Starting phenix.real_space_refine on Fri Aug 22 23:33:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u56_41913/08_2025/8u56_41913.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u56_41913/08_2025/8u56_41913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u56_41913/08_2025/8u56_41913.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u56_41913/08_2025/8u56_41913.map" model { file = "/net/cci-nas-00/data/ceres_data/8u56_41913/08_2025/8u56_41913.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u56_41913/08_2025/8u56_41913.cif" } resolution = 2.75 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= -0.003 sd= 0.036 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5814 2.51 5 N 1300 2.21 5 O 1418 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8588 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4253 Classifications: {'peptide': 541} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 521} Chain breaks: 5 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'LMN': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'Y01:plan-1': 1} Unresolved non-hydrogen planarities: 4 Restraints were copied for chains: B Time building chain proxies: 2.40, per 1000 atoms: 0.28 Number of scatterers: 8588 At special positions: 0 Unit cell: (101.215, 124.276, 75.5908, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1418 8.00 N 1300 7.00 C 5814 6.00 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=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 346.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2028 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 91.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 41 through 62 Processing helix chain 'A' and resid 66 through 80 removed outlier: 3.631A pdb=" N LYS A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 93 Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 99 through 125 Processing helix chain 'A' and resid 129 through 143 Proline residue: A 138 - end of helix Processing helix chain 'A' and resid 149 through 159 Processing helix chain 'A' and resid 164 through 194 removed outlier: 3.901A pdb=" N TYR A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE A 169 " --> pdb=" O TYR A 165 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Proline residue: A 174 - end of helix Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 204 through 216 Processing helix chain 'A' and resid 217 through 234 Processing helix chain 'A' and resid 238 through 265 removed outlier: 3.672A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLY A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 288 Processing helix chain 'A' and resid 288 through 302 Processing helix chain 'A' and resid 306 through 323 Processing helix chain 'A' and resid 326 through 336 removed outlier: 4.120A pdb=" N ALA A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 367 removed outlier: 3.617A pdb=" N ALA A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 368 through 370 No H-bonds generated for 'chain 'A' and resid 368 through 370' Processing helix chain 'A' and resid 371 through 404 Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 411 through 436 removed outlier: 3.576A pdb=" N PHE A 434 " --> pdb=" O MET A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 473 Processing helix chain 'A' and resid 482 through 501 removed outlier: 3.994A pdb=" N ILE A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) Proline residue: A 492 - end of helix removed outlier: 3.729A pdb=" N VAL A 496 " --> pdb=" O PRO A 492 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 543 Processing helix chain 'A' and resid 655 through 682 Processing helix chain 'A' and resid 689 through 712 removed outlier: 5.869A pdb=" N GLY A 704 " --> pdb=" O ASN A 700 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N PHE A 705 " --> pdb=" O PHE A 701 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 706 " --> pdb=" O GLY A 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 40 No H-bonds generated for 'chain 'B' and resid 38 through 40' Processing helix chain 'B' and resid 41 through 62 Processing helix chain 'B' and resid 66 through 80 removed outlier: 3.629A pdb=" N LYS B 71 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU B 73 " --> pdb=" O GLN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 93 Processing helix chain 'B' and resid 94 through 98 Processing helix chain 'B' and resid 99 through 125 Processing helix chain 'B' and resid 129 through 143 Proline residue: B 138 - end of helix Processing helix chain 'B' and resid 149 through 159 Processing helix chain 'B' and resid 164 through 194 removed outlier: 3.900A pdb=" N TYR B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE B 169 " --> pdb=" O TYR B 165 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Proline residue: B 174 - end of helix Proline residue: B 182 - end of helix Processing helix chain 'B' and resid 204 through 216 Processing helix chain 'B' and resid 217 through 234 Processing helix chain 'B' and resid 238 through 265 removed outlier: 3.670A pdb=" N PHE B 244 " --> pdb=" O TYR B 240 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLY B 254 " --> pdb=" O ASN B 250 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 288 Processing helix chain 'B' and resid 288 through 302 Processing helix chain 'B' and resid 306 through 323 Processing helix chain 'B' and resid 326 through 336 removed outlier: 4.120A pdb=" N ALA B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 367 removed outlier: 3.617A pdb=" N ALA B 355 " --> pdb=" O THR B 351 " (cutoff:3.500A) Proline residue: B 356 - end of helix Processing helix chain 'B' and resid 368 through 370 No H-bonds generated for 'chain 'B' and resid 368 through 370' Processing helix chain 'B' and resid 371 through 404 Processing helix chain 'B' and resid 405 through 409 Processing helix chain 'B' and resid 411 through 436 removed outlier: 3.577A pdb=" N PHE B 434 " --> pdb=" O MET B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 473 Processing helix chain 'B' and resid 482 through 501 removed outlier: 3.992A pdb=" N ILE B 491 " --> pdb=" O SER B 487 " (cutoff:3.500A) Proline residue: B 492 - end of helix removed outlier: 3.728A pdb=" N VAL B 496 " --> pdb=" O PRO B 492 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 543 Processing helix chain 'B' and resid 655 through 682 Processing helix chain 'B' and resid 689 through 712 removed outlier: 5.870A pdb=" N GLY B 704 " --> pdb=" O ASN B 700 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N PHE B 705 " --> pdb=" O PHE B 701 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 706 " --> pdb=" O GLY B 702 " (cutoff:3.500A) 722 hydrogen bonds defined for protein. 2142 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: 1.54 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1250 1.32 - 1.44: 2387 1.44 - 1.57: 5067 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 8794 Sorted by residual: bond pdb=" CD1 TYR A 320 " pdb=" CE1 TYR A 320 " ideal model delta sigma weight residual 1.382 1.337 0.045 3.00e-02 1.11e+03 2.25e+00 bond pdb=" CD1 TYR B 320 " pdb=" CE1 TYR B 320 " ideal model delta sigma weight residual 1.382 1.338 0.044 3.00e-02 1.11e+03 2.11e+00 bond pdb=" CB TYR A 320 " pdb=" CG TYR A 320 " ideal model delta sigma weight residual 1.512 1.481 0.031 2.20e-02 2.07e+03 2.02e+00 bond pdb=" C LEU B 665 " pdb=" O LEU B 665 " ideal model delta sigma weight residual 1.237 1.220 0.017 1.19e-02 7.06e+03 2.01e+00 bond pdb=" C SER B 251 " pdb=" O SER B 251 " ideal model delta sigma weight residual 1.236 1.253 -0.018 1.29e-02 6.01e+03 1.92e+00 ... (remaining 8789 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 11371 2.02 - 4.04: 484 4.04 - 6.05: 75 6.05 - 8.07: 8 8.07 - 10.09: 4 Bond angle restraints: 11942 Sorted by residual: angle pdb=" C GLU A 242 " pdb=" N ASN A 243 " pdb=" CA ASN A 243 " ideal model delta sigma weight residual 121.58 111.49 10.09 1.95e+00 2.63e-01 2.68e+01 angle pdb=" C GLU B 242 " pdb=" N ASN B 243 " pdb=" CA ASN B 243 " ideal model delta sigma weight residual 121.58 111.49 10.09 1.95e+00 2.63e-01 2.68e+01 angle pdb=" C VAL A 698 " pdb=" N PHE A 699 " pdb=" CA PHE A 699 " ideal model delta sigma weight residual 120.44 115.63 4.81 1.36e+00 5.41e-01 1.25e+01 angle pdb=" CA PHE A 221 " pdb=" CB PHE A 221 " pdb=" CG PHE A 221 " ideal model delta sigma weight residual 113.80 117.32 -3.52 1.00e+00 1.00e+00 1.24e+01 angle pdb=" CA PHE B 221 " pdb=" CB PHE B 221 " pdb=" CG PHE B 221 " ideal model delta sigma weight residual 113.80 117.32 -3.52 1.00e+00 1.00e+00 1.24e+01 ... (remaining 11937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.86: 5020 23.86 - 47.73: 156 47.73 - 71.59: 30 71.59 - 95.45: 2 95.45 - 119.31: 6 Dihedral angle restraints: 5214 sinusoidal: 2076 harmonic: 3138 Sorted by residual: dihedral pdb=" CA GLN A 143 " pdb=" C GLN A 143 " pdb=" N SER A 144 " pdb=" CA SER A 144 " ideal model delta harmonic sigma weight residual -180.00 -153.38 -26.62 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA GLN B 143 " pdb=" C GLN B 143 " pdb=" N SER B 144 " pdb=" CA SER B 144 " ideal model delta harmonic sigma weight residual -180.00 -153.60 -26.40 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA TYR B 516 " pdb=" C TYR B 516 " pdb=" N GLY B 517 " pdb=" CA GLY B 517 " ideal model delta harmonic sigma weight residual 180.00 156.84 23.16 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 5211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1048 0.052 - 0.103: 314 0.103 - 0.155: 74 0.155 - 0.206: 4 0.206 - 0.258: 8 Chirality restraints: 1448 Sorted by residual: chirality pdb=" CA ASN B 243 " pdb=" N ASN B 243 " pdb=" C ASN B 243 " pdb=" CB ASN B 243 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA ASN A 243 " pdb=" N ASN A 243 " pdb=" C ASN A 243 " pdb=" CB ASN A 243 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB VAL B 425 " pdb=" CA VAL B 425 " pdb=" CG1 VAL B 425 " pdb=" CG2 VAL B 425 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1445 not shown) Planarity restraints: 1406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 320 " 0.056 2.00e-02 2.50e+03 2.89e-02 1.67e+01 pdb=" CG TYR B 320 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR B 320 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR B 320 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR B 320 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 320 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 320 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR B 320 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 320 " 0.056 2.00e-02 2.50e+03 2.85e-02 1.63e+01 pdb=" CG TYR A 320 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR A 320 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR A 320 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR A 320 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 320 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 320 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 320 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 221 " 0.029 2.00e-02 2.50e+03 2.24e-02 8.75e+00 pdb=" CG PHE B 221 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE B 221 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 221 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 221 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 221 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 221 " 0.005 2.00e-02 2.50e+03 ... (remaining 1403 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 3367 2.90 - 3.40: 9559 3.40 - 3.90: 15526 3.90 - 4.40: 17942 4.40 - 4.90: 29501 Nonbonded interactions: 75895 Sorted by model distance: nonbonded pdb=" CG1 VAL B 348 " pdb=" CBQ LMN B 901 " model vdw 2.398 3.860 nonbonded pdb=" CG1 VAL A 348 " pdb=" CBQ LMN A 901 " model vdw 2.399 3.860 nonbonded pdb=" CE MET A 264 " pdb=" CBL LMN A 901 " model vdw 2.448 3.860 nonbonded pdb=" CE MET B 264 " pdb=" CBL LMN B 901 " model vdw 2.449 3.860 nonbonded pdb=" O GLN B 520 " pdb=" OG1 THR B 524 " model vdw 2.476 3.040 ... (remaining 75890 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.510 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.070 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 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 : 0.007 0.049 8794 Z= 0.330 Angle : 0.963 10.090 11942 Z= 0.546 Chirality : 0.053 0.258 1448 Planarity : 0.008 0.072 1406 Dihedral : 13.549 119.315 3186 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.73 (0.24), residues: 1058 helix: -0.39 (0.15), residues: 894 sheet: None (None), residues: 0 loop : 0.01 (0.54), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 295 TYR 0.056 0.005 TYR B 320 PHE 0.050 0.005 PHE A 221 TRP 0.025 0.005 TRP B 100 HIS 0.007 0.003 HIS B 310 Details of bonding type rmsd covalent geometry : bond 0.00707 ( 8794) covalent geometry : angle 0.96323 (11942) hydrogen bonds : bond 0.10975 ( 722) hydrogen bonds : angle 6.41557 ( 2142) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TYR cc_start: 0.7773 (m-10) cc_final: 0.7428 (m-10) REVERT: A 246 ASP cc_start: 0.7917 (m-30) cc_final: 0.7551 (m-30) REVERT: A 347 MET cc_start: 0.8862 (tmm) cc_final: 0.8661 (tmm) REVERT: B 104 TYR cc_start: 0.7701 (m-10) cc_final: 0.7489 (m-10) REVERT: B 136 LEU cc_start: 0.8481 (mt) cc_final: 0.8112 (mt) REVERT: B 246 ASP cc_start: 0.7902 (m-30) cc_final: 0.7597 (m-30) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.4079 time to fit residues: 136.9246 Evaluate side-chains 167 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 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 310 HIS A 409 GLN A 672 ASN A 716 HIS B 310 HIS B 409 GLN B 716 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.136686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.110368 restraints weight = 16134.572| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.47 r_work: 0.3513 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8794 Z= 0.207 Angle : 0.755 7.917 11942 Z= 0.385 Chirality : 0.044 0.166 1448 Planarity : 0.005 0.040 1406 Dihedral : 6.934 78.000 1280 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 4.03 % Allowed : 14.33 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.64 (0.26), residues: 1058 helix: 1.19 (0.17), residues: 884 sheet: None (None), residues: 0 loop : 1.04 (0.57), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 213 TYR 0.013 0.002 TYR A 168 PHE 0.032 0.002 PHE B 221 TRP 0.011 0.002 TRP B 489 HIS 0.002 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 8794) covalent geometry : angle 0.75459 (11942) hydrogen bonds : bond 0.05818 ( 722) hydrogen bonds : angle 5.35464 ( 2142) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 209 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.8286 (ptp-170) cc_final: 0.7918 (ptp-170) REVERT: A 179 MET cc_start: 0.8482 (mtm) cc_final: 0.8078 (mtm) REVERT: A 212 LEU cc_start: 0.8898 (tm) cc_final: 0.8584 (mt) REVERT: A 213 ARG cc_start: 0.8771 (mtp85) cc_final: 0.8362 (mtp85) REVERT: A 296 GLU cc_start: 0.8821 (tp30) cc_final: 0.8347 (tp30) REVERT: A 352 PHE cc_start: 0.8393 (t80) cc_final: 0.7958 (t80) REVERT: A 396 TRP cc_start: 0.7630 (t60) cc_final: 0.7183 (t60) REVERT: A 413 MET cc_start: 0.8254 (ptm) cc_final: 0.7808 (ttp) REVERT: A 417 ASN cc_start: 0.8825 (m-40) cc_final: 0.8217 (m110) REVERT: A 469 PHE cc_start: 0.8261 (t80) cc_final: 0.7831 (t80) REVERT: B 130 ARG cc_start: 0.8129 (ptp90) cc_final: 0.7741 (ptp-170) REVERT: B 179 MET cc_start: 0.8474 (mtm) cc_final: 0.8090 (mtm) REVERT: B 296 GLU cc_start: 0.8779 (tp30) cc_final: 0.8379 (tp30) REVERT: B 352 PHE cc_start: 0.8415 (t80) cc_final: 0.7949 (t80) REVERT: B 396 TRP cc_start: 0.7714 (t60) cc_final: 0.7352 (t60) REVERT: B 413 MET cc_start: 0.8169 (ptm) cc_final: 0.7938 (ttp) REVERT: B 417 ASN cc_start: 0.8766 (m-40) cc_final: 0.8429 (m110) REVERT: B 469 PHE cc_start: 0.8224 (t80) cc_final: 0.7767 (t80) outliers start: 38 outliers final: 3 residues processed: 227 average time/residue: 0.4101 time to fit residues: 100.6155 Evaluate side-chains 170 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 167 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 288 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 0.2980 chunk 61 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 HIS ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 716 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.135730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.109356 restraints weight = 16105.323| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.49 r_work: 0.3500 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8794 Z= 0.201 Angle : 0.731 10.211 11942 Z= 0.366 Chirality : 0.044 0.238 1448 Planarity : 0.005 0.037 1406 Dihedral : 6.499 71.953 1280 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 3.61 % Allowed : 17.62 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.10 (0.26), residues: 1058 helix: 1.57 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 0.80 (0.56), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 657 TYR 0.013 0.002 TYR B 455 PHE 0.028 0.002 PHE B 384 TRP 0.011 0.002 TRP B 363 HIS 0.002 0.001 HIS B 716 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 8794) covalent geometry : angle 0.73062 (11942) hydrogen bonds : bond 0.05286 ( 722) hydrogen bonds : angle 5.17012 ( 2142) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8924 (mmm-85) cc_final: 0.7987 (mtp85) REVERT: A 130 ARG cc_start: 0.8235 (ptp-170) cc_final: 0.7906 (ptp-170) REVERT: A 211 LEU cc_start: 0.9284 (mt) cc_final: 0.9014 (mt) REVERT: A 215 LEU cc_start: 0.9324 (mt) cc_final: 0.9097 (mm) REVERT: A 413 MET cc_start: 0.8152 (ptm) cc_final: 0.7746 (ttp) REVERT: A 417 ASN cc_start: 0.8734 (m-40) cc_final: 0.8119 (m110) REVERT: A 430 MET cc_start: 0.7584 (mtp) cc_final: 0.7371 (mtp) REVERT: A 458 TYR cc_start: 0.7670 (m-10) cc_final: 0.7465 (m-80) REVERT: A 514 PHE cc_start: 0.7767 (m-80) cc_final: 0.7178 (m-80) REVERT: B 41 ARG cc_start: 0.8931 (mmm-85) cc_final: 0.8005 (mtp85) REVERT: B 130 ARG cc_start: 0.8264 (ptp90) cc_final: 0.7862 (ptp-170) REVERT: B 212 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8438 (tm) REVERT: B 296 GLU cc_start: 0.8748 (tp30) cc_final: 0.8271 (tp30) REVERT: B 297 MET cc_start: 0.8563 (mmt) cc_final: 0.8278 (mpt) REVERT: B 299 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7599 (mm-30) REVERT: B 400 ILE cc_start: 0.8885 (mm) cc_final: 0.8670 (mt) REVERT: B 413 MET cc_start: 0.8148 (ptm) cc_final: 0.7771 (ttp) REVERT: B 417 ASN cc_start: 0.8767 (m-40) cc_final: 0.8164 (m110) REVERT: B 514 PHE cc_start: 0.7713 (m-80) cc_final: 0.7132 (m-80) outliers start: 34 outliers final: 7 residues processed: 216 average time/residue: 0.4088 time to fit residues: 95.6346 Evaluate side-chains 176 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 168 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 395 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 0.0770 chunk 48 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 99 optimal weight: 0.0050 chunk 8 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 overall best weight: 0.5152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 HIS ** 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 = 0.4031 r_free = 0.4031 target = 0.136298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.110262 restraints weight = 16418.147| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.54 r_work: 0.3514 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8794 Z= 0.178 Angle : 0.713 12.979 11942 Z= 0.355 Chirality : 0.043 0.282 1448 Planarity : 0.004 0.037 1406 Dihedral : 6.471 71.526 1280 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 4.56 % Allowed : 18.05 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.47 (0.26), residues: 1058 helix: 1.82 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 0.93 (0.57), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 657 TYR 0.011 0.001 TYR B 455 PHE 0.030 0.002 PHE A 221 TRP 0.012 0.002 TRP A 363 HIS 0.002 0.001 HIS B 716 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 8794) covalent geometry : angle 0.71335 (11942) hydrogen bonds : bond 0.04997 ( 722) hydrogen bonds : angle 5.04199 ( 2142) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 182 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8611 (mmm-85) cc_final: 0.8357 (mtm-85) REVERT: A 130 ARG cc_start: 0.8233 (ptp-170) cc_final: 0.7887 (ptp-170) REVERT: A 159 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7888 (pm20) REVERT: A 215 LEU cc_start: 0.9269 (mt) cc_final: 0.9029 (mm) REVERT: A 296 GLU cc_start: 0.8796 (tp30) cc_final: 0.8365 (tp30) REVERT: A 370 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.6963 (mmm) REVERT: A 413 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7732 (ttp) REVERT: A 417 ASN cc_start: 0.8751 (m-40) cc_final: 0.8160 (m110) REVERT: A 469 PHE cc_start: 0.8213 (t80) cc_final: 0.7841 (t80) REVERT: B 41 ARG cc_start: 0.8635 (mmm-85) cc_final: 0.8386 (mtm-85) REVERT: B 130 ARG cc_start: 0.8285 (ptp90) cc_final: 0.7884 (ptp-170) REVERT: B 159 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7938 (pm20) REVERT: B 370 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.6913 (mmm) REVERT: B 409 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.6492 (mp10) REVERT: B 413 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7716 (ttp) REVERT: B 417 ASN cc_start: 0.8753 (m-40) cc_final: 0.8163 (m110) REVERT: B 469 PHE cc_start: 0.8189 (t80) cc_final: 0.7820 (t80) REVERT: B 691 GLU cc_start: 0.8729 (mp0) cc_final: 0.8523 (mp0) outliers start: 43 outliers final: 8 residues processed: 205 average time/residue: 0.4282 time to fit residues: 95.1769 Evaluate side-chains 183 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 413 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 22 optimal weight: 0.0770 chunk 35 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.136217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.109927 restraints weight = 16387.845| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.58 r_work: 0.3510 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8794 Z= 0.187 Angle : 0.716 8.294 11942 Z= 0.358 Chirality : 0.044 0.275 1448 Planarity : 0.004 0.029 1406 Dihedral : 6.398 74.441 1280 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 3.50 % Allowed : 20.28 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.51 (0.26), residues: 1058 helix: 1.87 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 0.85 (0.56), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 657 TYR 0.023 0.002 TYR A 458 PHE 0.031 0.002 PHE A 384 TRP 0.013 0.002 TRP A 363 HIS 0.001 0.000 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 8794) covalent geometry : angle 0.71585 (11942) hydrogen bonds : bond 0.04915 ( 722) hydrogen bonds : angle 5.04020 ( 2142) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.8326 (ptp-170) cc_final: 0.8005 (ptp-170) REVERT: A 215 LEU cc_start: 0.9279 (mt) cc_final: 0.9036 (mm) REVERT: A 296 GLU cc_start: 0.8767 (tp30) cc_final: 0.8328 (tp30) REVERT: A 413 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7612 (ttp) REVERT: A 417 ASN cc_start: 0.8743 (m-40) cc_final: 0.8148 (m110) REVERT: A 430 MET cc_start: 0.7544 (mmm) cc_final: 0.7213 (mmm) REVERT: A 469 PHE cc_start: 0.8215 (t80) cc_final: 0.7877 (t80) REVERT: B 130 ARG cc_start: 0.8312 (ptp90) cc_final: 0.7928 (ptp-170) REVERT: B 296 GLU cc_start: 0.8707 (tp30) cc_final: 0.8341 (tp30) REVERT: B 370 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.6892 (mmm) REVERT: B 409 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.6444 (mp10) REVERT: B 413 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7594 (ttp) REVERT: B 417 ASN cc_start: 0.8750 (m-40) cc_final: 0.8165 (m110) REVERT: B 469 PHE cc_start: 0.8228 (t80) cc_final: 0.7869 (t80) REVERT: B 691 GLU cc_start: 0.8714 (mp0) cc_final: 0.8505 (mp0) outliers start: 33 outliers final: 11 residues processed: 198 average time/residue: 0.4533 time to fit residues: 97.3315 Evaluate side-chains 179 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 413 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 43 optimal weight: 0.1980 chunk 83 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 45 optimal weight: 0.0050 chunk 6 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 63 optimal weight: 0.1980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 HIS ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 716 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.138141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.112658 restraints weight = 16203.726| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.49 r_work: 0.3549 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8794 Z= 0.163 Angle : 0.698 8.166 11942 Z= 0.352 Chirality : 0.043 0.229 1448 Planarity : 0.004 0.029 1406 Dihedral : 6.335 75.621 1280 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 3.61 % Allowed : 21.87 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.61 (0.26), residues: 1058 helix: 1.97 (0.17), residues: 886 sheet: None (None), residues: 0 loop : 0.64 (0.54), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 657 TYR 0.015 0.001 TYR A 359 PHE 0.027 0.002 PHE A 221 TRP 0.012 0.001 TRP B 363 HIS 0.001 0.000 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 8794) covalent geometry : angle 0.69839 (11942) hydrogen bonds : bond 0.04697 ( 722) hydrogen bonds : angle 4.96651 ( 2142) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.8304 (ptp-170) cc_final: 0.8002 (ptp-170) REVERT: A 215 LEU cc_start: 0.9220 (mt) cc_final: 0.9019 (mm) REVERT: A 246 ASP cc_start: 0.8539 (m-30) cc_final: 0.8163 (m-30) REVERT: A 296 GLU cc_start: 0.8747 (tp30) cc_final: 0.8311 (tp30) REVERT: A 370 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.6732 (mmm) REVERT: A 413 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7640 (ttp) REVERT: A 417 ASN cc_start: 0.8724 (m-40) cc_final: 0.8136 (m110) REVERT: A 459 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8411 (mt) REVERT: A 469 PHE cc_start: 0.8251 (t80) cc_final: 0.7911 (t80) REVERT: B 130 ARG cc_start: 0.8262 (ptp90) cc_final: 0.7927 (ptp-170) REVERT: B 296 GLU cc_start: 0.8710 (tp30) cc_final: 0.8327 (tp30) REVERT: B 409 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.6513 (mp10) REVERT: B 413 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7658 (ttp) REVERT: B 417 ASN cc_start: 0.8733 (m-40) cc_final: 0.8159 (m110) REVERT: B 458 TYR cc_start: 0.7532 (m-10) cc_final: 0.6747 (m-10) REVERT: B 469 PHE cc_start: 0.8265 (t80) cc_final: 0.7902 (t80) REVERT: B 657 ARG cc_start: 0.7905 (ttm-80) cc_final: 0.7679 (ttm110) REVERT: B 691 GLU cc_start: 0.8714 (mp0) cc_final: 0.8467 (mp0) REVERT: B 714 ASP cc_start: 0.7933 (t0) cc_final: 0.7713 (t0) outliers start: 34 outliers final: 7 residues processed: 212 average time/residue: 0.4657 time to fit residues: 106.4127 Evaluate side-chains 181 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 413 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 82 optimal weight: 0.1980 chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 GLN A 703 GLN B 337 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 GLN B 716 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.136371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.110259 restraints weight = 16254.974| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.54 r_work: 0.3512 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8794 Z= 0.196 Angle : 0.733 8.006 11942 Z= 0.368 Chirality : 0.044 0.236 1448 Planarity : 0.004 0.032 1406 Dihedral : 6.227 77.815 1280 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 4.03 % Allowed : 22.40 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.57 (0.26), residues: 1058 helix: 1.92 (0.17), residues: 890 sheet: None (None), residues: 0 loop : 0.73 (0.54), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 657 TYR 0.014 0.002 TYR A 451 PHE 0.034 0.002 PHE B 384 TRP 0.011 0.001 TRP B 363 HIS 0.002 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 8794) covalent geometry : angle 0.73274 (11942) hydrogen bonds : bond 0.04805 ( 722) hydrogen bonds : angle 5.03407 ( 2142) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.8326 (ptp-170) cc_final: 0.8039 (ptp-170) REVERT: A 213 ARG cc_start: 0.8692 (ptm-80) cc_final: 0.8315 (ptm-80) REVERT: A 215 LEU cc_start: 0.9266 (mt) cc_final: 0.9053 (mm) REVERT: A 296 GLU cc_start: 0.8750 (tp30) cc_final: 0.8322 (tp30) REVERT: A 370 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.6903 (mmm) REVERT: A 413 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7552 (ttp) REVERT: A 417 ASN cc_start: 0.8730 (m-40) cc_final: 0.8151 (m110) REVERT: A 430 MET cc_start: 0.7581 (mmm) cc_final: 0.7326 (mpp) REVERT: A 459 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8405 (mt) REVERT: A 657 ARG cc_start: 0.7889 (ttm-80) cc_final: 0.7615 (ttm110) REVERT: A 703 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8470 (pm20) REVERT: B 130 ARG cc_start: 0.8309 (ptp90) cc_final: 0.7980 (ptp-170) REVERT: B 213 ARG cc_start: 0.8835 (ptm-80) cc_final: 0.8315 (ptm160) REVERT: B 296 GLU cc_start: 0.8699 (tp30) cc_final: 0.8288 (tp30) REVERT: B 370 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.6927 (mmm) REVERT: B 373 LYS cc_start: 0.9001 (ttmm) cc_final: 0.8763 (tppt) REVERT: B 409 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7573 (pp30) REVERT: B 413 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7625 (ttp) REVERT: B 417 ASN cc_start: 0.8718 (m-40) cc_final: 0.8121 (m110) REVERT: B 459 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8415 (mt) REVERT: B 539 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8094 (mp) REVERT: B 657 ARG cc_start: 0.7950 (ttm-80) cc_final: 0.7685 (ttm110) REVERT: B 691 GLU cc_start: 0.8694 (mp0) cc_final: 0.8450 (mp0) REVERT: B 703 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8431 (pm20) REVERT: B 714 ASP cc_start: 0.7784 (t0) cc_final: 0.7103 (t0) REVERT: B 716 HIS cc_start: 0.6498 (m90) cc_final: 0.6268 (m-70) outliers start: 38 outliers final: 12 residues processed: 192 average time/residue: 0.4492 time to fit residues: 92.8965 Evaluate side-chains 183 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 703 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 99 optimal weight: 0.0370 chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 0.0970 chunk 10 optimal weight: 0.2980 chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 45 optimal weight: 0.0050 chunk 66 optimal weight: 0.3980 chunk 40 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 overall best weight: 0.1670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 GLN A 716 HIS B 409 GLN B 433 ASN B 520 GLN B 703 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.139730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.114872 restraints weight = 16065.140| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.46 r_work: 0.3584 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8794 Z= 0.157 Angle : 0.732 9.483 11942 Z= 0.368 Chirality : 0.043 0.224 1448 Planarity : 0.004 0.028 1406 Dihedral : 6.283 76.975 1280 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.55 % Allowed : 24.31 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.69 (0.26), residues: 1058 helix: 2.02 (0.17), residues: 890 sheet: None (None), residues: 0 loop : 0.69 (0.54), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 657 TYR 0.019 0.001 TYR A 451 PHE 0.031 0.002 PHE A 384 TRP 0.010 0.001 TRP A 460 HIS 0.002 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8794) covalent geometry : angle 0.73191 (11942) hydrogen bonds : bond 0.04578 ( 722) hydrogen bonds : angle 4.94412 ( 2142) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.8229 (ptp-170) cc_final: 0.7938 (ptp-170) REVERT: A 213 ARG cc_start: 0.8645 (ptm-80) cc_final: 0.8303 (ptm-80) REVERT: A 296 GLU cc_start: 0.8646 (tp30) cc_final: 0.8239 (tp30) REVERT: A 370 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.6682 (mmm) REVERT: A 373 LYS cc_start: 0.9038 (ttmm) cc_final: 0.8616 (tppt) REVERT: A 413 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7699 (ttp) REVERT: A 417 ASN cc_start: 0.8701 (m-40) cc_final: 0.8142 (m110) REVERT: A 469 PHE cc_start: 0.8185 (t80) cc_final: 0.7790 (t80) REVERT: A 657 ARG cc_start: 0.7887 (ttm-80) cc_final: 0.7645 (ttm110) REVERT: A 692 LEU cc_start: 0.9155 (mt) cc_final: 0.8866 (pp) REVERT: A 703 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8367 (pm20) REVERT: A 714 ASP cc_start: 0.7926 (t0) cc_final: 0.7277 (t0) REVERT: A 716 HIS cc_start: 0.6275 (m170) cc_final: 0.5979 (m90) REVERT: B 130 ARG cc_start: 0.8247 (ptp90) cc_final: 0.7929 (ptp-170) REVERT: B 212 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8930 (mp) REVERT: B 296 GLU cc_start: 0.8656 (tp30) cc_final: 0.8234 (tp30) REVERT: B 370 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.6671 (mmm) REVERT: B 373 LYS cc_start: 0.9085 (ttmm) cc_final: 0.8675 (tppt) REVERT: B 409 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.6448 (mp10) REVERT: B 413 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7631 (ttp) REVERT: B 417 ASN cc_start: 0.8679 (m-40) cc_final: 0.8097 (m110) REVERT: B 455 TYR cc_start: 0.7844 (m-80) cc_final: 0.7320 (m-80) REVERT: B 458 TYR cc_start: 0.7431 (m-10) cc_final: 0.6755 (m-10) REVERT: B 469 PHE cc_start: 0.8234 (t80) cc_final: 0.7418 (t80) REVERT: B 521 MET cc_start: 0.4863 (tpt) cc_final: 0.4558 (tpt) REVERT: B 657 ARG cc_start: 0.7929 (ttm-80) cc_final: 0.7690 (ttm110) REVERT: B 700 ASN cc_start: 0.7588 (m-40) cc_final: 0.7354 (m110) REVERT: B 703 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8321 (pm20) REVERT: B 714 ASP cc_start: 0.7811 (t0) cc_final: 0.7052 (t0) REVERT: B 716 HIS cc_start: 0.6237 (m90) cc_final: 0.6037 (m-70) outliers start: 24 outliers final: 6 residues processed: 202 average time/residue: 0.4323 time to fit residues: 94.1919 Evaluate side-chains 181 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 703 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 6 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 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 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 GLN B 703 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.137650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.111913 restraints weight = 16073.207| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.47 r_work: 0.3542 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8794 Z= 0.194 Angle : 0.754 8.378 11942 Z= 0.382 Chirality : 0.045 0.215 1448 Planarity : 0.004 0.029 1406 Dihedral : 6.183 78.735 1280 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.44 % Allowed : 24.84 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.66 (0.26), residues: 1058 helix: 2.00 (0.17), residues: 890 sheet: None (None), residues: 0 loop : 0.63 (0.54), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 657 TYR 0.014 0.002 TYR B 455 PHE 0.034 0.002 PHE B 701 TRP 0.016 0.001 TRP B 100 HIS 0.003 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 8794) covalent geometry : angle 0.75431 (11942) hydrogen bonds : bond 0.04723 ( 722) hydrogen bonds : angle 5.00093 ( 2142) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.8319 (ptp-170) cc_final: 0.8051 (ptp-170) REVERT: A 296 GLU cc_start: 0.8553 (tp30) cc_final: 0.8173 (tp30) REVERT: A 299 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8386 (mp0) REVERT: A 370 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.6896 (mmm) REVERT: A 373 LYS cc_start: 0.8946 (ttmm) cc_final: 0.8736 (tppt) REVERT: A 417 ASN cc_start: 0.8661 (m-40) cc_final: 0.8141 (m110) REVERT: A 469 PHE cc_start: 0.8208 (t80) cc_final: 0.7845 (t80) REVERT: A 539 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7719 (mp) REVERT: A 657 ARG cc_start: 0.7945 (ttm-80) cc_final: 0.7607 (ttm110) REVERT: A 703 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8532 (pm20) REVERT: A 714 ASP cc_start: 0.7964 (t0) cc_final: 0.7291 (t0) REVERT: B 130 ARG cc_start: 0.8275 (ptp90) cc_final: 0.8009 (ptp-170) REVERT: B 212 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8904 (mp) REVERT: B 296 GLU cc_start: 0.8637 (tp30) cc_final: 0.8236 (tp30) REVERT: B 370 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.6867 (mmm) REVERT: B 413 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7683 (ptp) REVERT: B 417 ASN cc_start: 0.8658 (m-40) cc_final: 0.8160 (m110) REVERT: B 455 TYR cc_start: 0.7859 (m-80) cc_final: 0.7546 (m-80) REVERT: B 458 TYR cc_start: 0.7625 (m-10) cc_final: 0.6817 (m-10) REVERT: B 469 PHE cc_start: 0.8246 (t80) cc_final: 0.7867 (t80) REVERT: B 521 MET cc_start: 0.4992 (tpt) cc_final: 0.4670 (tpt) REVERT: B 657 ARG cc_start: 0.7974 (ttm-80) cc_final: 0.7737 (ttm110) REVERT: B 703 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8514 (pm20) REVERT: B 714 ASP cc_start: 0.7711 (t0) cc_final: 0.7026 (t0) outliers start: 23 outliers final: 8 residues processed: 189 average time/residue: 0.4596 time to fit residues: 93.9473 Evaluate side-chains 180 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 703 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.1980 chunk 33 optimal weight: 0.6980 chunk 85 optimal weight: 0.4980 chunk 63 optimal weight: 0.0980 chunk 44 optimal weight: 0.0010 chunk 103 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 GLN A 716 HIS B 337 ASN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.139991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.114243 restraints weight = 16006.424| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.48 r_work: 0.3579 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8794 Z= 0.172 Angle : 0.778 9.590 11942 Z= 0.392 Chirality : 0.044 0.239 1448 Planarity : 0.004 0.031 1406 Dihedral : 6.236 77.229 1280 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.34 % Allowed : 25.58 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.60 (0.26), residues: 1058 helix: 1.96 (0.17), residues: 890 sheet: None (None), residues: 0 loop : 0.61 (0.54), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 235 TYR 0.022 0.001 TYR A 451 PHE 0.034 0.002 PHE B 701 TRP 0.017 0.002 TRP B 460 HIS 0.006 0.001 HIS A 716 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 8794) covalent geometry : angle 0.77758 (11942) hydrogen bonds : bond 0.04658 ( 722) hydrogen bonds : angle 4.97533 ( 2142) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.8279 (ptp-170) cc_final: 0.8026 (ptp-170) REVERT: A 213 ARG cc_start: 0.8619 (ptm160) cc_final: 0.8404 (ptm-80) REVERT: A 296 GLU cc_start: 0.8490 (tp30) cc_final: 0.8077 (tp30) REVERT: A 299 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8415 (mp0) REVERT: A 301 LEU cc_start: 0.8083 (pt) cc_final: 0.7751 (pp) REVERT: A 370 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7316 (mmm) REVERT: A 373 LYS cc_start: 0.9024 (ttmm) cc_final: 0.8654 (tppt) REVERT: A 413 MET cc_start: 0.7916 (ptt) cc_final: 0.7583 (ttp) REVERT: A 417 ASN cc_start: 0.8665 (m-40) cc_final: 0.8090 (m110) REVERT: A 420 ILE cc_start: 0.8821 (mp) cc_final: 0.8366 (tp) REVERT: A 469 PHE cc_start: 0.8195 (t80) cc_final: 0.7819 (t80) REVERT: A 514 PHE cc_start: 0.6381 (p90) cc_final: 0.5927 (p90) REVERT: A 539 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7733 (mp) REVERT: A 657 ARG cc_start: 0.7969 (ttm-80) cc_final: 0.7637 (ttm110) REVERT: A 716 HIS cc_start: 0.6023 (m90) cc_final: 0.5619 (m90) REVERT: B 130 ARG cc_start: 0.8228 (ptp90) cc_final: 0.7950 (ptp-170) REVERT: B 212 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8877 (mp) REVERT: B 296 GLU cc_start: 0.8554 (tp30) cc_final: 0.8169 (tp30) REVERT: B 370 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.7183 (mmm) REVERT: B 413 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7676 (pmm) REVERT: B 417 ASN cc_start: 0.8660 (m-40) cc_final: 0.8142 (m110) REVERT: B 455 TYR cc_start: 0.7823 (m-80) cc_final: 0.7499 (m-80) REVERT: B 458 TYR cc_start: 0.7582 (m-10) cc_final: 0.6835 (m-10) REVERT: B 469 PHE cc_start: 0.8234 (t80) cc_final: 0.7872 (t80) REVERT: B 521 MET cc_start: 0.4705 (tpt) cc_final: 0.4480 (tpt) REVERT: B 657 ARG cc_start: 0.7990 (ttm-80) cc_final: 0.7754 (ttm110) REVERT: B 716 HIS cc_start: 0.6116 (m-70) cc_final: 0.5668 (m90) outliers start: 22 outliers final: 8 residues processed: 191 average time/residue: 0.4677 time to fit residues: 96.4737 Evaluate side-chains 184 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 414 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 22 optimal weight: 0.0670 chunk 28 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 25 optimal weight: 0.1980 chunk 61 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 ASN B 716 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.139415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.113196 restraints weight = 15962.434| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.51 r_work: 0.3562 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8794 Z= 0.188 Angle : 0.784 8.681 11942 Z= 0.395 Chirality : 0.045 0.218 1448 Planarity : 0.005 0.048 1406 Dihedral : 6.159 77.378 1280 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.02 % Allowed : 25.48 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.51 (0.26), residues: 1058 helix: 1.92 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 0.52 (0.53), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 213 TYR 0.016 0.002 TYR B 455 PHE 0.033 0.002 PHE B 185 TRP 0.018 0.002 TRP B 460 HIS 0.007 0.001 HIS B 716 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 8794) covalent geometry : angle 0.78395 (11942) hydrogen bonds : bond 0.04738 ( 722) hydrogen bonds : angle 5.00812 ( 2142) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3162.69 seconds wall clock time: 54 minutes 50.72 seconds (3290.72 seconds total)