Starting phenix.real_space_refine on Mon Jul 28 08:57:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xha_33192/07_2025/7xha_33192.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xha_33192/07_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_33192/07_2025/7xha_33192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xha_33192/07_2025/7xha_33192.map" model { file = "/net/cci-nas-00/data/ceres_data/7xha_33192/07_2025/7xha_33192.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xha_33192/07_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-5711/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: 6.26, per 1000 atoms: 0.62 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 1.6 seconds 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2360 Finding SS restraints... 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: 1.15 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: 2.94 Time building geometry restraints manager: 2.99 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: 1.690 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.690 Find NCS groups from input model: 0.100 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.120 ------------------------------------------------------------------------------- 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 : 0.012 0.672 10276 Z= 1.041 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 Details of bonding type rmsd hydrogen bonds : bond 0.09928 ( 610) hydrogen bonds : angle 6.01405 ( 1806) covalent geometry : bond 0.00815 (10274) covalent geometry : angle 1.06280 (13873) Misc. bond : bond 0.66450 ( 2) *********************** 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 : 1.061 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: 0.2526 time to fit residues: 85.9574 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 : 1.185 ------------------------------------------------------------------------------- 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 = 0.153353 restraints weight = 12657.280| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.52 r_work: 0.3592 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 10276 Z= 0.151 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 Details of bonding type rmsd hydrogen bonds : bond 0.04410 ( 610) hydrogen bonds : angle 4.63236 ( 1806) covalent geometry : bond 0.00338 (10274) covalent geometry : angle 0.61636 (13873) Misc. bond : bond 0.00123 ( 2) *********************** 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 : 1.159 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: 0.8933 (OUTLIER) cc_final: 0.8407 (mtmm) REVERT: A 189 MET cc_start: 0.8299 (mtp) cc_final: 0.8092 (mtp) REVERT: A 194 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7913 (pm20) REVERT: A 273 PHE cc_start: 0.7984 (m-10) cc_final: 0.7667 (m-80) REVERT: A 331 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7832 (mm-30) REVERT: A 350 MET cc_start: 0.8822 (pmm) cc_final: 0.8504 (ptp) REVERT: A 362 ARG cc_start: 0.8737 (mmm-85) cc_final: 0.8533 (mmm-85) REVERT: A 560 ARG cc_start: 0.7769 (ptt90) cc_final: 0.7560 (ptt90) REVERT: A 707 GLN cc_start: 0.8157 (mm110) cc_final: 0.7898 (mt0) REVERT: A 762 HIS cc_start: 0.7725 (m-70) cc_final: 0.7506 (m-70) REVERT: A 769 ASP cc_start: 0.8258 (m-30) cc_final: 0.7823 (m-30) REVERT: E 44 PHE cc_start: 0.8911 (m-80) cc_final: 0.8525 (m-80) outliers start: 20 outliers final: 12 residues processed: 198 average time/residue: 0.2429 time to fit residues: 65.8927 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 : 1.066 ------------------------------------------------------------------------------- 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: 1.9990 chunk 76 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.4229 r_free = 0.4229 target = 0.192087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.152016 restraints weight = 12925.790| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.15 r_work: 0.3588 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10276 Z= 0.152 Angle : 0.586 9.470 13873 Z= 0.303 Chirality : 0.042 0.208 1583 Planarity : 0.004 0.047 1773 Dihedral : 6.119 112.353 1399 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.32 % Allowed : 10.94 % Favored : 86.75 % 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: -0.44 (0.24), residues: 1256 helix: 0.76 (0.18), residues: 804 sheet: -1.82 (0.50), residues: 100 loop : -2.23 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 98 HIS 0.005 0.001 HIS A 93 PHE 0.025 0.001 PHE A 703 TYR 0.014 0.002 TYR Y 245 ARG 0.004 0.000 ARG A 528 Details of bonding type rmsd hydrogen bonds : bond 0.04221 ( 610) hydrogen bonds : angle 4.42149 ( 1806) covalent geometry : bond 0.00348 (10274) covalent geometry : angle 0.58608 (13873) Misc. bond : bond 0.00073 ( 2) *********************** 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 198 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8436 (mtmm) REVERT: A 189 MET cc_start: 0.8453 (mtp) cc_final: 0.8008 (mtp) REVERT: A 273 PHE cc_start: 0.8115 (m-10) cc_final: 0.7661 (m-80) REVERT: A 331 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8083 (mm-30) REVERT: A 373 THR cc_start: 0.9049 (p) cc_final: 0.8745 (p) REVERT: A 500 LYS cc_start: 0.8413 (ptpp) cc_final: 0.8035 (mtpt) REVERT: A 624 ARG cc_start: 0.8173 (ttm170) cc_final: 0.7962 (ttm-80) REVERT: A 657 LEU cc_start: 0.7950 (tp) cc_final: 0.7710 (tt) REVERT: A 707 GLN cc_start: 0.8297 (mm110) cc_final: 0.7941 (mt0) REVERT: A 731 MET cc_start: 0.8794 (tpt) cc_final: 0.8305 (tpt) REVERT: A 762 HIS cc_start: 0.7907 (m-70) cc_final: 0.7599 (m-70) REVERT: Y 10 ARG cc_start: 0.7605 (mmt180) cc_final: 0.6445 (tpp80) REVERT: Y 429 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.7117 (pp) outliers start: 25 outliers final: 12 residues processed: 187 average time/residue: 0.2402 time to fit residues: 62.1357 Evaluate side-chains 171 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 163 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: 0.5980 chunk 123 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 124 optimal weight: 0.3980 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 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.185839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.146186 restraints weight = 12867.259| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.39 r_work: 0.3519 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10276 Z= 0.145 Angle : 0.570 11.177 13873 Z= 0.296 Chirality : 0.042 0.204 1583 Planarity : 0.004 0.047 1773 Dihedral : 6.034 114.270 1399 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.22 % Allowed : 12.23 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.24), residues: 1256 helix: 1.15 (0.18), residues: 804 sheet: -1.81 (0.50), residues: 100 loop : -2.06 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 165 HIS 0.003 0.001 HIS A 93 PHE 0.036 0.001 PHE A 703 TYR 0.012 0.001 TYR Y 245 ARG 0.004 0.000 ARG A 362 Details of bonding type rmsd hydrogen bonds : bond 0.04089 ( 610) hydrogen bonds : angle 4.30947 ( 1806) covalent geometry : bond 0.00330 (10274) covalent geometry : angle 0.56998 (13873) Misc. bond : bond 0.00063 ( 2) *********************** 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 194 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8728 (m-30) cc_final: 0.8488 (p0) REVERT: A 106 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8239 (mtmm) REVERT: A 189 MET cc_start: 0.8319 (mtp) cc_final: 0.7925 (mtp) REVERT: A 273 PHE cc_start: 0.7775 (m-10) cc_final: 0.7570 (m-10) REVERT: A 331 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7776 (mm-30) REVERT: A 373 THR cc_start: 0.9018 (p) cc_final: 0.8705 (p) REVERT: A 460 ASN cc_start: 0.7675 (m-40) cc_final: 0.7437 (m110) REVERT: A 500 LYS cc_start: 0.8295 (ptpp) cc_final: 0.8012 (mtmm) REVERT: A 624 ARG cc_start: 0.7984 (ttm170) cc_final: 0.7621 (ttt-90) REVERT: A 707 GLN cc_start: 0.8254 (mm110) cc_final: 0.7912 (mt0) REVERT: A 762 HIS cc_start: 0.7645 (m-70) cc_final: 0.7322 (m-70) REVERT: Y 10 ARG cc_start: 0.7672 (mmt180) cc_final: 0.6541 (tpp80) REVERT: Y 429 ILE cc_start: 0.7437 (OUTLIER) cc_final: 0.7023 (pp) outliers start: 24 outliers final: 16 residues processed: 180 average time/residue: 0.2540 time to fit residues: 62.6003 Evaluate side-chains 172 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 1.157 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 109 optimal weight: 0.9990 chunk 61 optimal weight: 0.2980 chunk 63 optimal weight: 0.0270 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 0.2980 chunk 29 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.187357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.147697 restraints weight = 12896.059| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.07 r_work: 0.3545 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10276 Z= 0.124 Angle : 0.548 10.711 13873 Z= 0.283 Chirality : 0.041 0.188 1583 Planarity : 0.003 0.047 1773 Dihedral : 5.860 114.547 1399 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.13 % Allowed : 13.16 % Favored : 84.71 % 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: 0.37 (0.24), residues: 1256 helix: 1.40 (0.18), residues: 804 sheet: -1.69 (0.53), residues: 95 loop : -1.87 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Y 165 HIS 0.003 0.000 HIS A 93 PHE 0.034 0.001 PHE A 703 TYR 0.010 0.001 TYR Y 326 ARG 0.003 0.000 ARG A 362 Details of bonding type rmsd hydrogen bonds : bond 0.03801 ( 610) hydrogen bonds : angle 4.18660 ( 1806) covalent geometry : bond 0.00271 (10274) covalent geometry : angle 0.54849 (13873) Misc. bond : bond 0.00045 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8934 (m-30) cc_final: 0.8570 (p0) REVERT: A 106 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8297 (mtmm) REVERT: A 189 MET cc_start: 0.8318 (mtp) cc_final: 0.8048 (mtp) REVERT: A 273 PHE cc_start: 0.7899 (m-10) cc_final: 0.7452 (m-10) REVERT: A 373 THR cc_start: 0.9027 (p) cc_final: 0.8707 (p) REVERT: A 500 LYS cc_start: 0.8353 (ptpp) cc_final: 0.8100 (mtpt) REVERT: A 600 ASP cc_start: 0.7547 (t70) cc_final: 0.7299 (t70) REVERT: A 707 GLN cc_start: 0.8309 (mm110) cc_final: 0.7939 (mt0) REVERT: A 708 MET cc_start: 0.8093 (tpt) cc_final: 0.7853 (tpt) REVERT: A 762 HIS cc_start: 0.7841 (m-70) cc_final: 0.7484 (m-70) REVERT: Y 10 ARG cc_start: 0.7713 (mmt180) cc_final: 0.6506 (tpp80) REVERT: Y 254 PRO cc_start: 0.8111 (Cg_endo) cc_final: 0.7736 (Cg_exo) REVERT: Y 429 ILE cc_start: 0.7542 (OUTLIER) cc_final: 0.7166 (pp) outliers start: 23 outliers final: 14 residues processed: 180 average time/residue: 0.2353 time to fit residues: 58.8419 Evaluate side-chains 175 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 54 optimal weight: 0.8980 chunk 92 optimal weight: 0.3980 chunk 119 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 73 optimal weight: 0.0770 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Y 7 ASN ** Y 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.185265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.144145 restraints weight = 12782.669| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.26 r_work: 0.3530 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10276 Z= 0.134 Angle : 0.567 10.876 13873 Z= 0.290 Chirality : 0.042 0.188 1583 Planarity : 0.003 0.047 1773 Dihedral : 5.815 115.221 1399 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.22 % Allowed : 13.81 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.24), residues: 1256 helix: 1.49 (0.18), residues: 802 sheet: -1.62 (0.53), residues: 95 loop : -1.79 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Y 165 HIS 0.003 0.001 HIS A 93 PHE 0.033 0.001 PHE A 703 TYR 0.011 0.001 TYR Y 326 ARG 0.004 0.000 ARG A 75 Details of bonding type rmsd hydrogen bonds : bond 0.03871 ( 610) hydrogen bonds : angle 4.18098 ( 1806) covalent geometry : bond 0.00302 (10274) covalent geometry : angle 0.56657 (13873) Misc. bond : bond 0.00052 ( 2) *********************** 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 187 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8231 (mtmm) REVERT: A 189 MET cc_start: 0.8308 (mtp) cc_final: 0.8028 (mtp) REVERT: A 273 PHE cc_start: 0.7738 (m-10) cc_final: 0.7420 (m-80) REVERT: A 373 THR cc_start: 0.8984 (p) cc_final: 0.8669 (p) REVERT: A 500 LYS cc_start: 0.8229 (ptpp) cc_final: 0.8023 (mtpt) REVERT: A 600 ASP cc_start: 0.7277 (t70) cc_final: 0.7036 (t70) REVERT: A 707 GLN cc_start: 0.8239 (mm110) cc_final: 0.7892 (mt0) REVERT: A 754 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7689 (mmm) REVERT: A 762 HIS cc_start: 0.7612 (m-70) cc_final: 0.7279 (m-70) REVERT: Y 10 ARG cc_start: 0.7820 (mmt180) cc_final: 0.6589 (tpp80) REVERT: Y 254 PRO cc_start: 0.8165 (Cg_endo) cc_final: 0.7802 (Cg_exo) REVERT: Y 429 ILE cc_start: 0.7480 (OUTLIER) cc_final: 0.7095 (pp) outliers start: 24 outliers final: 16 residues processed: 178 average time/residue: 0.2307 time to fit residues: 57.0602 Evaluate side-chains 173 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 133 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 110 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 34 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.184939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.144595 restraints weight = 12950.809| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.21 r_work: 0.3515 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10276 Z= 0.137 Angle : 0.565 9.879 13873 Z= 0.291 Chirality : 0.042 0.197 1583 Planarity : 0.003 0.047 1773 Dihedral : 5.824 115.279 1399 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.50 % Allowed : 14.74 % Favored : 82.76 % 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: 1.54 (0.18), residues: 806 sheet: -1.53 (0.54), residues: 93 loop : -1.77 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Y 165 HIS 0.003 0.001 HIS A 93 PHE 0.034 0.001 PHE A 703 TYR 0.011 0.001 TYR Y 233 ARG 0.005 0.000 ARG A 624 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 610) hydrogen bonds : angle 4.17723 ( 1806) covalent geometry : bond 0.00312 (10274) covalent geometry : angle 0.56457 (13873) Misc. bond : bond 0.00061 ( 2) *********************** 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 186 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.8346 (mtp) cc_final: 0.8075 (mtp) REVERT: A 273 PHE cc_start: 0.7784 (m-10) cc_final: 0.7408 (m-80) REVERT: A 373 THR cc_start: 0.8987 (p) cc_final: 0.8655 (p) REVERT: A 600 ASP cc_start: 0.7296 (t70) cc_final: 0.7037 (t70) REVERT: A 707 GLN cc_start: 0.8306 (mm110) cc_final: 0.8005 (mt0) REVERT: A 762 HIS cc_start: 0.7612 (m-70) cc_final: 0.7248 (m-70) REVERT: Y 10 ARG cc_start: 0.7757 (mmt180) cc_final: 0.6586 (tpp80) REVERT: Y 254 PRO cc_start: 0.8136 (Cg_endo) cc_final: 0.7766 (Cg_exo) REVERT: Y 302 ARG cc_start: 0.8079 (mtp180) cc_final: 0.7298 (mtm-85) REVERT: Y 429 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.7073 (pp) outliers start: 27 outliers final: 20 residues processed: 174 average time/residue: 0.2392 time to fit residues: 57.5087 Evaluate side-chains 175 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 114 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 117 optimal weight: 0.3980 chunk 47 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 58 optimal weight: 0.2980 chunk 74 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Y 7 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.182072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.143386 restraints weight = 12639.072| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.17 r_work: 0.3537 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10276 Z= 0.133 Angle : 0.574 10.417 13873 Z= 0.294 Chirality : 0.042 0.194 1583 Planarity : 0.003 0.047 1773 Dihedral : 5.779 115.405 1399 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.04 % Allowed : 15.01 % Favored : 82.95 % 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: 0.67 (0.24), residues: 1256 helix: 1.61 (0.18), residues: 807 sheet: -1.44 (0.54), residues: 93 loop : -1.75 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Y 165 HIS 0.003 0.001 HIS A 93 PHE 0.028 0.001 PHE A 703 TYR 0.011 0.001 TYR Y 245 ARG 0.005 0.000 ARG A 624 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 610) hydrogen bonds : angle 4.16733 ( 1806) covalent geometry : bond 0.00300 (10274) covalent geometry : angle 0.57431 (13873) Misc. bond : bond 0.00056 ( 2) *********************** 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 185 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 1.177 Fit side-chains revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8899 (m-30) cc_final: 0.8586 (p0) REVERT: A 106 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8330 (mtmm) REVERT: A 189 MET cc_start: 0.8375 (mtp) cc_final: 0.8127 (mtp) REVERT: A 273 PHE cc_start: 0.7971 (m-10) cc_final: 0.7407 (m-80) REVERT: A 373 THR cc_start: 0.9018 (p) cc_final: 0.8714 (p) REVERT: A 572 LYS cc_start: 0.8215 (mttp) cc_final: 0.7972 (ttmm) REVERT: A 600 ASP cc_start: 0.7550 (t70) cc_final: 0.7275 (t70) REVERT: A 707 GLN cc_start: 0.8403 (mm110) cc_final: 0.8083 (mt0) REVERT: A 762 HIS cc_start: 0.7807 (m-70) cc_final: 0.7460 (m-70) REVERT: A 770 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8295 (tm-30) REVERT: Y 10 ARG cc_start: 0.7812 (mmt180) cc_final: 0.6606 (tpp80) REVERT: Y 254 PRO cc_start: 0.8157 (Cg_endo) cc_final: 0.7824 (Cg_exo) REVERT: Y 302 ARG cc_start: 0.7992 (mtp180) cc_final: 0.7186 (mtm-85) REVERT: Y 429 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7236 (pp) outliers start: 22 outliers final: 18 residues processed: 173 average time/residue: 0.2403 time to fit residues: 57.9542 Evaluate side-chains 176 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 133 ASN Chi-restraints excluded: chain Y residue 151 LEU Chi-restraints excluded: chain Y residue 163 LEU 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: 0.9980 chunk 37 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 95 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 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 = 0.4143 r_free = 0.4143 target = 0.181591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.142665 restraints weight = 12793.953| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.24 r_work: 0.3513 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10276 Z= 0.162 Angle : 0.601 9.588 13873 Z= 0.309 Chirality : 0.043 0.199 1583 Planarity : 0.004 0.047 1773 Dihedral : 5.849 114.303 1399 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.41 % Allowed : 15.11 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.24), residues: 1256 helix: 1.55 (0.18), residues: 808 sheet: -1.57 (0.54), residues: 93 loop : -1.79 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 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 233 ARG 0.005 0.000 ARG A 624 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 610) hydrogen bonds : angle 4.23309 ( 1806) covalent geometry : bond 0.00377 (10274) covalent geometry : angle 0.60100 (13873) Misc. bond : bond 0.00084 ( 2) *********************** 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 179 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 1.138 Fit side-chains revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8863 (m-30) cc_final: 0.8551 (p0) REVERT: A 106 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8353 (mtmm) REVERT: A 154 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8538 (tt) REVERT: A 189 MET cc_start: 0.8387 (mtp) cc_final: 0.8100 (mtp) REVERT: A 273 PHE cc_start: 0.8042 (m-10) cc_final: 0.7680 (m-10) REVERT: A 373 THR cc_start: 0.9041 (p) cc_final: 0.8772 (p) REVERT: A 572 LYS cc_start: 0.8380 (mttp) cc_final: 0.8148 (ttmm) REVERT: A 600 ASP cc_start: 0.7556 (t70) cc_final: 0.7293 (t70) REVERT: A 707 GLN cc_start: 0.8351 (mm110) cc_final: 0.8032 (mt0) REVERT: A 762 HIS cc_start: 0.7845 (m-70) cc_final: 0.7488 (m-70) REVERT: Y 10 ARG cc_start: 0.7822 (mmt180) cc_final: 0.6595 (tpp80) REVERT: Y 254 PRO cc_start: 0.8149 (Cg_endo) cc_final: 0.7798 (Cg_exo) REVERT: Y 302 ARG cc_start: 0.7980 (mtp180) cc_final: 0.7166 (mtm-85) REVERT: Y 429 ILE cc_start: 0.7669 (OUTLIER) cc_final: 0.7251 (pp) outliers start: 26 outliers final: 19 residues processed: 167 average time/residue: 0.2435 time to fit residues: 56.4212 Evaluate side-chains 174 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 154 LEU 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 133 ASN Chi-restraints excluded: chain Y residue 151 LEU Chi-restraints excluded: chain Y residue 163 LEU 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: 0.9980 chunk 50 optimal weight: 0.7980 chunk 1 optimal weight: 0.4980 chunk 87 optimal weight: 7.9990 chunk 108 optimal weight: 0.0770 chunk 48 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 83 optimal weight: 0.0670 chunk 76 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 7 ASN ** 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 = 0.4165 r_free = 0.4165 target = 0.185150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.143930 restraints weight = 12817.002| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.30 r_work: 0.3539 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10276 Z= 0.130 Angle : 0.581 10.133 13873 Z= 0.297 Chirality : 0.042 0.196 1583 Planarity : 0.003 0.047 1773 Dihedral : 5.780 115.417 1399 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.76 % Allowed : 15.57 % Favored : 82.67 % 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: 0.78 (0.24), residues: 1256 helix: 1.67 (0.18), residues: 808 sheet: -1.50 (0.58), residues: 78 loop : -1.66 (0.32), residues: 370 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 0.031 0.001 PHE A 703 TYR 0.011 0.001 TYR Y 233 ARG 0.005 0.000 ARG A 624 Details of bonding type rmsd hydrogen bonds : bond 0.03758 ( 610) hydrogen bonds : angle 4.14352 ( 1806) covalent geometry : bond 0.00291 (10274) covalent geometry : angle 0.58052 (13873) Misc. bond : bond 0.00050 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8239 (mtmm) REVERT: A 154 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8454 (tt) REVERT: A 189 MET cc_start: 0.8341 (mtp) cc_final: 0.8116 (mtp) REVERT: A 273 PHE cc_start: 0.7756 (m-10) cc_final: 0.7474 (m-80) REVERT: A 373 THR cc_start: 0.8974 (p) cc_final: 0.8665 (p) REVERT: A 572 LYS cc_start: 0.8236 (mttp) cc_final: 0.8029 (ttmm) REVERT: A 600 ASP cc_start: 0.7266 (t70) cc_final: 0.7018 (t70) REVERT: A 657 LEU cc_start: 0.7997 (tp) cc_final: 0.7698 (tt) REVERT: A 707 GLN cc_start: 0.8297 (mm110) cc_final: 0.8047 (mt0) REVERT: A 762 HIS cc_start: 0.7563 (m-70) cc_final: 0.7211 (m-70) REVERT: A 770 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8143 (tm-30) REVERT: Y 10 ARG cc_start: 0.7702 (mmt180) cc_final: 0.6539 (tpp80) REVERT: Y 429 ILE cc_start: 0.7504 (OUTLIER) cc_final: 0.7139 (pp) outliers start: 19 outliers final: 15 residues processed: 175 average time/residue: 0.2471 time to fit residues: 59.7689 Evaluate side-chains 175 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 154 LEU 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 Y residue 133 ASN 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: 0.1980 chunk 58 optimal weight: 0.2980 chunk 6 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 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 = 0.4156 r_free = 0.4156 target = 0.184201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.143978 restraints weight = 12854.209| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.34 r_work: 0.3551 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10276 Z= 0.143 Angle : 0.595 10.064 13873 Z= 0.305 Chirality : 0.042 0.197 1583 Planarity : 0.004 0.048 1773 Dihedral : 5.801 115.876 1399 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.76 % Allowed : 16.50 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.24), residues: 1256 helix: 1.68 (0.18), residues: 806 sheet: -1.54 (0.58), residues: 78 loop : -1.64 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP Y 165 HIS 0.003 0.001 HIS A 93 PHE 0.032 0.001 PHE A 703 TYR 0.012 0.001 TYR Y 233 ARG 0.006 0.000 ARG A 242 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 610) hydrogen bonds : angle 4.14906 ( 1806) covalent geometry : bond 0.00328 (10274) covalent geometry : angle 0.59548 (13873) Misc. bond : bond 0.00059 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5482.10 seconds wall clock time: 94 minutes 28.58 seconds (5668.58 seconds total)