Starting phenix.real_space_refine on Sat Jul 4 06:14:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8b14_15802/07_2026/8b14_15802.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b14_15802/07_2026/8b14_15802.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8b14_15802/07_2026/8b14_15802.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b14_15802/07_2026/8b14_15802.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8b14_15802/07_2026/8b14_15802.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8b14_15802/07_2026/8b14_15802.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8b14_15802/07_2026/8b14_15802.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b14_15802/07_2026/8b14_15802.map" } resolution = 2.6 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= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 36 5.16 5 C 6114 2.51 5 N 1631 2.21 5 O 1915 1.98 5 H 9112 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18810 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 10595 Classifications: {'peptide': 696} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 662} Chain breaks: 1 Chain: "B" Number of atoms: 8065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 8065 Classifications: {'peptide': 547} Link IDs: {'PTRANS': 25, 'TRANS': 521} Chain breaks: 3 Chain: "A" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 150 Unusual residues: {'DDQ': 1, 'LU9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.20, per 1000 atoms: 0.17 Number of scatterers: 18810 At special positions: 0 Unit cell: (102.044, 108.356, 137.812, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 2 15.00 O 1915 8.00 N 1631 7.00 C 6114 6.00 H 9112 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 701 " - pdb=" SG CYS A 707 " distance=2.03 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: 1.75 Conformation dependent library (CDL) restraints added in 591.0 milliseconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2218 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 17 sheets defined 8.3% alpha, 50.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 21 through 28 removed outlier: 3.530A pdb=" N ALA A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A 27 " --> pdb=" O GLY A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 55 through 62 Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.657A pdb=" N SER A 101 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 124 No H-bonds generated for 'chain 'A' and resid 122 through 124' Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 320 through 324 Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 335 through 338 removed outlier: 3.667A pdb=" N GLY A 338 " --> pdb=" O ALA A 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 335 through 338' Processing helix chain 'B' and resid 68 through 78 Processing helix chain 'B' and resid 146 through 151 Processing helix chain 'B' and resid 152 through 154 No H-bonds generated for 'chain 'B' and resid 152 through 154' Processing helix chain 'B' and resid 176 through 182 Processing helix chain 'B' and resid 195 through 199 removed outlier: 3.511A pdb=" N THR B 199 " --> pdb=" O ASP B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 207 removed outlier: 3.563A pdb=" N VAL B 207 " --> pdb=" O SER B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 511 Processing helix chain 'B' and resid 518 through 523 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33 Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 54 removed outlier: 3.513A pdb=" N ARG A 128 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TYR A 105 " --> pdb=" O MET A 151 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N SER A 153 " --> pdb=" O TYR A 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 77 Processing sheet with id=AA4, first strand: chain 'A' and resid 397 through 401 removed outlier: 4.924A pdb=" N ARG A 343 " --> pdb=" O PRO A 398 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TYR A 340 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL A 317 " --> pdb=" O TYR A 340 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ALA A 342 " --> pdb=" O TYR A 315 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N TYR A 275 " --> pdb=" O GLU A 240 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU A 240 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLN A 211 " --> pdb=" O PRO A 239 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR A 241 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N GLU A 209 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 173 " --> pdb=" O GLY A 169 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS A 162 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLU A 573 " --> pdb=" O THR A 605 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER A 568 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA A 560 " --> pdb=" O SER A 568 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N GLU A 570 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU A 558 " --> pdb=" O GLU A 570 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLY A 572 " --> pdb=" O ASN A 556 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP A 487 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE A 509 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 9.352A pdb=" N PHE A 485 " --> pdb=" O PHE A 509 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 397 through 401 removed outlier: 4.924A pdb=" N ARG A 343 " --> pdb=" O PRO A 398 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR A 345 " --> pdb=" O GLY A 392 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 651 through 652 Processing sheet with id=AA7, first strand: chain 'A' and resid 698 through 701 removed outlier: 3.910A pdb=" N SER A 700 " --> pdb=" O PHE A 708 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 325 through 327 removed outlier: 5.102A pdb=" N VAL B 82 " --> pdb=" O THR B 316 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ARG B 94 " --> pdb=" O ASP B 376 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY B 378 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ASN B 380 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN B 420 " --> pdb=" O CYS B 379 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU B 381 " --> pdb=" O HIS B 418 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N HIS B 418 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N ILE B 45 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ASN B 317 " --> pdb=" O ILE B 45 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 63 through 66 Processing sheet with id=AB1, first strand: chain 'B' and resid 112 through 113 removed outlier: 4.528A pdb=" N ARG B 274 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N GLY B 252 " --> pdb=" O ARG B 274 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 112 through 113 removed outlier: 7.265A pdb=" N TYR B 556 " --> pdb=" O ASN B 605 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ASN B 605 " --> pdb=" O TYR B 556 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N MET B 603 " --> pdb=" O PRO B 558 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE B 560 " --> pdb=" O TYR B 601 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE B 611 " --> pdb=" O THR B 484 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR B 484 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE B 613 " --> pdb=" O VAL B 482 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 183 through 184 Processing sheet with id=AB4, first strand: chain 'B' and resid 229 through 231 Processing sheet with id=AB5, first strand: chain 'B' and resid 245 through 247 Processing sheet with id=AB6, first strand: chain 'B' and resid 398 through 401 Processing sheet with id=AB7, first strand: chain 'B' and resid 464 through 468 removed outlier: 4.558A pdb=" N LYS B 543 " --> pdb=" O PHE B 503 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 471 through 474 485 hydrogen bonds defined for protein. 1311 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: 5.00 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9105 1.03 - 1.23: 69 1.23 - 1.42: 4263 1.42 - 1.62: 5539 1.62 - 1.81: 65 Bond restraints: 19041 Sorted by residual: bond pdb=" C81 LU9 A 802 " pdb=" O81 LU9 A 802 " ideal model delta sigma weight residual 1.204 1.395 -0.191 2.00e-02 2.50e+03 9.11e+01 bond pdb=" C01 LU9 A 802 " pdb=" O03 LU9 A 802 " ideal model delta sigma weight residual 1.243 1.414 -0.171 2.00e-02 2.50e+03 7.35e+01 bond pdb=" C71 LU9 A 802 " pdb=" O71 LU9 A 802 " ideal model delta sigma weight residual 1.203 1.372 -0.169 2.00e-02 2.50e+03 7.16e+01 bond pdb=" NB2 LU9 A 802 " pdb=" C51 LU9 A 802 " ideal model delta sigma weight residual 1.347 1.512 -0.165 2.00e-02 2.50e+03 6.81e+01 bond pdb=" C11 LU9 A 802 " pdb=" NA2 LU9 A 802 " ideal model delta sigma weight residual 1.344 1.507 -0.163 2.00e-02 2.50e+03 6.65e+01 ... (remaining 19036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.34: 33957 4.34 - 8.69: 115 8.69 - 13.03: 3 13.03 - 17.37: 5 17.37 - 21.72: 1 Bond angle restraints: 34081 Sorted by residual: angle pdb=" C19 LU9 A 802 " pdb="C110 LU9 A 802 " pdb="C111 LU9 A 802 " ideal model delta sigma weight residual 114.73 136.45 -21.72 3.00e+00 1.11e-01 5.24e+01 angle pdb=" C82 LU9 A 802 " pdb=" C81 LU9 A 802 " pdb=" O81 LU9 A 802 " ideal model delta sigma weight residual 125.22 109.26 15.96 3.00e+00 1.11e-01 2.83e+01 angle pdb=" O02 LU9 A 802 " pdb=" C01 LU9 A 802 " pdb=" O03 LU9 A 802 " ideal model delta sigma weight residual 127.57 112.42 15.15 3.00e+00 1.11e-01 2.55e+01 angle pdb=" OB3 LU9 A 802 " pdb=" C71 LU9 A 802 " pdb=" O71 LU9 A 802 " ideal model delta sigma weight residual 124.63 109.70 14.93 3.00e+00 1.11e-01 2.48e+01 angle pdb=" C72 LU9 A 802 " pdb=" C71 LU9 A 802 " pdb=" O71 LU9 A 802 " ideal model delta sigma weight residual 123.61 108.96 14.65 3.00e+00 1.11e-01 2.38e+01 ... (remaining 34076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 8217 17.78 - 35.55: 698 35.55 - 53.33: 265 53.33 - 71.10: 77 71.10 - 88.88: 19 Dihedral angle restraints: 9276 sinusoidal: 5036 harmonic: 4240 Sorted by residual: dihedral pdb=" N ASN B 609 " pdb=" C ASN B 609 " pdb=" CA ASN B 609 " pdb=" CB ASN B 609 " ideal model delta harmonic sigma weight residual 122.80 130.94 -8.14 0 2.50e+00 1.60e-01 1.06e+01 dihedral pdb=" CB GLU A 56 " pdb=" CG GLU A 56 " pdb=" CD GLU A 56 " pdb=" OE1 GLU A 56 " ideal model delta sinusoidal sigma weight residual 0.00 85.93 -85.93 1 3.00e+01 1.11e-03 9.91e+00 dihedral pdb=" CG ARG B 225 " pdb=" CD ARG B 225 " pdb=" NE ARG B 225 " pdb=" CZ ARG B 225 " ideal model delta sinusoidal sigma weight residual 90.00 132.23 -42.23 2 1.50e+01 4.44e-03 9.64e+00 ... (remaining 9273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1180 0.056 - 0.112: 223 0.112 - 0.168: 30 0.168 - 0.224: 4 0.224 - 0.281: 1 Chirality restraints: 1438 Sorted by residual: chirality pdb=" C2 LU9 A 802 " pdb=" C3 LU9 A 802 " pdb=" O05 LU9 A 802 " pdb=" O6 LU9 A 802 " both_signs ideal model delta sigma weight residual False -2.31 -2.60 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA ASN B 609 " pdb=" N ASN B 609 " pdb=" C ASN B 609 " pdb=" CB ASN B 609 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA5 LU9 A 802 " pdb=" CA4 LU9 A 802 " pdb=" CA6 LU9 A 802 " pdb=" OA5 LU9 A 802 " both_signs ideal model delta sigma weight residual False -2.32 -2.51 0.20 2.00e-01 2.50e+01 9.65e-01 ... (remaining 1435 not shown) Planarity restraints: 2941 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C81 LU9 A 802 " 0.362 2.00e-02 2.50e+03 2.09e-01 4.36e+02 pdb=" C82 LU9 A 802 " -0.112 2.00e-02 2.50e+03 pdb=" O73 LU9 A 802 " -0.124 2.00e-02 2.50e+03 pdb=" O81 LU9 A 802 " -0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" OB3 LU9 A 802 " -0.124 2.00e-02 2.50e+03 2.08e-01 4.32e+02 pdb=" C71 LU9 A 802 " 0.360 2.00e-02 2.50e+03 pdb=" C72 LU9 A 802 " -0.108 2.00e-02 2.50e+03 pdb=" O71 LU9 A 802 " -0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 LU9 A 802 " -0.351 2.00e-02 2.50e+03 2.02e-01 4.10e+02 pdb=" C02 LU9 A 802 " 0.108 2.00e-02 2.50e+03 pdb=" O02 LU9 A 802 " 0.121 2.00e-02 2.50e+03 pdb=" O03 LU9 A 802 " 0.122 2.00e-02 2.50e+03 ... (remaining 2938 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.08: 565 2.08 - 2.71: 31543 2.71 - 3.34: 53748 3.34 - 3.97: 76937 3.97 - 4.60: 117859 Nonbonded interactions: 280652 Sorted by model distance: nonbonded pdb=" O PRO B 237 " pdb=" HG SER B 269 " model vdw 1.456 2.450 nonbonded pdb="HH11 ARG A 384 " pdb=" O07 LU9 A 802 " model vdw 1.457 2.450 nonbonded pdb=" HH TYR A 87 " pdb=" HH TYR A 275 " model vdw 1.466 2.100 nonbonded pdb=" HZ2 LYS B 383 " pdb=" O SER B 385 " model vdw 1.469 2.450 nonbonded pdb=" O GLY B 198 " pdb=" HH TYR B 268 " model vdw 1.492 2.450 ... (remaining 280647 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: 8.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.120 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.720 Find NCS groups from input model: 0.070 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:7.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.191 9931 Z= 0.398 Angle : 0.754 21.715 13480 Z= 0.345 Chirality : 0.047 0.281 1438 Planarity : 0.009 0.209 1761 Dihedral : 15.298 88.876 3704 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.79 % Allowed : 14.17 % Favored : 85.04 % 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 are not related in a simple way. whole: 0.27 (0.24), residues: 1231 helix: -2.15 (0.58), residues: 69 sheet: 0.86 (0.24), residues: 540 loop : -0.07 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 167 TYR 0.025 0.002 TYR B 192 PHE 0.011 0.001 PHE B 89 TRP 0.025 0.002 TRP B 187 HIS 0.004 0.001 HIS B 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00822 / 0.40 ( 9929) covalent geometry : angle 0.75441 / 0.34 (13476) SS BOND : bond 0.00199 / 0.09 ( 2) SS BOND : angle 0.18035 / 0.10 ( 4) hydrogen bonds : bond 0.18739 / 12.77 ( 469) hydrogen bonds : angle 8.49851 / 5.90 ( 1311) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 216 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8183 (ttmt) cc_final: 0.7978 (ttmm) REVERT: A 127 GLU cc_start: 0.7478 (tp30) cc_final: 0.7196 (tp30) REVERT: A 308 SER cc_start: 0.8581 (t) cc_final: 0.8370 (p) REVERT: A 353 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.7598 (mp-120) REVERT: A 379 ASP cc_start: 0.7789 (t0) cc_final: 0.7568 (t70) REVERT: A 510 GLU cc_start: 0.7481 (tt0) cc_final: 0.7262 (tt0) REVERT: A 534 VAL cc_start: 0.8920 (t) cc_final: 0.8674 (p) REVERT: A 556 ASN cc_start: 0.8564 (t0) cc_final: 0.8334 (t0) REVERT: A 592 ASN cc_start: 0.8437 (m110) cc_final: 0.8183 (m110) REVERT: A 668 ASP cc_start: 0.7892 (m-30) cc_final: 0.7691 (m-30) REVERT: B 41 SER cc_start: 0.7618 (m) cc_final: 0.7161 (p) REVERT: B 73 GLN cc_start: 0.7695 (tm-30) cc_final: 0.7398 (tm-30) REVERT: B 134 LEU cc_start: 0.8451 (mt) cc_final: 0.8221 (mt) REVERT: B 385 SER cc_start: 0.8237 (t) cc_final: 0.7926 (p) REVERT: B 610 ASN cc_start: 0.7658 (m-40) cc_final: 0.7324 (m110) outliers start: 8 outliers final: 3 residues processed: 221 average time/residue: 1.1596 time to fit residues: 276.8800 Evaluate side-chains 193 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 189 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain B residue 112 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 chunk 117 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 GLN A 353 GLN A 354 ASN A 362 GLN A 592 ASN A 714 GLN B 115 GLN B 360 ASN B 475 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.103462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.093471 restraints weight = 39020.074| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.53 r_work: 0.3185 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 9931 Z= 0.299 Angle : 0.611 5.376 13480 Z= 0.325 Chirality : 0.048 0.152 1438 Planarity : 0.005 0.056 1761 Dihedral : 6.230 45.208 1588 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.26 % Allowed : 15.55 % Favored : 82.19 % 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 are not related in a simple way. whole: -0.01 (0.24), residues: 1231 helix: -2.45 (0.55), residues: 71 sheet: 0.69 (0.23), residues: 530 loop : -0.24 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 199 TYR 0.015 0.002 TYR B 597 PHE 0.016 0.002 PHE A 365 TRP 0.019 0.002 TRP B 187 HIS 0.004 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.30 ( 9929) covalent geometry : angle 0.61140 / 0.33 (13476) SS BOND : bond 0.00490 / 0.23 ( 2) SS BOND : angle 0.49533 / 0.28 ( 4) hydrogen bonds : bond 0.05041 / 3.42 ( 469) hydrogen bonds : angle 6.34613 / 4.41 ( 1311) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7816 (mp0) cc_final: 0.7484 (mp0) REVERT: A 127 GLU cc_start: 0.7439 (tp30) cc_final: 0.7186 (tp30) REVERT: A 199 ARG cc_start: 0.8270 (ttt-90) cc_final: 0.8064 (ttp80) REVERT: A 478 ASP cc_start: 0.7438 (m-30) cc_final: 0.7192 (m-30) REVERT: A 510 GLU cc_start: 0.7618 (tt0) cc_final: 0.7404 (tt0) REVERT: A 534 VAL cc_start: 0.8843 (t) cc_final: 0.8589 (p) REVERT: B 41 SER cc_start: 0.7896 (m) cc_final: 0.7540 (p) REVERT: B 131 ASP cc_start: 0.7755 (t70) cc_final: 0.7509 (t0) REVERT: B 359 ILE cc_start: 0.8685 (mt) cc_final: 0.8474 (mm) REVERT: B 360 ASN cc_start: 0.8152 (t0) cc_final: 0.7916 (t0) REVERT: B 385 SER cc_start: 0.8558 (t) cc_final: 0.8321 (p) REVERT: B 405 ASN cc_start: 0.8196 (m-40) cc_final: 0.7964 (m-40) REVERT: B 610 ASN cc_start: 0.7757 (m-40) cc_final: 0.7537 (m-40) outliers start: 23 outliers final: 16 residues processed: 213 average time/residue: 1.1374 time to fit residues: 261.9724 Evaluate side-chains 213 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 197 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain B residue 570 CYS Chi-restraints excluded: chain B residue 585 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 4 optimal weight: 0.0570 chunk 49 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 118 optimal weight: 0.0050 chunk 103 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 76 optimal weight: 0.0670 overall best weight: 0.4050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN A 114 ASN A 436 ASN A 690 ASN A 714 GLN B 115 GLN B 475 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.104423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.094441 restraints weight = 38852.723| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.54 r_work: 0.3199 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 9931 Z= 0.206 Angle : 0.546 4.359 13480 Z= 0.290 Chirality : 0.046 0.149 1438 Planarity : 0.004 0.065 1761 Dihedral : 5.446 39.837 1581 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.46 % Allowed : 16.14 % Favored : 81.40 % 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 are not related in a simple way. whole: -0.17 (0.24), residues: 1231 helix: -2.32 (0.55), residues: 72 sheet: 0.43 (0.22), residues: 534 loop : -0.21 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 199 TYR 0.012 0.001 TYR B 192 PHE 0.012 0.001 PHE A 365 TRP 0.014 0.001 TRP B 187 HIS 0.003 0.001 HIS B 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.21 ( 9929) covalent geometry : angle 0.54647 / 0.29 (13476) SS BOND : bond 0.00330 / 0.16 ( 2) SS BOND : angle 0.46583 / 0.26 ( 4) hydrogen bonds : bond 0.04026 / 2.72 ( 469) hydrogen bonds : angle 5.96371 / 4.17 ( 1311) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7815 (mp0) cc_final: 0.7517 (mp0) REVERT: A 127 GLU cc_start: 0.7429 (tp30) cc_final: 0.7169 (tp30) REVERT: A 159 GLU cc_start: 0.7678 (mp0) cc_final: 0.7448 (pm20) REVERT: A 291 ASN cc_start: 0.8592 (OUTLIER) cc_final: 0.8379 (p0) REVERT: A 308 SER cc_start: 0.8496 (m) cc_final: 0.8291 (t) REVERT: A 478 ASP cc_start: 0.7401 (m-30) cc_final: 0.7162 (m-30) REVERT: A 510 GLU cc_start: 0.7611 (tt0) cc_final: 0.7400 (tt0) REVERT: A 534 VAL cc_start: 0.8832 (t) cc_final: 0.8571 (p) REVERT: A 592 ASN cc_start: 0.8447 (m-40) cc_final: 0.8214 (m110) REVERT: B 41 SER cc_start: 0.7922 (m) cc_final: 0.7606 (p) REVERT: B 73 GLN cc_start: 0.7847 (tm-30) cc_final: 0.7580 (tm-30) REVERT: B 359 ILE cc_start: 0.8682 (mt) cc_final: 0.8456 (mm) REVERT: B 385 SER cc_start: 0.8589 (t) cc_final: 0.8356 (p) REVERT: B 405 ASN cc_start: 0.8153 (m-40) cc_final: 0.7925 (m-40) REVERT: B 610 ASN cc_start: 0.7775 (m-40) cc_final: 0.7543 (m-40) REVERT: B 619 MET cc_start: 0.8770 (mtp) cc_final: 0.8558 (mtp) outliers start: 25 outliers final: 13 residues processed: 215 average time/residue: 1.1414 time to fit residues: 265.7858 Evaluate side-chains 214 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain B residue 570 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 114 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 7 optimal weight: 0.0970 chunk 73 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 63 optimal weight: 0.4980 chunk 53 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 ASN B 475 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.103476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.093556 restraints weight = 38777.213| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.53 r_work: 0.3189 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 9931 Z= 0.305 Angle : 0.585 5.211 13480 Z= 0.309 Chirality : 0.048 0.152 1438 Planarity : 0.004 0.070 1761 Dihedral : 5.582 39.940 1581 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.66 % Allowed : 16.34 % Favored : 81.00 % 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 are not related in a simple way. whole: -0.31 (0.24), residues: 1231 helix: -2.44 (0.54), residues: 73 sheet: 0.30 (0.22), residues: 535 loop : -0.26 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 577 TYR 0.016 0.002 TYR B 597 PHE 0.013 0.002 PHE A 365 TRP 0.014 0.002 TRP B 187 HIS 0.004 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00690 / 0.30 ( 9929) covalent geometry : angle 0.58473 / 0.31 (13476) SS BOND : bond 0.00391 / 0.19 ( 2) SS BOND : angle 0.59305 / 0.32 ( 4) hydrogen bonds : bond 0.03967 / 2.66 ( 469) hydrogen bonds : angle 5.91430 / 4.15 ( 1311) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 203 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7870 (mp0) cc_final: 0.7552 (mp0) REVERT: A 127 GLU cc_start: 0.7414 (tp30) cc_final: 0.7158 (tp30) REVERT: A 238 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7623 (mt-10) REVERT: A 478 ASP cc_start: 0.7395 (m-30) cc_final: 0.7150 (m-30) REVERT: A 534 VAL cc_start: 0.8776 (t) cc_final: 0.8510 (p) REVERT: B 41 SER cc_start: 0.7942 (m) cc_final: 0.7619 (p) REVERT: B 54 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8177 (ptm160) REVERT: B 73 GLN cc_start: 0.7854 (tm-30) cc_final: 0.7553 (tm-30) REVERT: B 359 ILE cc_start: 0.8713 (mt) cc_final: 0.8496 (mm) REVERT: B 405 ASN cc_start: 0.8265 (m-40) cc_final: 0.8027 (m-40) REVERT: B 610 ASN cc_start: 0.7783 (m-40) cc_final: 0.7568 (m-40) REVERT: B 619 MET cc_start: 0.8811 (mtp) cc_final: 0.8595 (mtp) outliers start: 27 outliers final: 13 residues processed: 219 average time/residue: 1.1430 time to fit residues: 270.1491 Evaluate side-chains 214 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain B residue 570 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 40 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 119 optimal weight: 0.1980 chunk 24 optimal weight: 0.3980 chunk 43 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN A 114 ASN A 714 GLN B 475 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.103905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.094037 restraints weight = 38580.633| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.53 r_work: 0.3203 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9931 Z= 0.234 Angle : 0.548 5.279 13480 Z= 0.290 Chirality : 0.046 0.146 1438 Planarity : 0.004 0.071 1761 Dihedral : 5.369 39.173 1581 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.46 % Allowed : 16.83 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.24), residues: 1231 helix: -2.32 (0.55), residues: 73 sheet: 0.23 (0.22), residues: 537 loop : -0.24 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 638 TYR 0.014 0.001 TYR B 597 PHE 0.011 0.001 PHE A 365 TRP 0.014 0.001 TRP B 187 HIS 0.004 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.23 ( 9929) covalent geometry : angle 0.54830 / 0.29 (13476) SS BOND : bond 0.00371 / 0.18 ( 2) SS BOND : angle 0.52523 / 0.28 ( 4) hydrogen bonds : bond 0.03579 / 2.40 ( 469) hydrogen bonds : angle 5.79019 / 4.08 ( 1311) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7856 (mp0) cc_final: 0.7547 (mp0) REVERT: A 127 GLU cc_start: 0.7416 (tp30) cc_final: 0.7171 (tp30) REVERT: A 238 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7602 (mt-10) REVERT: A 478 ASP cc_start: 0.7399 (m-30) cc_final: 0.7149 (m-30) REVERT: A 534 VAL cc_start: 0.8823 (t) cc_final: 0.8551 (p) REVERT: B 41 SER cc_start: 0.7915 (m) cc_final: 0.7587 (p) REVERT: B 54 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8159 (ptm160) REVERT: B 359 ILE cc_start: 0.8689 (mt) cc_final: 0.8466 (mm) REVERT: B 610 ASN cc_start: 0.7789 (m-40) cc_final: 0.7582 (m-40) outliers start: 25 outliers final: 15 residues processed: 215 average time/residue: 1.1712 time to fit residues: 271.9209 Evaluate side-chains 217 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain B residue 570 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 28 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 17 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 115 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN A 114 ASN A 291 ASN A 714 GLN B 115 GLN B 475 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.103747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.093637 restraints weight = 38766.917| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.56 r_work: 0.3181 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 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 : 0.008 0.056 9931 Z= 0.339 Angle : 0.594 5.125 13480 Z= 0.313 Chirality : 0.048 0.151 1438 Planarity : 0.005 0.072 1761 Dihedral : 5.644 40.078 1581 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.95 % Allowed : 16.54 % Favored : 80.51 % 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 are not related in a simple way. whole: -0.44 (0.24), residues: 1231 helix: -2.35 (0.54), residues: 72 sheet: 0.14 (0.22), residues: 536 loop : -0.30 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 577 TYR 0.018 0.002 TYR B 597 PHE 0.014 0.002 PHE A 365 TRP 0.015 0.002 TRP B 187 HIS 0.006 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00774 / 0.34 ( 9929) covalent geometry : angle 0.59358 / 0.31 (13476) SS BOND : bond 0.00522 / 0.25 ( 2) SS BOND : angle 0.62330 / 0.34 ( 4) hydrogen bonds : bond 0.03824 / 2.56 ( 469) hydrogen bonds : angle 5.85857 / 4.14 ( 1311) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7836 (mp0) cc_final: 0.7536 (mp0) REVERT: A 127 GLU cc_start: 0.7399 (tp30) cc_final: 0.7148 (tp30) REVERT: A 238 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7572 (mt-10) REVERT: A 478 ASP cc_start: 0.7464 (m-30) cc_final: 0.7208 (m-30) REVERT: A 534 VAL cc_start: 0.8770 (t) cc_final: 0.8499 (p) REVERT: B 41 SER cc_start: 0.7930 (m) cc_final: 0.7584 (p) REVERT: B 359 ILE cc_start: 0.8703 (mt) cc_final: 0.8480 (mm) REVERT: B 610 ASN cc_start: 0.7800 (m-40) cc_final: 0.7578 (m-40) outliers start: 30 outliers final: 21 residues processed: 216 average time/residue: 1.1620 time to fit residues: 271.0569 Evaluate side-chains 224 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain B residue 570 CYS Chi-restraints excluded: chain B residue 625 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 100 optimal weight: 0.0970 chunk 36 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 23 optimal weight: 0.1980 chunk 32 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 51 optimal weight: 0.0980 chunk 34 optimal weight: 0.3980 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN A 114 ASN A 291 ASN A 556 ASN A 714 GLN B 115 GLN B 475 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.105752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.095740 restraints weight = 38484.161| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.55 r_work: 0.3197 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 9931 Z= 0.157 Angle : 0.525 5.217 13480 Z= 0.277 Chirality : 0.045 0.152 1438 Planarity : 0.004 0.071 1761 Dihedral : 5.181 37.537 1581 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.48 % Allowed : 18.11 % Favored : 80.41 % 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 are not related in a simple way. whole: -0.35 (0.24), residues: 1231 helix: -2.15 (0.56), residues: 73 sheet: 0.15 (0.22), residues: 537 loop : -0.21 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 646 TYR 0.009 0.001 TYR B 597 PHE 0.010 0.001 PHE A 115 TRP 0.014 0.001 TRP B 187 HIS 0.003 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 9929) covalent geometry : angle 0.52482 / 0.28 (13476) SS BOND : bond 0.00251 / 0.12 ( 2) SS BOND : angle 0.44947 / 0.24 ( 4) hydrogen bonds : bond 0.03210 / 2.17 ( 469) hydrogen bonds : angle 5.68086 / 4.02 ( 1311) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 199 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7825 (mp0) cc_final: 0.7529 (mp0) REVERT: A 62 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7671 (mm110) REVERT: A 127 GLU cc_start: 0.7405 (tp30) cc_final: 0.7154 (tp30) REVERT: A 478 ASP cc_start: 0.7387 (m-30) cc_final: 0.7133 (m-30) REVERT: A 534 VAL cc_start: 0.8819 (t) cc_final: 0.8540 (p) REVERT: B 41 SER cc_start: 0.7914 (m) cc_final: 0.7593 (p) REVERT: B 359 ILE cc_start: 0.8683 (mt) cc_final: 0.8461 (mm) REVERT: B 610 ASN cc_start: 0.7796 (m-40) cc_final: 0.7579 (m-40) outliers start: 15 outliers final: 12 residues processed: 207 average time/residue: 1.1852 time to fit residues: 265.2682 Evaluate side-chains 208 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 196 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 547 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 54 optimal weight: 0.9980 chunk 41 optimal weight: 0.3980 chunk 65 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 77 optimal weight: 0.0980 chunk 6 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 ASN A 714 GLN B 475 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.105049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.095020 restraints weight = 38615.058| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.55 r_work: 0.3199 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 9931 Z= 0.244 Angle : 0.548 5.105 13480 Z= 0.289 Chirality : 0.046 0.147 1438 Planarity : 0.004 0.072 1761 Dihedral : 5.301 37.578 1581 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.17 % Allowed : 17.81 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.24), residues: 1231 helix: -2.23 (0.55), residues: 73 sheet: 0.13 (0.22), residues: 537 loop : -0.21 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 488 TYR 0.014 0.001 TYR B 597 PHE 0.013 0.001 PHE A 115 TRP 0.014 0.001 TRP B 187 HIS 0.005 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.24 ( 9929) covalent geometry : angle 0.54850 / 0.29 (13476) SS BOND : bond 0.00372 / 0.18 ( 2) SS BOND : angle 0.52588 / 0.28 ( 4) hydrogen bonds : bond 0.03454 / 2.31 ( 469) hydrogen bonds : angle 5.68411 / 4.02 ( 1311) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7879 (mp0) cc_final: 0.7571 (mp0) REVERT: A 478 ASP cc_start: 0.7378 (m-30) cc_final: 0.7120 (m-30) REVERT: A 534 VAL cc_start: 0.8777 (t) cc_final: 0.8498 (p) REVERT: B 41 SER cc_start: 0.7932 (m) cc_final: 0.7597 (p) REVERT: B 359 ILE cc_start: 0.8686 (mt) cc_final: 0.8456 (mm) REVERT: B 610 ASN cc_start: 0.7913 (m-40) cc_final: 0.7677 (m-40) outliers start: 22 outliers final: 16 residues processed: 209 average time/residue: 1.1499 time to fit residues: 259.7745 Evaluate side-chains 217 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain B residue 570 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 120 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 65 optimal weight: 0.0670 chunk 91 optimal weight: 0.0170 chunk 102 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 chunk 110 optimal weight: 0.2980 chunk 24 optimal weight: 0.0020 overall best weight: 0.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN A 556 ASN A 592 ASN A 714 GLN B 475 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.105309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.095493 restraints weight = 38558.777| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.53 r_work: 0.3222 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9931 Z= 0.126 Angle : 0.509 5.368 13480 Z= 0.268 Chirality : 0.045 0.152 1438 Planarity : 0.004 0.071 1761 Dihedral : 4.916 35.338 1581 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.28 % Allowed : 18.80 % Favored : 79.92 % 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 are not related in a simple way. whole: -0.26 (0.24), residues: 1231 helix: -2.01 (0.57), residues: 73 sheet: 0.18 (0.22), residues: 539 loop : -0.12 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 638 TYR 0.008 0.001 TYR B 192 PHE 0.011 0.001 PHE A 115 TRP 0.013 0.001 TRP B 187 HIS 0.002 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 9929) covalent geometry : angle 0.50923 / 0.27 (13476) SS BOND : bond 0.00202 / 0.10 ( 2) SS BOND : angle 0.39870 / 0.21 ( 4) hydrogen bonds : bond 0.02996 / 2.03 ( 469) hydrogen bonds : angle 5.54406 / 3.93 ( 1311) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 204 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7820 (mp0) cc_final: 0.7528 (mp0) REVERT: A 478 ASP cc_start: 0.7335 (m-30) cc_final: 0.7081 (m-30) REVERT: A 534 VAL cc_start: 0.8819 (t) cc_final: 0.8540 (p) REVERT: B 41 SER cc_start: 0.7934 (m) cc_final: 0.7622 (p) REVERT: B 54 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7553 (ptt90) REVERT: B 303 HIS cc_start: 0.8562 (t-90) cc_final: 0.8249 (t-90) REVERT: B 359 ILE cc_start: 0.8672 (mt) cc_final: 0.8446 (mm) REVERT: B 610 ASN cc_start: 0.7813 (m-40) cc_final: 0.7592 (m-40) outliers start: 13 outliers final: 8 residues processed: 210 average time/residue: 1.1447 time to fit residues: 259.7520 Evaluate side-chains 213 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 204 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 112 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 46 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 51 optimal weight: 0.0970 chunk 20 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 chunk 60 optimal weight: 0.2980 chunk 94 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 ASN A 592 ASN A 714 GLN B 475 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.104274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.094441 restraints weight = 38775.136| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.53 r_work: 0.3204 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9931 Z= 0.227 Angle : 0.543 5.114 13480 Z= 0.286 Chirality : 0.046 0.157 1438 Planarity : 0.004 0.072 1761 Dihedral : 5.098 36.057 1581 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.48 % Allowed : 18.90 % Favored : 79.63 % 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 are not related in a simple way. whole: -0.28 (0.24), residues: 1231 helix: -2.18 (0.55), residues: 73 sheet: 0.20 (0.22), residues: 536 loop : -0.15 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 638 TYR 0.014 0.001 TYR B 597 PHE 0.011 0.001 PHE A 365 TRP 0.013 0.001 TRP B 187 HIS 0.004 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.23 ( 9929) covalent geometry : angle 0.54326 / 0.29 (13476) SS BOND : bond 0.00378 / 0.18 ( 2) SS BOND : angle 0.51922 / 0.28 ( 4) hydrogen bonds : bond 0.03322 / 2.23 ( 469) hydrogen bonds : angle 5.58469 / 3.95 ( 1311) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 205 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7797 (mp0) cc_final: 0.7470 (mp0) REVERT: A 478 ASP cc_start: 0.7351 (m-30) cc_final: 0.7091 (m-30) REVERT: A 534 VAL cc_start: 0.8815 (t) cc_final: 0.8539 (p) REVERT: B 41 SER cc_start: 0.7979 (m) cc_final: 0.7635 (p) REVERT: B 54 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7587 (ptt90) REVERT: B 303 HIS cc_start: 0.8560 (t-90) cc_final: 0.8255 (t-90) REVERT: B 610 ASN cc_start: 0.7913 (m-40) cc_final: 0.7678 (m-40) outliers start: 15 outliers final: 10 residues processed: 212 average time/residue: 1.1130 time to fit residues: 254.8130 Evaluate side-chains 213 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 202 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain B residue 570 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 97 optimal weight: 0.0470 chunk 109 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 92 optimal weight: 0.1980 chunk 18 optimal weight: 0.9980 chunk 12 optimal weight: 0.1980 chunk 63 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 96 optimal weight: 0.0770 chunk 34 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.2236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN A 592 ASN A 714 GLN B 475 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.105520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.095779 restraints weight = 38634.931| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.51 r_work: 0.3227 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9931 Z= 0.135 Angle : 0.513 5.230 13480 Z= 0.270 Chirality : 0.045 0.157 1438 Planarity : 0.004 0.071 1761 Dihedral : 4.856 35.086 1581 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.28 % Allowed : 19.19 % Favored : 79.53 % 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 are not related in a simple way. whole: -0.21 (0.24), residues: 1231 helix: -1.99 (0.57), residues: 73 sheet: 0.25 (0.22), residues: 534 loop : -0.13 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 638 TYR 0.009 0.001 TYR B 192 PHE 0.009 0.001 PHE A 115 TRP 0.013 0.001 TRP B 187 HIS 0.003 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 9929) covalent geometry : angle 0.51297 / 0.27 (13476) SS BOND : bond 0.00210 / 0.10 ( 2) SS BOND : angle 0.42829 / 0.23 ( 4) hydrogen bonds : bond 0.02999 / 2.04 ( 469) hydrogen bonds : angle 5.49166 / 3.90 ( 1311) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7696.37 seconds wall clock time: 130 minutes 58.72 seconds (7858.72 seconds total)