: 17 residues processed: 177 average time/residue: 0.2592 time to fit residues: 62.7676 Evaluate side-chains 176 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 224 SER 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 636 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 163 LEU Chi-restraints excluded: chain Y residue 219 LEU Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain Y residue 429 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 66 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 GLN ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 7 ASN ** Y 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 424 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.182424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.140612 restraints weight = 12829.223| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.27 r_work: 0.3488 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10274 Z= 0.242 Angle : 0.594 10.508 13873 Z= 0.306 Chirality : 0.043 0.209 1583 Planarity : 0.004 0.047 1773 Dihedral : 6.033 113.926 1399 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.59 % Allowed : 12.97 % Favored : 84.43 % 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: 0.07 (0.24), residues: 1256 helix: 1.19 (0.18), residues: 803 sheet: -1.87 (0.49), residues: 100 loop : -2.02 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 165 HIS 0.004 0.001 HIS A 93 PHE 0.034 0.001 PHE A 703 TYR 0.013 0.001 TYR Y 245 ARG 0.004 0.000 ARG A 362 *********************** 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 193 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8290 (mtmm) REVERT: A 189 MET cc_start: 0.8389 (mtp) cc_final: 0.8005 (mtp) REVERT: A 331 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7768 (mm-30) REVERT: A 373 THR cc_start: 0.9043 (p) cc_final: 0.8774 (p) REVERT: A 500 LYS cc_start: 0.8312 (ptpp) cc_final: 0.8007 (mtmm) REVERT: A 707 GLN cc_start: 0.8283 (mm110) cc_final: 0.7948 (mt0) REVERT: A 762 HIS cc_start: 0.7647 (m-70) cc_final: 0.7368 (m-70) REVERT: A 777 LYS cc_start: 0.7502 (ttmt) cc_final: 0.7220 (ttmt) REVERT: Y 10 ARG cc_start: 0.7775 (mmt180) cc_final: 0.6570 (tpp80) REVERT: Y 429 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7133 (pp) outliers start: 28 outliers final: 19 residues processed: 180 average time/residue: 0.2499 time to fit residues: 62.4981 Evaluate side-chains 178 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 224 SER 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 636 GLU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 151 LEU Chi-restraints excluded: chain Y residue 163 LEU Chi-restraints excluded: chain Y residue 219 LEU Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain Y residue 429 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 54 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 48 optimal weight: 0.1980 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 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 7 ASN ** Y 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 424 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.183229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.142765 restraints weight = 12795.366| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.19 r_work: 0.3502 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3054 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= 0.204 Angle : 0.575 10.881 13873 Z= 0.297 Chirality : 0.042 0.200 1583 Planarity : 0.004 0.047 1773 Dihedral : 5.895 113.359 1399 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.78 % Allowed : 13.72 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.24), residues: 1256 helix: 1.31 (0.18), residues: 805 sheet: -1.80 (0.52), residues: 90 loop : -1.86 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Y 165 HIS 0.003 0.001 HIS A 93 PHE 0.027 0.001 PHE E 43 TYR 0.012 0.001 TYR Y 149 ARG 0.004 0.000 ARG A 362 *********************** 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 198 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 MET cc_start: 0.8284 (mtp) cc_final: 0.8004 (mtp) REVERT: A 331 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7742 (mm-30) REVERT: A 373 THR cc_start: 0.9040 (p) cc_final: 0.8762 (p) REVERT: A 500 LYS cc_start: 0.8289 (ptpp) cc_final: 0.8029 (mtmm) REVERT: A 600 ASP cc_start: 0.7292 (t70) cc_final: 0.7037 (t70) REVERT: A 707 GLN cc_start: 0.8233 (mm110) cc_final: 0.7941 (mt0) REVERT: A 754 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7761 (mmm) REVERT: A 762 HIS cc_start: 0.7616 (m-70) cc_final: 0.7335 (m-70) REVERT: Y 10 ARG cc_start: 0.7753 (mmt180) cc_final: 0.6546 (tpp80) REVERT: Y 254 PRO cc_start: 0.8162 (Cg_endo) cc_final: 0.7771 (Cg_exo) REVERT: Y 429 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.7015 (pp) outliers start: 30 outliers final: 19 residues processed: 181 average time/residue: 0.2441 time to fit residues: 60.7265 Evaluate side-chains 179 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 224 SER 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 642 TYR Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 725 MET 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 163 LEU Chi-restraints excluded: chain Y residue 219 LEU Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain Y residue 429 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 110 optimal weight: 0.3980 chunk 105 optimal weight: 0.2980 chunk 28 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN A 736 GLN Y 7 ASN ** Y 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 424 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.181821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.142596 restraints weight = 12651.477| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.19 r_work: 0.3536 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10274 Z= 0.189 Angle : 0.573 10.072 13873 Z= 0.293 Chirality : 0.042 0.194 1583 Planarity : 0.003 0.047 1773 Dihedral : 5.779 114.123 1399 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.59 % Allowed : 15.11 % Favored : 82.30 % 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: 0.48 (0.24), residues: 1256 helix: 1.44 (0.18), residues: 807 sheet: -1.59 (0.54), residues: 88 loop : -1.75 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Y 165 HIS 0.003 0.000 HIS A 93 PHE 0.023 0.001 PHE E 43 TYR 0.010 0.001 TYR Y 326 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 189 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 MET cc_start: 0.8315 (mtp) cc_final: 0.8064 (mtp) REVERT: A 331 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7989 (mm-30) REVERT: A 373 THR cc_start: 0.9054 (p) cc_final: 0.8778 (p) REVERT: A 500 LYS cc_start: 0.8367 (ptpp) cc_final: 0.8131 (mtpt) REVERT: A 600 ASP cc_start: 0.7531 (t70) cc_final: 0.7267 (t70) REVERT: A 707 GLN cc_start: 0.8331 (mm110) cc_final: 0.8022 (mt0) REVERT: A 754 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.7983 (mmm) REVERT: A 762 HIS cc_start: 0.7820 (m-70) cc_final: 0.7512 (m-70) REVERT: A 770 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8334 (tm-30) REVERT: Y 10 ARG cc_start: 0.7768 (mmt180) cc_final: 0.6536 (tpp80) REVERT: Y 254 PRO cc_start: 0.8108 (Cg_endo) cc_final: 0.7723 (Cg_exo) REVERT: Y 429 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7269 (pp) outliers start: 28 outliers final: 22 residues processed: 175 average time/residue: 0.2428 time to fit residues: 58.7148 Evaluate side-chains 180 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 224 SER 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 636 GLU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain Y residue 23 LEU Chi-restraints excluded: chain Y residue 133 ASN Chi-restraints excluded: chain Y residue 151 LEU Chi-restraints excluded: chain Y residue 163 LEU Chi-restraints excluded: chain Y residue 219 LEU Chi-restraints excluded: chain Y residue 323 THR Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain Y residue 429 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 75 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 30 optimal weight: 0.0030 chunk 117 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 7 ASN ** Y 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 424 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.184022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.142725 restraints weight = 12933.911| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.23 r_work: 0.3514 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10274 Z= 0.205 Angle : 0.583 10.891 13873 Z= 0.297 Chirality : 0.042 0.196 1583 Planarity : 0.003 0.047 1773 Dihedral : 5.733 114.597 1399 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.50 % Allowed : 15.20 % Favored : 82.30 % 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: 0.56 (0.24), residues: 1256 helix: 1.51 (0.18), residues: 808 sheet: -1.53 (0.55), residues: 88 loop : -1.74 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Y 165 HIS 0.003 0.001 HIS A 93 PHE 0.025 0.001 PHE A 703 TYR 0.012 0.001 TYR Y 245 ARG 0.005 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 190 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 1.055 Fit side-chains REVERT: A 39 ASP cc_start: 0.8885 (m-30) cc_final: 0.8585 (p0) REVERT: A 189 MET cc_start: 0.8385 (mtp) cc_final: 0.8127 (mtp) REVERT: A 331 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7960 (mm-30) REVERT: A 373 THR cc_start: 0.9075 (p) cc_final: 0.8796 (p) REVERT: A 500 LYS cc_start: 0.8364 (ptpp) cc_final: 0.8145 (mtpt) REVERT: A 600 ASP cc_start: 0.7560 (t70) cc_final: 0.7295 (t70) REVERT: A 707 GLN cc_start: 0.8402 (mm110) cc_final: 0.8084 (mt0) REVERT: A 754 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.7936 (mmm) REVERT: A 762 HIS cc_start: 0.7838 (m-70) cc_final: 0.7498 (m-70) REVERT: A 770 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8360 (tm-30) REVERT: Y 10 ARG cc_start: 0.7820 (mmt180) cc_final: 0.6600 (tpp80) REVERT: Y 254 PRO cc_start: 0.8166 (Cg_endo) cc_final: 0.7815 (Cg_exo) REVERT: Y 302 ARG cc_start: 0.7992 (mtp180) cc_final: 0.7195 (mtm-85) REVERT: Y 429 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7166 (pp) outliers start: 27 outliers final: 22 residues processed: 176 average time/residue: 0.2460 time to fit residues: 60.1146 Evaluate side-chains 179 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 224 SER 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 636 GLU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain Y residue 23 LEU Chi-restraints excluded: chain Y residue 133 ASN Chi-restraints excluded: chain Y residue 151 LEU Chi-restraints excluded: chain Y residue 163 LEU Chi-restraints excluded: chain Y residue 323 THR 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 17 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 124 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 95 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 7 ASN ** Y 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 424 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.183506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.143477 restraints weight = 12943.455| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.23 r_work: 0.3507 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10274 Z= 0.225 Angle : 0.597 9.801 13873 Z= 0.305 Chirality : 0.042 0.200 1583 Planarity : 0.003 0.047 1773 Dihedral : 5.760 114.693 1399 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.59 % Allowed : 15.29 % Favored : 82.11 % 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: 0.58 (0.24), residues: 1256 helix: 1.51 (0.18), residues: 808 sheet: -1.49 (0.57), residues: 81 loop : -1.73 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP Y 165 HIS 0.003 0.001 HIS A 93 PHE 0.027 0.001 PHE A 703 TYR 0.013 0.001 TYR Y 245 ARG 0.004 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 184 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8897 (m-30) cc_final: 0.8568 (p0) REVERT: A 189 MET cc_start: 0.8384 (mtp) cc_final: 0.8119 (mtp) REVERT: A 331 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7966 (mm-30) REVERT: A 373 THR cc_start: 0.9068 (p) cc_final: 0.8750 (p) REVERT: A 500 LYS cc_start: 0.8371 (ptpp) cc_final: 0.8151 (mtpt) REVERT: A 600 ASP cc_start: 0.7557 (t70) cc_final: 0.7293 (t70) REVERT: A 707 GLN cc_start: 0.8335 (mm110) cc_final: 0.8034 (mt0) REVERT: A 754 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8034 (mmm) REVERT: A 762 HIS cc_start: 0.7848 (m-70) cc_final: 0.7499 (m-70) REVERT: Y 10 ARG cc_start: 0.7796 (mmt180) cc_final: 0.6546 (tpp80) REVERT: Y 254 PRO cc_start: 0.8146 (Cg_endo) cc_final: 0.7788 (Cg_exo) REVERT: Y 429 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7229 (pp) outliers start: 28 outliers final: 21 residues processed: 170 average time/residue: 0.2823 time to fit residues: 67.0631 Evaluate side-chains 177 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 224 SER 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 636 GLU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain Y residue 23 LEU Chi-restraints excluded: chain Y residue 133 ASN Chi-restraints excluded: chain Y residue 151 LEU Chi-restraints excluded: chain Y residue 163 LEU Chi-restraints excluded: chain Y residue 323 THR 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 9 optimal weight: 0.6980 chunk 50 optimal weight: 0.0570 chunk 1 optimal weight: 0.0970 chunk 87 optimal weight: 6.9990 chunk 108 optimal weight: 0.0980 chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 83 optimal weight: 0.0060 chunk 76 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.1912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 GLN Y 7 ASN ** Y 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 424 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.188644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.149255 restraints weight = 12876.726| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.16 r_work: 0.3579 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10274 Z= 0.161 Angle : 0.579 10.201 13873 Z= 0.292 Chirality : 0.041 0.198 1583 Planarity : 0.003 0.047 1773 Dihedral : 5.577 116.009 1399 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.95 % Allowed : 16.50 % Favored : 81.56 % 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: 0.93 (0.25), residues: 1256 helix: 1.74 (0.18), residues: 807 sheet: -1.05 (0.59), residues: 78 loop : -1.56 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP Y 165 HIS 0.002 0.000 HIS A 93 PHE 0.029 0.001 PHE A 703 TYR 0.009 0.001 TYR A 174 ARG 0.005 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 192 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8792 (m-30) cc_final: 0.8474 (p0) REVERT: A 189 MET cc_start: 0.8315 (mtp) cc_final: 0.7908 (mtp) REVERT: A 373 THR cc_start: 0.9042 (p) cc_final: 0.8743 (p) REVERT: A 600 ASP cc_start: 0.7871 (t70) cc_final: 0.7609 (t70) REVERT: A 707 GLN cc_start: 0.8336 (mm110) cc_final: 0.8053 (mt0) REVERT: A 731 MET cc_start: 0.8699 (tpt) cc_final: 0.8221 (tpt) REVERT: A 762 HIS cc_start: 0.7774 (m-70) cc_final: 0.7411 (m-70) REVERT: A 770 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8317 (tm-30) REVERT: Y 10 ARG cc_start: 0.7740 (mmt180) cc_final: 0.6551 (tpp80) REVERT: Y 365 TYR cc_start: 0.7478 (m-10) cc_final: 0.7175 (m-10) REVERT: Y 429 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.7208 (pp) outliers start: 21 outliers final: 14 residues processed: 182 average time/residue: 0.2520 time to fit residues: 64.2015 Evaluate side-chains 168 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 129 VAL 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 642 TYR Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain Y residue 133 ASN Chi-restraints excluded: chain Y residue 323 THR 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 98 optimal weight: 0.0670 chunk 58 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN A 736 GLN ** Y 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 236 GLN Y 424 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.184774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.144242 restraints weight = 12867.211| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.37 r_work: 0.3529 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10274 Z= 0.207 Angle : 0.597 10.005 13873 Z= 0.302 Chirality : 0.042 0.202 1583 Planarity : 0.004 0.047 1773 Dihedral : 5.609 116.200 1399 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.85 % Allowed : 17.33 % Favored : 80.82 % 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: 0.88 (0.24), residues: 1256 helix: 1.68 (0.18), residues: 809 sheet: -0.99 (0.59), residues: 77 loop : -1.56 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP Y 165 HIS 0.003 0.001 HIS A 93 PHE 0.030 0.001 PHE A 703 TYR 0.013 0.001 TYR Y 245 ARG 0.007 0.000 ARG A 637 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5289.17 seconds wall clock time: 94 minutes 27.52 seconds (5667.52 seconds total)