Starting phenix.real_space_refine on Wed Sep 17 17:49:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xha_33192/09_2025/7xha_33192.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xha_33192/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7xha_33192/09_2025/7xha_33192.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xha_33192/09_2025/7xha_33192.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xha_33192/09_2025/7xha_33192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xha_33192/09_2025/7xha_33192.map" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.63, per 1000 atoms: 0.26 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: 0.88 Conformation dependent library (CDL) restraints added in 433.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.36 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: 1.69 Time building geometry restraints manager: 1.23 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: 3.330 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.610 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.780 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG A 593 TYR 0.034 0.003 TYR B 53 PHE 0.043 0.003 PHE A 48 TRP 0.015 0.003 TRP Y 299 HIS 0.008 0.002 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00815 (10274) covalent geometry : angle 1.06280 (13873) hydrogen bonds : bond 0.09928 ( 610) hydrogen bonds : angle 6.01405 ( 1806) 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 : 0.395 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: 0.1203 time to fit residues: 40.9959 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 : 0.387 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.0970 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 65 optimal weight: 0.0670 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 157 ASN A 198 GLN ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 GLN A 430 GLN A 457 GLN A 529 GLN A 622 ASN A 733 GLN ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 7 ASN Y 169 GLN ** Y 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 308 HIS Y 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 = 0.4267 r_free = 0.4267 target = 0.195590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.155715 restraints weight = 12825.193| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.54 r_work: 0.3619 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10276 Z= 0.132 Angle : 0.603 11.815 13873 Z= 0.311 Chirality : 0.042 0.220 1583 Planarity : 0.005 0.052 1773 Dihedral : 7.073 132.705 1404 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.67 % Allowed : 10.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.22), residues: 1256 helix: 0.05 (0.17), residues: 793 sheet: -1.57 (0.53), residues: 91 loop : -2.43 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 466 TYR 0.011 0.001 TYR Y 245 PHE 0.024 0.001 PHE A 703 TRP 0.011 0.001 TRP Y 98 HIS 0.005 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00282 (10274) covalent geometry : angle 0.60311 (13873) hydrogen bonds : bond 0.04220 ( 610) hydrogen bonds : angle 4.63208 ( 1806) Misc. bond : bond 0.00086 ( 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 209 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 HIS cc_start: 0.8563 (t70) cc_final: 0.8325 (t-90) REVERT: A 106 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8338 (mtmm) REVERT: A 189 MET cc_start: 0.8287 (mtp) cc_final: 0.7977 (mtp) REVERT: A 273 PHE cc_start: 0.7972 (m-10) cc_final: 0.7655 (m-80) REVERT: A 331 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7792 (mm-30) REVERT: A 350 MET cc_start: 0.8828 (pmm) cc_final: 0.8535 (ptp) REVERT: A 469 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7637 (tt0) REVERT: A 560 ARG cc_start: 0.7785 (ptt90) cc_final: 0.7574 (ptt90) REVERT: A 707 GLN cc_start: 0.8130 (mm110) cc_final: 0.7894 (mt0) REVERT: A 762 HIS cc_start: 0.7708 (m-70) cc_final: 0.7470 (m-70) REVERT: A 769 ASP cc_start: 0.8290 (m-30) cc_final: 0.7875 (m-30) REVERT: E 44 PHE cc_start: 0.8888 (m-80) cc_final: 0.8546 (m-80) outliers start: 18 outliers final: 10 residues processed: 200 average time/residue: 0.1105 time to fit residues: 30.5320 Evaluate side-chains 181 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 23 LEU Chi-restraints excluded: chain Y residue 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 62 optimal weight: 0.7980 chunk 120 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN A 198 GLN ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 7 ASN Y 253 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.191540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.152054 restraints weight = 12928.340| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.17 r_work: 0.3581 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10276 Z= 0.164 Angle : 0.593 9.447 13873 Z= 0.309 Chirality : 0.043 0.209 1583 Planarity : 0.004 0.047 1773 Dihedral : 6.397 113.368 1402 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.69 % Allowed : 10.84 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.24), residues: 1256 helix: 0.75 (0.18), residues: 804 sheet: -1.84 (0.50), residues: 100 loop : -2.22 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 425 TYR 0.016 0.002 TYR Y 245 PHE 0.024 0.002 PHE A 703 TRP 0.009 0.001 TRP Y 98 HIS 0.005 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00381 (10274) covalent geometry : angle 0.59304 (13873) hydrogen bonds : bond 0.04348 ( 610) hydrogen bonds : angle 4.47698 ( 1806) Misc. bond : bond 0.00083 ( 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 202 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8436 (mtmm) REVERT: A 139 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6749 (mt-10) REVERT: A 189 MET cc_start: 0.8525 (mtp) cc_final: 0.8093 (mtp) REVERT: A 273 PHE cc_start: 0.7931 (m-10) cc_final: 0.7525 (m-10) REVERT: A 300 MET cc_start: 0.7362 (ptp) cc_final: 0.7155 (ptp) REVERT: A 331 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8062 (mm-30) REVERT: A 373 THR cc_start: 0.9050 (p) cc_final: 0.8738 (p) REVERT: A 469 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7772 (tt0) REVERT: A 657 LEU cc_start: 0.7956 (tp) cc_final: 0.7706 (tt) REVERT: A 707 GLN cc_start: 0.8342 (mm110) cc_final: 0.7982 (mt0) REVERT: A 731 MET cc_start: 0.8789 (tpt) cc_final: 0.8321 (tpt) REVERT: A 762 HIS cc_start: 0.7918 (m-70) cc_final: 0.7629 (m-70) REVERT: Y 10 ARG cc_start: 0.7608 (mmt180) cc_final: 0.6463 (tpp80) REVERT: Y 429 ILE cc_start: 0.7601 (OUTLIER) cc_final: 0.7159 (pp) outliers start: 29 outliers final: 12 residues processed: 189 average time/residue: 0.1137 time to fit residues: 29.7718 Evaluate side-chains 174 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 469 GLN 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 401 SER 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 48 optimal weight: 0.0040 chunk 54 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 chunk 37 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.187015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.146217 restraints weight = 12965.984| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.40 r_work: 0.3547 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2693 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= 0.131 Angle : 0.569 11.160 13873 Z= 0.292 Chirality : 0.042 0.200 1583 Planarity : 0.004 0.046 1773 Dihedral : 6.223 113.860 1402 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.04 % Allowed : 12.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.24), residues: 1256 helix: 1.15 (0.18), residues: 803 sheet: -1.75 (0.50), residues: 100 loop : -2.01 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.011 0.001 TYR Y 245 PHE 0.036 0.001 PHE A 703 TRP 0.010 0.001 TRP Y 165 HIS 0.004 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00292 (10274) covalent geometry : angle 0.56853 (13873) hydrogen bonds : bond 0.03933 ( 610) hydrogen bonds : angle 4.33009 ( 1806) Misc. bond : bond 0.00052 ( 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 195 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8719 (m-30) cc_final: 0.8492 (p0) REVERT: A 106 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8315 (mtmm) REVERT: A 141 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7945 (mmm) REVERT: A 189 MET cc_start: 0.8350 (mtp) cc_final: 0.7998 (mtp) REVERT: A 273 PHE cc_start: 0.7728 (m-10) cc_final: 0.7492 (m-10) REVERT: A 300 MET cc_start: 0.7223 (ptp) cc_final: 0.6994 (ptp) REVERT: A 331 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7741 (mm-30) REVERT: A 373 THR cc_start: 0.8997 (p) cc_final: 0.8659 (p) REVERT: A 469 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7564 (tt0) REVERT: A 500 LYS cc_start: 0.8293 (ptpp) cc_final: 0.8011 (mtmm) REVERT: A 555 MET cc_start: 0.8095 (mmt) cc_final: 0.7865 (mmt) REVERT: A 707 GLN cc_start: 0.8235 (mm110) cc_final: 0.7912 (mt0) REVERT: A 762 HIS cc_start: 0.7604 (m-70) cc_final: 0.7272 (m-70) REVERT: Y 10 ARG cc_start: 0.7664 (mmt180) cc_final: 0.6513 (tpp80) outliers start: 22 outliers final: 16 residues processed: 182 average time/residue: 0.1120 time to fit residues: 28.2187 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 : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 141 MET 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 469 GLN 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 219 LEU Chi-restraints excluded: chain Y residue 401 SER Chi-restraints excluded: chain Y residue 421 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 76 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN A 469 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.182538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.141782 restraints weight = 12941.758| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.45 r_work: 0.3487 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10276 Z= 0.168 Angle : 0.594 10.711 13873 Z= 0.305 Chirality : 0.043 0.200 1583 Planarity : 0.004 0.046 1773 Dihedral : 6.214 114.065 1402 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.41 % Allowed : 13.90 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.24), residues: 1256 helix: 1.23 (0.18), residues: 805 sheet: -1.77 (0.50), residues: 100 loop : -1.94 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 425 TYR 0.014 0.002 TYR Y 245 PHE 0.032 0.002 PHE A 703 TRP 0.010 0.001 TRP Y 165 HIS 0.004 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00394 (10274) covalent geometry : angle 0.59391 (13873) hydrogen bonds : bond 0.04223 ( 610) hydrogen bonds : angle 4.33685 ( 1806) Misc. bond : bond 0.00088 ( 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 185 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8725 (m-30) cc_final: 0.8515 (p0) REVERT: A 106 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8290 (mtmm) REVERT: A 189 MET cc_start: 0.8437 (mtp) cc_final: 0.8072 (mtp) REVERT: A 273 PHE cc_start: 0.7895 (m-10) cc_final: 0.7661 (m-10) REVERT: A 300 MET cc_start: 0.7266 (ptp) cc_final: 0.7009 (ptp) REVERT: A 331 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7784 (mm-30) REVERT: A 373 THR cc_start: 0.9007 (p) cc_final: 0.8686 (p) REVERT: A 500 LYS cc_start: 0.8300 (ptpp) cc_final: 0.8030 (mtmm) REVERT: A 707 GLN cc_start: 0.8301 (mm110) cc_final: 0.7966 (mt0) REVERT: A 762 HIS cc_start: 0.7673 (m-70) cc_final: 0.7367 (m-70) REVERT: Y 10 ARG cc_start: 0.7632 (mmt180) cc_final: 0.6497 (tpp80) REVERT: Y 254 PRO cc_start: 0.8161 (Cg_endo) cc_final: 0.7758 (Cg_exo) REVERT: Y 429 ILE cc_start: 0.7524 (OUTLIER) cc_final: 0.7102 (pp) outliers start: 26 outliers final: 18 residues processed: 174 average time/residue: 0.1130 time to fit residues: 27.1284 Evaluate side-chains 175 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 151 LEU Chi-restraints excluded: chain Y residue 163 LEU Chi-restraints excluded: chain Y residue 401 SER Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain Y residue 429 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 69 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 65 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 460 ASN ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 7 ASN ** Y 101 GLN ** 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 = 0.4139 r_free = 0.4139 target = 0.182604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.141411 restraints weight = 13003.318| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.34 r_work: 0.3487 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10276 Z= 0.164 Angle : 0.592 10.450 13873 Z= 0.305 Chirality : 0.043 0.217 1583 Planarity : 0.004 0.047 1773 Dihedral : 5.941 113.062 1399 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.04 % Allowed : 14.83 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.24), residues: 1256 helix: 1.29 (0.18), residues: 804 sheet: -1.78 (0.53), residues: 88 loop : -1.83 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 75 TYR 0.012 0.001 TYR Y 245 PHE 0.033 0.001 PHE A 703 TRP 0.012 0.001 TRP Y 165 HIS 0.003 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00383 (10274) covalent geometry : angle 0.59215 (13873) hydrogen bonds : bond 0.04178 ( 610) hydrogen bonds : angle 4.31341 ( 1806) Misc. bond : bond 0.00085 ( 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 185 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 MET cc_start: 0.8428 (mtp) cc_final: 0.8154 (mtp) REVERT: A 273 PHE cc_start: 0.7951 (m-10) cc_final: 0.7742 (m-10) REVERT: A 300 MET cc_start: 0.7247 (ptp) cc_final: 0.6969 (ptp) REVERT: A 331 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7764 (mm-30) REVERT: A 373 THR cc_start: 0.9008 (p) cc_final: 0.8683 (p) REVERT: A 500 LYS cc_start: 0.8293 (ptpp) cc_final: 0.8037 (mtmm) REVERT: A 707 GLN cc_start: 0.8312 (mm110) cc_final: 0.7982 (mt0) REVERT: A 754 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7846 (mmm) REVERT: A 762 HIS cc_start: 0.7638 (m-70) cc_final: 0.7350 (m-70) REVERT: Y 10 ARG cc_start: 0.7765 (mmt180) cc_final: 0.6559 (tpp80) REVERT: Y 254 PRO cc_start: 0.8164 (Cg_endo) cc_final: 0.7769 (Cg_exo) REVERT: Y 429 ILE cc_start: 0.7650 (OUTLIER) cc_final: 0.7269 (pp) outliers start: 22 outliers final: 17 residues processed: 176 average time/residue: 0.1078 time to fit residues: 26.6296 Evaluate side-chains 170 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 151 LEU Chi-restraints excluded: chain Y residue 163 LEU Chi-restraints excluded: chain Y residue 401 SER Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain Y residue 429 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 101 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 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 = 0.4133 r_free = 0.4133 target = 0.181825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.142084 restraints weight = 12798.241| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.27 r_work: 0.3486 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10276 Z= 0.167 Angle : 0.605 10.202 13873 Z= 0.310 Chirality : 0.043 0.214 1583 Planarity : 0.004 0.046 1773 Dihedral : 5.966 113.292 1399 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.41 % Allowed : 15.76 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.24), residues: 1256 helix: 1.33 (0.18), residues: 805 sheet: -1.76 (0.53), residues: 88 loop : -1.78 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 75 TYR 0.012 0.002 TYR Y 233 PHE 0.024 0.001 PHE A 703 TRP 0.014 0.001 TRP Y 165 HIS 0.004 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00392 (10274) covalent geometry : angle 0.60545 (13873) hydrogen bonds : bond 0.04201 ( 610) hydrogen bonds : angle 4.29626 ( 1806) Misc. bond : bond 0.00088 ( 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 180 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8309 (mtmm) REVERT: A 189 MET cc_start: 0.8419 (mtp) cc_final: 0.8146 (mtp) REVERT: A 300 MET cc_start: 0.7224 (ptp) cc_final: 0.6923 (ptp) REVERT: A 373 THR cc_start: 0.9023 (p) cc_final: 0.8745 (p) REVERT: A 500 LYS cc_start: 0.8288 (ptpp) cc_final: 0.8035 (mtmm) REVERT: A 624 ARG cc_start: 0.8022 (ttm170) cc_final: 0.7682 (ttt-90) REVERT: A 707 GLN cc_start: 0.8312 (mm110) cc_final: 0.8048 (mt0) REVERT: A 754 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7813 (mmm) REVERT: A 762 HIS cc_start: 0.7653 (m-70) cc_final: 0.7390 (m-70) REVERT: Y 10 ARG cc_start: 0.7733 (mmt180) cc_final: 0.6540 (tpp80) REVERT: Y 254 PRO cc_start: 0.8158 (Cg_endo) cc_final: 0.7755 (Cg_exo) REVERT: Y 429 ILE cc_start: 0.7663 (OUTLIER) cc_final: 0.7269 (pp) outliers start: 26 outliers final: 18 residues processed: 168 average time/residue: 0.1151 time to fit residues: 27.0163 Evaluate side-chains 170 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 133 ASN Chi-restraints excluded: chain Y residue 151 LEU Chi-restraints excluded: chain Y residue 163 LEU Chi-restraints excluded: chain Y residue 401 SER Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain Y residue 429 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 28 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 80 optimal weight: 8.9990 chunk 5 optimal weight: 0.6980 chunk 110 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 GLN Y 7 ASN ** Y 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 133 ASN Y 424 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.179666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.140751 restraints weight = 12591.567| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.14 r_work: 0.3533 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10276 Z= 0.156 Angle : 0.603 10.089 13873 Z= 0.308 Chirality : 0.042 0.212 1583 Planarity : 0.004 0.047 1773 Dihedral : 5.929 113.252 1399 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.41 % Allowed : 16.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.24), residues: 1256 helix: 1.40 (0.18), residues: 805 sheet: -1.74 (0.53), residues: 88 loop : -1.74 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 75 TYR 0.012 0.001 TYR Y 233 PHE 0.024 0.001 PHE A 703 TRP 0.017 0.002 TRP Y 165 HIS 0.003 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00362 (10274) covalent geometry : angle 0.60273 (13873) hydrogen bonds : bond 0.04113 ( 610) hydrogen bonds : angle 4.27390 ( 1806) Misc. bond : bond 0.00080 ( 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 181 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8944 (m-30) cc_final: 0.8626 (p0) REVERT: A 106 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8310 (mtmm) REVERT: A 189 MET cc_start: 0.8436 (mtp) cc_final: 0.8186 (mtp) REVERT: A 300 MET cc_start: 0.7402 (ptp) cc_final: 0.7090 (ptp) REVERT: A 373 THR cc_start: 0.9050 (p) cc_final: 0.8778 (p) REVERT: A 500 LYS cc_start: 0.8381 (ptpp) cc_final: 0.8153 (mtmm) REVERT: A 707 GLN cc_start: 0.8432 (mm110) cc_final: 0.8130 (mt0) REVERT: A 754 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8032 (mmm) REVERT: A 762 HIS cc_start: 0.7816 (m-70) cc_final: 0.7531 (m-70) REVERT: A 770 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8404 (tm-30) REVERT: Y 10 ARG cc_start: 0.7777 (mmt180) cc_final: 0.6556 (tpp80) REVERT: Y 254 PRO cc_start: 0.8159 (Cg_endo) cc_final: 0.7787 (Cg_exo) REVERT: Y 429 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7416 (pp) outliers start: 26 outliers final: 17 residues processed: 168 average time/residue: 0.1119 time to fit residues: 26.3293 Evaluate side-chains 171 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 151 LEU Chi-restraints excluded: chain Y residue 323 THR Chi-restraints excluded: chain Y residue 401 SER Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain Y residue 429 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.182513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.141960 restraints weight = 12840.838| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.33 r_work: 0.3493 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10276 Z= 0.154 Angle : 0.599 9.928 13873 Z= 0.307 Chirality : 0.042 0.210 1583 Planarity : 0.003 0.047 1773 Dihedral : 5.913 113.375 1399 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.22 % Allowed : 16.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.24), residues: 1256 helix: 1.44 (0.18), residues: 806 sheet: -1.62 (0.56), residues: 81 loop : -1.75 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 75 TYR 0.012 0.001 TYR Y 245 PHE 0.026 0.001 PHE A 703 TRP 0.020 0.002 TRP Y 165 HIS 0.003 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00358 (10274) covalent geometry : angle 0.59932 (13873) hydrogen bonds : bond 0.04064 ( 610) hydrogen bonds : angle 4.24874 ( 1806) Misc. bond : bond 0.00075 ( 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: 24 poor density : 155 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8942 (m-30) cc_final: 0.8594 (p0) REVERT: A 106 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8314 (mtmm) REVERT: A 189 MET cc_start: 0.8443 (mtp) cc_final: 0.8194 (mtp) REVERT: A 300 MET cc_start: 0.7444 (ptp) cc_final: 0.7121 (ptp) REVERT: A 373 THR cc_start: 0.9026 (p) cc_final: 0.8760 (p) REVERT: A 500 LYS cc_start: 0.8402 (ptpp) cc_final: 0.8185 (mtmm) REVERT: A 600 ASP cc_start: 0.7605 (t70) cc_final: 0.7351 (t70) REVERT: A 624 ARG cc_start: 0.8195 (ttm170) cc_final: 0.7824 (ttt-90) REVERT: A 707 GLN cc_start: 0.8368 (mm110) cc_final: 0.8071 (mt0) REVERT: A 754 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8081 (mmm) REVERT: A 762 HIS cc_start: 0.7888 (m-70) cc_final: 0.7590 (m-70) REVERT: Y 10 ARG cc_start: 0.7778 (mmt180) cc_final: 0.6540 (tpp80) REVERT: Y 254 PRO cc_start: 0.8159 (Cg_endo) cc_final: 0.7791 (Cg_exo) REVERT: Y 429 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7368 (pp) outliers start: 24 outliers final: 17 residues processed: 168 average time/residue: 0.1104 time to fit residues: 25.9508 Evaluate side-chains 172 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 151 LEU Chi-restraints excluded: chain Y residue 323 THR Chi-restraints excluded: chain Y residue 401 SER Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain Y residue 429 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 82 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 662 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.181446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.141835 restraints weight = 12693.811| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.22 r_work: 0.3481 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10276 Z= 0.171 Angle : 0.623 9.885 13873 Z= 0.318 Chirality : 0.043 0.219 1583 Planarity : 0.004 0.047 1773 Dihedral : 5.965 113.411 1399 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.50 % Allowed : 16.13 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.24), residues: 1256 helix: 1.40 (0.18), residues: 807 sheet: -1.65 (0.56), residues: 81 loop : -1.80 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 75 TYR 0.015 0.001 TYR Y 245 PHE 0.027 0.001 PHE A 703 TRP 0.027 0.002 TRP Y 165 HIS 0.003 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00404 (10274) covalent geometry : angle 0.62265 (13873) hydrogen bonds : bond 0.04217 ( 610) hydrogen bonds : angle 4.27977 ( 1806) Misc. bond : bond 0.00087 ( 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 176 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.400 Fit side-chains REVERT: A 39 ASP cc_start: 0.8887 (m-30) cc_final: 0.8565 (p0) REVERT: A 106 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8334 (mtmm) REVERT: A 189 MET cc_start: 0.8470 (mtp) cc_final: 0.8206 (mtp) REVERT: A 300 MET cc_start: 0.7450 (ptp) cc_final: 0.7149 (ptp) REVERT: A 373 THR cc_start: 0.9066 (p) cc_final: 0.8769 (p) REVERT: A 500 LYS cc_start: 0.8429 (ptpp) cc_final: 0.8158 (mtmm) REVERT: A 600 ASP cc_start: 0.7608 (t70) cc_final: 0.7357 (t70) REVERT: A 624 ARG cc_start: 0.8194 (ttm170) cc_final: 0.7892 (ttt-90) REVERT: A 707 GLN cc_start: 0.8391 (mm110) cc_final: 0.8090 (mt0) REVERT: A 762 HIS cc_start: 0.7904 (m-70) cc_final: 0.7619 (m-70) REVERT: A 770 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8427 (tm-30) REVERT: Y 10 ARG cc_start: 0.7781 (mmt180) cc_final: 0.6526 (tpp80) REVERT: Y 254 PRO cc_start: 0.8151 (Cg_endo) cc_final: 0.7791 (Cg_exo) REVERT: Y 429 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7323 (pp) REVERT: E 13 ARG cc_start: 0.8490 (ttm110) cc_final: 0.8211 (ttp-110) outliers start: 27 outliers final: 22 residues processed: 165 average time/residue: 0.1006 time to fit residues: 23.1578 Evaluate side-chains 172 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 255 LYS 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 598 GLN 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 163 LEU Chi-restraints excluded: chain Y residue 323 THR Chi-restraints excluded: chain Y residue 401 SER Chi-restraints excluded: chain Y residue 421 VAL Chi-restraints excluded: chain Y residue 429 ILE Chi-restraints excluded: chain E residue 19 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 46 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 99 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 122 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 61 optimal weight: 0.0170 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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 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 = 0.4140 r_free = 0.4140 target = 0.180847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.142232 restraints weight = 12582.339| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.13 r_work: 0.3552 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10276 Z= 0.139 Angle : 0.600 9.901 13873 Z= 0.305 Chirality : 0.042 0.202 1583 Planarity : 0.003 0.046 1773 Dihedral : 5.886 113.790 1399 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.13 % Allowed : 16.68 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.24), residues: 1256 helix: 1.54 (0.18), residues: 807 sheet: -1.53 (0.57), residues: 81 loop : -1.75 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 75 TYR 0.011 0.001 TYR Y 233 PHE 0.027 0.001 PHE A 703 TRP 0.027 0.002 TRP Y 165 HIS 0.003 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00320 (10274) covalent geometry : angle 0.59955 (13873) hydrogen bonds : bond 0.03890 ( 610) hydrogen bonds : angle 4.20410 ( 1806) Misc. bond : bond 0.00060 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2770.01 seconds wall clock time: 48 minutes 8.26 seconds (2888.26 seconds total)