Starting phenix.real_space_refine on Fri Aug 22 19:40:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qlo_18486/08_2025/8qlo_18486.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qlo_18486/08_2025/8qlo_18486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qlo_18486/08_2025/8qlo_18486.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qlo_18486/08_2025/8qlo_18486.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qlo_18486/08_2025/8qlo_18486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qlo_18486/08_2025/8qlo_18486.map" } resolution = 2.57 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= 0.008 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 22 5.16 5 C 4726 2.51 5 N 1203 2.21 5 O 1331 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 7282 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3657 Classifications: {'peptide': 455} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 431} Chain breaks: 1 Chain: "A" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3625 Classifications: {'peptide': 437} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 419} Time building chain proxies: 1.71, per 1000 atoms: 0.23 Number of scatterers: 7282 At special positions: 0 Unit cell: (80.6, 81.25, 124.8, 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 22 16.00 O 1331 8.00 N 1203 7.00 C 4726 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: 0.46 Conformation dependent library (CDL) restraints added in 402.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1688 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 12 sheets defined 41.9% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 22 through 30 Processing helix chain 'B' and resid 46 through 60 Processing helix chain 'B' and resid 77 through 82 Processing helix chain 'B' and resid 97 through 106 removed outlier: 3.580A pdb=" N ILE B 101 " --> pdb=" O THR B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 132 removed outlier: 3.731A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 151 removed outlier: 3.694A pdb=" N TYR B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 248 through 264 removed outlier: 3.688A pdb=" N ALA B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 351 Processing helix chain 'B' and resid 366 through 377 removed outlier: 3.612A pdb=" N TRP B 370 " --> pdb=" O ASN B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 465 removed outlier: 3.731A pdb=" N LEU B 465 " --> pdb=" O ALA B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 482 removed outlier: 4.258A pdb=" N PHE B 482 " --> pdb=" O VAL B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 493 removed outlier: 3.706A pdb=" N SER B 493 " --> pdb=" O ILE B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 506 No H-bonds generated for 'chain 'B' and resid 504 through 506' Processing helix chain 'A' and resid 14 through 28 Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 71 through 89 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.743A pdb=" N ILE A 113 " --> pdb=" O PRO A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 138 Processing helix chain 'A' and resid 146 through 159 removed outlier: 3.721A pdb=" N SER A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 222 through 226 removed outlier: 4.330A pdb=" N HIS A 225 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 257 through 280 Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 353 through 368 Processing helix chain 'A' and resid 369 through 385 Processing helix chain 'A' and resid 423 through 436 Processing sheet with id=AA1, first strand: chain 'B' and resid 2 through 3 removed outlier: 6.430A pdb=" N LYS B 2 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 5 through 6 removed outlier: 6.607A pdb=" N SER B 417 " --> pdb=" O VAL B 413 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ILE B 443 " --> pdb=" O THR B 389 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR B 389 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ILE B 445 " --> pdb=" O THR B 387 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR B 387 " --> pdb=" O ILE B 445 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL B 386 " --> pdb=" O ILE B 359 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 19 through 20 Processing sheet with id=AA4, first strand: chain 'B' and resid 91 through 95 removed outlier: 6.116A pdb=" N SER B 41 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LYS B 94 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL B 43 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLY B 42 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL B 142 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL B 44 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 286 through 287 Processing sheet with id=AA6, first strand: chain 'B' and resid 321 through 322 Processing sheet with id=AA7, first strand: chain 'B' and resid 425 through 426 Processing sheet with id=AA8, first strand: chain 'A' and resid 31 through 33 removed outlier: 8.307A pdb=" N LEU A 61 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N PHE A 6 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ALA A 63 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N SER A 8 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE A 60 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU A 97 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU A 62 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL A 118 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 283 through 285 Processing sheet with id=AB1, first strand: chain 'A' and resid 283 through 285 removed outlier: 7.438A pdb=" N TRP A 175 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLU A 406 " --> pdb=" O TRP A 175 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N SER A 177 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR A 402 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 208 through 210 Processing sheet with id=AB3, first strand: chain 'A' and resid 304 through 305 338 hydrogen bonds defined for protein. 912 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: 1.09 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1216 1.30 - 1.43: 1942 1.43 - 1.55: 4274 1.55 - 1.68: 0 1.68 - 1.81: 34 Bond restraints: 7466 Sorted by residual: bond pdb=" C PRO B 404 " pdb=" O PRO B 404 " ideal model delta sigma weight residual 1.235 1.169 0.066 1.30e-02 5.92e+03 2.55e+01 bond pdb=" C PRO B 268 " pdb=" O PRO B 268 " ideal model delta sigma weight residual 1.235 1.173 0.062 1.30e-02 5.92e+03 2.25e+01 bond pdb=" C PRO B 76 " pdb=" O PRO B 76 " ideal model delta sigma weight residual 1.238 1.174 0.064 1.35e-02 5.49e+03 2.24e+01 bond pdb=" CA TYR B 425 " pdb=" C TYR B 425 " ideal model delta sigma weight residual 1.521 1.471 0.051 1.19e-02 7.06e+03 1.81e+01 bond pdb=" C PRO B 499 " pdb=" O PRO B 499 " ideal model delta sigma weight residual 1.240 1.193 0.047 1.12e-02 7.97e+03 1.78e+01 ... (remaining 7461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 8839 1.83 - 3.66: 1100 3.66 - 5.49: 119 5.49 - 7.32: 26 7.32 - 9.15: 6 Bond angle restraints: 10090 Sorted by residual: angle pdb=" N LEU A 37 " pdb=" CA LEU A 37 " pdb=" C LEU A 37 " ideal model delta sigma weight residual 113.15 104.98 8.17 1.19e+00 7.06e-01 4.72e+01 angle pdb=" N PRO B 499 " pdb=" CA PRO B 499 " pdb=" C PRO B 499 " ideal model delta sigma weight residual 110.70 103.30 7.40 1.22e+00 6.72e-01 3.68e+01 angle pdb=" N ILE A 58 " pdb=" CA ILE A 58 " pdb=" C ILE A 58 " ideal model delta sigma weight residual 113.07 105.02 8.05 1.36e+00 5.41e-01 3.51e+01 angle pdb=" N TYR B 472 " pdb=" CA TYR B 472 " pdb=" C TYR B 472 " ideal model delta sigma weight residual 111.33 104.31 7.02 1.21e+00 6.83e-01 3.37e+01 angle pdb=" N ILE B 70 " pdb=" CA ILE B 70 " pdb=" C ILE B 70 " ideal model delta sigma weight residual 111.56 106.68 4.88 8.60e-01 1.35e+00 3.22e+01 ... (remaining 10085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.89: 3833 14.89 - 29.79: 441 29.79 - 44.68: 141 44.68 - 59.57: 37 59.57 - 74.47: 21 Dihedral angle restraints: 4473 sinusoidal: 1858 harmonic: 2615 Sorted by residual: dihedral pdb=" C TYR B 425 " pdb=" N TYR B 425 " pdb=" CA TYR B 425 " pdb=" CB TYR B 425 " ideal model delta harmonic sigma weight residual -122.60 -111.27 -11.33 0 2.50e+00 1.60e-01 2.06e+01 dihedral pdb=" CA ARG B 213 " pdb=" C ARG B 213 " pdb=" N LEU B 214 " pdb=" CA LEU B 214 " ideal model delta harmonic sigma weight residual 180.00 163.03 16.97 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" N ALA A 63 " pdb=" C ALA A 63 " pdb=" CA ALA A 63 " pdb=" CB ALA A 63 " ideal model delta harmonic sigma weight residual 122.90 114.66 8.24 0 2.50e+00 1.60e-01 1.09e+01 ... (remaining 4470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 633 0.051 - 0.103: 238 0.103 - 0.154: 137 0.154 - 0.205: 58 0.205 - 0.257: 10 Chirality restraints: 1076 Sorted by residual: chirality pdb=" CA VAL B 423 " pdb=" N VAL B 423 " pdb=" C VAL B 423 " pdb=" CB VAL B 423 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB VAL A 334 " pdb=" CA VAL A 334 " pdb=" CG1 VAL A 334 " pdb=" CG2 VAL A 334 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ILE B 122 " pdb=" N ILE B 122 " pdb=" C ILE B 122 " pdb=" CB ILE B 122 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 1073 not shown) Planarity restraints: 1288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 40 " 0.016 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C LYS B 40 " -0.059 2.00e-02 2.50e+03 pdb=" O LYS B 40 " 0.022 2.00e-02 2.50e+03 pdb=" N SER B 41 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 24 " -0.272 9.50e-02 1.11e+02 1.22e-01 9.09e+00 pdb=" NE ARG B 24 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 24 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 24 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 24 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 315 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.55e+00 pdb=" C GLY B 315 " 0.041 2.00e-02 2.50e+03 pdb=" O GLY B 315 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU B 316 " -0.014 2.00e-02 2.50e+03 ... (remaining 1285 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 742 2.75 - 3.29: 7331 3.29 - 3.82: 12272 3.82 - 4.36: 15855 4.36 - 4.90: 25514 Nonbonded interactions: 61714 Sorted by model distance: nonbonded pdb=" N GLU A 284 " pdb=" OE1 GLU A 284 " model vdw 2.209 3.120 nonbonded pdb=" O LEU A 227 " pdb=" OG1 THR A 230 " model vdw 2.223 3.040 nonbonded pdb=" OD1 ASN B 307 " pdb=" N ASP B 309 " model vdw 2.264 3.120 nonbonded pdb=" N GLU B 132 " pdb=" OE1 GLU B 132 " model vdw 2.296 3.120 nonbonded pdb=" OG SER A 173 " pdb=" O VAL A 408 " model vdw 2.321 3.040 ... (remaining 61709 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: 0.010 Normalize map: mean=0, sd=1: 3.250 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: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.900 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 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 : 0.009 0.069 7466 Z= 0.651 Angle : 1.180 9.151 10090 Z= 0.854 Chirality : 0.076 0.257 1076 Planarity : 0.007 0.122 1288 Dihedral : 15.285 74.466 2785 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.51 % Favored : 95.37 % Rotamer: Outliers : 2.16 % Allowed : 17.15 % Favored : 80.69 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.50 % 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: -1.41 (0.27), residues: 886 helix: -0.42 (0.28), residues: 307 sheet: -1.11 (0.39), residues: 171 loop : -1.14 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 209 TYR 0.021 0.002 TYR B 472 PHE 0.022 0.002 PHE B 373 TRP 0.022 0.002 TRP B 370 HIS 0.003 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00895 ( 7466) covalent geometry : angle 1.17977 (10090) hydrogen bonds : bond 0.17684 ( 332) hydrogen bonds : angle 7.99214 ( 912) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.8138 (m-10) cc_final: 0.7779 (p90) REVERT: B 87 ASP cc_start: 0.8225 (t0) cc_final: 0.7190 (t70) REVERT: B 89 ASP cc_start: 0.7473 (m-30) cc_final: 0.6974 (m-30) REVERT: B 135 LYS cc_start: 0.7348 (mttt) cc_final: 0.7081 (pptt) REVERT: B 225 ARG cc_start: 0.7472 (mtp180) cc_final: 0.7137 (mtp180) REVERT: A 44 ASP cc_start: 0.6514 (OUTLIER) cc_final: 0.6240 (p0) REVERT: A 54 ARG cc_start: 0.7702 (mtm110) cc_final: 0.7428 (ptp-110) REVERT: A 84 VAL cc_start: 0.8370 (t) cc_final: 0.8097 (p) REVERT: A 90 ASP cc_start: 0.7941 (t0) cc_final: 0.7270 (t0) REVERT: A 91 ASP cc_start: 0.8109 (m-30) cc_final: 0.7782 (t70) REVERT: A 263 ARG cc_start: 0.7609 (ttp80) cc_final: 0.7117 (tmm-80) REVERT: A 267 GLN cc_start: 0.8385 (mm110) cc_final: 0.7828 (mp10) outliers start: 17 outliers final: 8 residues processed: 157 average time/residue: 0.4503 time to fit residues: 75.0814 Evaluate side-chains 101 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 255 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 HIS B 439 ASN A 15 ASN A 155 GLN A 364 GLN A 434 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.120156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.090937 restraints weight = 12481.822| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 3.39 r_work: 0.3241 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7466 Z= 0.198 Angle : 0.630 6.519 10090 Z= 0.329 Chirality : 0.044 0.232 1076 Planarity : 0.004 0.038 1288 Dihedral : 5.726 49.092 971 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.56 % Allowed : 20.08 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.31 (0.28), residues: 886 helix: 0.84 (0.28), residues: 322 sheet: -0.99 (0.39), residues: 163 loop : -0.62 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 209 TYR 0.015 0.002 TYR B 285 PHE 0.017 0.002 PHE A 158 TRP 0.021 0.002 TRP B 370 HIS 0.004 0.001 HIS A 9 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 7466) covalent geometry : angle 0.63048 (10090) hydrogen bonds : bond 0.05045 ( 332) hydrogen bonds : angle 5.56261 ( 912) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.8551 (m-10) cc_final: 0.7858 (p90) REVERT: B 87 ASP cc_start: 0.8710 (t0) cc_final: 0.8013 (t70) REVERT: B 135 LYS cc_start: 0.7645 (mttt) cc_final: 0.7248 (pptt) REVERT: B 148 TYR cc_start: 0.6919 (OUTLIER) cc_final: 0.6306 (m-80) REVERT: B 400 GLU cc_start: 0.7448 (mt-10) cc_final: 0.6912 (mp0) REVERT: B 471 ILE cc_start: 0.8310 (mt) cc_final: 0.7984 (mp) REVERT: A 54 ARG cc_start: 0.7981 (mtm110) cc_final: 0.7615 (ptp-110) REVERT: A 88 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8423 (mm) REVERT: A 91 ASP cc_start: 0.8719 (m-30) cc_final: 0.8343 (t0) REVERT: A 398 GLU cc_start: 0.8727 (mp0) cc_final: 0.7993 (tm-30) outliers start: 28 outliers final: 12 residues processed: 116 average time/residue: 0.4918 time to fit residues: 60.8183 Evaluate side-chains 96 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 423 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 26 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 0.0980 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 75 optimal weight: 0.0980 chunk 54 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.122862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.093812 restraints weight = 12347.140| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 3.39 r_work: 0.3294 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7466 Z= 0.125 Angle : 0.561 6.462 10090 Z= 0.291 Chirality : 0.042 0.239 1076 Planarity : 0.004 0.038 1288 Dihedral : 4.766 36.269 960 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.18 % Allowed : 21.09 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.09 (0.28), residues: 886 helix: 1.14 (0.28), residues: 326 sheet: -0.94 (0.39), residues: 163 loop : -0.29 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 263 TYR 0.012 0.001 TYR A 293 PHE 0.020 0.001 PHE A 259 TRP 0.017 0.001 TRP B 370 HIS 0.003 0.001 HIS A 9 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7466) covalent geometry : angle 0.56121 (10090) hydrogen bonds : bond 0.04283 ( 332) hydrogen bonds : angle 5.19612 ( 912) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.8538 (m-10) cc_final: 0.7830 (p90) REVERT: B 87 ASP cc_start: 0.8689 (t0) cc_final: 0.8054 (t70) REVERT: B 135 LYS cc_start: 0.7673 (mttt) cc_final: 0.7127 (pptt) REVERT: B 148 TYR cc_start: 0.6881 (OUTLIER) cc_final: 0.6197 (m-80) REVERT: B 400 GLU cc_start: 0.7364 (mt-10) cc_final: 0.6749 (mp0) REVERT: B 471 ILE cc_start: 0.8326 (mt) cc_final: 0.7988 (mp) REVERT: A 38 PHE cc_start: 0.7997 (m-80) cc_final: 0.7768 (m-80) REVERT: A 41 LYS cc_start: 0.5542 (OUTLIER) cc_final: 0.4826 (mtmm) REVERT: A 54 ARG cc_start: 0.7972 (mtm110) cc_final: 0.7711 (ptp-110) REVERT: A 77 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6918 (mm-30) REVERT: A 88 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8376 (mm) REVERT: A 345 LYS cc_start: 0.8412 (mptt) cc_final: 0.8002 (mmtm) REVERT: A 398 GLU cc_start: 0.8735 (mp0) cc_final: 0.7957 (tm-30) outliers start: 25 outliers final: 7 residues processed: 109 average time/residue: 0.5476 time to fit residues: 63.4226 Evaluate side-chains 93 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 423 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.114443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.085458 restraints weight = 12739.449| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.34 r_work: 0.3146 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 7466 Z= 0.309 Angle : 0.686 8.785 10090 Z= 0.354 Chirality : 0.046 0.242 1076 Planarity : 0.004 0.057 1288 Dihedral : 5.270 42.342 959 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.83 % Allowed : 21.35 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.19 (0.27), residues: 886 helix: 0.77 (0.27), residues: 323 sheet: -0.86 (0.38), residues: 171 loop : -0.41 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 263 TYR 0.017 0.002 TYR B 285 PHE 0.017 0.002 PHE A 38 TRP 0.018 0.002 TRP B 370 HIS 0.009 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00720 ( 7466) covalent geometry : angle 0.68580 (10090) hydrogen bonds : bond 0.05380 ( 332) hydrogen bonds : angle 5.53808 ( 912) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 95 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.8613 (m-10) cc_final: 0.7951 (p90) REVERT: B 87 ASP cc_start: 0.8765 (t0) cc_final: 0.8190 (t70) REVERT: B 135 LYS cc_start: 0.7785 (mttt) cc_final: 0.7144 (pptt) REVERT: B 148 TYR cc_start: 0.7233 (OUTLIER) cc_final: 0.6403 (m-80) REVERT: B 330 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7158 (pp) REVERT: B 400 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7453 (mp0) REVERT: B 471 ILE cc_start: 0.8429 (mt) cc_final: 0.8103 (mp) REVERT: A 5 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.8063 (mp) REVERT: A 41 LYS cc_start: 0.5656 (OUTLIER) cc_final: 0.4980 (mtmm) REVERT: A 54 ARG cc_start: 0.7947 (mtm110) cc_final: 0.7637 (ptp-110) REVERT: A 88 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8451 (mm) REVERT: A 91 ASP cc_start: 0.8693 (m-30) cc_final: 0.8452 (t0) REVERT: A 212 ASN cc_start: 0.8850 (t0) cc_final: 0.8325 (t0) REVERT: A 267 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8210 (mm-40) REVERT: A 345 LYS cc_start: 0.8434 (mptt) cc_final: 0.7976 (mmtm) REVERT: A 398 GLU cc_start: 0.8783 (mp0) cc_final: 0.8010 (tm-30) outliers start: 38 outliers final: 14 residues processed: 121 average time/residue: 0.4411 time to fit residues: 57.5015 Evaluate side-chains 101 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 423 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.0980 chunk 53 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 54 optimal weight: 0.0770 chunk 66 optimal weight: 0.3980 chunk 48 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN A 234 ASN A 364 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.121032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.092037 restraints weight = 12414.354| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 3.37 r_work: 0.3263 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7466 Z= 0.119 Angle : 0.566 7.917 10090 Z= 0.292 Chirality : 0.042 0.315 1076 Planarity : 0.004 0.059 1288 Dihedral : 4.856 41.586 959 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.43 % Allowed : 23.00 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.26 (0.28), residues: 886 helix: 1.21 (0.28), residues: 325 sheet: -0.63 (0.39), residues: 163 loop : -0.22 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 263 TYR 0.012 0.001 TYR A 293 PHE 0.018 0.001 PHE A 259 TRP 0.019 0.001 TRP B 370 HIS 0.007 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7466) covalent geometry : angle 0.56591 (10090) hydrogen bonds : bond 0.04046 ( 332) hydrogen bonds : angle 5.05831 ( 912) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.8576 (m-10) cc_final: 0.7892 (p90) REVERT: B 148 TYR cc_start: 0.7105 (OUTLIER) cc_final: 0.6222 (m-80) REVERT: B 330 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.6972 (pp) REVERT: B 400 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7129 (mp0) REVERT: A 41 LYS cc_start: 0.5675 (OUTLIER) cc_final: 0.5081 (mtmm) REVERT: A 54 ARG cc_start: 0.7843 (mtm110) cc_final: 0.7389 (ptp-110) REVERT: A 87 GLN cc_start: 0.9077 (tm-30) cc_final: 0.8734 (tm-30) REVERT: A 91 ASP cc_start: 0.8671 (m-30) cc_final: 0.8440 (t0) REVERT: A 184 GLU cc_start: 0.8317 (pt0) cc_final: 0.7589 (tm-30) REVERT: A 186 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6997 (mtt-85) REVERT: A 212 ASN cc_start: 0.8880 (t0) cc_final: 0.8331 (t0) REVERT: A 398 GLU cc_start: 0.8736 (mp0) cc_final: 0.7866 (tm-30) outliers start: 27 outliers final: 9 residues processed: 115 average time/residue: 0.4625 time to fit residues: 56.9693 Evaluate side-chains 100 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 423 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 53 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** 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 = 0.3787 r_free = 0.3787 target = 0.116565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.087673 restraints weight = 12607.734| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 3.35 r_work: 0.3176 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7466 Z= 0.228 Angle : 0.624 7.945 10090 Z= 0.324 Chirality : 0.045 0.286 1076 Planarity : 0.004 0.067 1288 Dihedral : 5.039 43.804 959 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.32 % Allowed : 22.74 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.13 (0.28), residues: 886 helix: 1.01 (0.27), residues: 324 sheet: -0.65 (0.39), residues: 166 loop : -0.22 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 263 TYR 0.013 0.001 TYR B 285 PHE 0.016 0.002 PHE A 259 TRP 0.014 0.002 TRP B 370 HIS 0.008 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00533 ( 7466) covalent geometry : angle 0.62356 (10090) hydrogen bonds : bond 0.04729 ( 332) hydrogen bonds : angle 5.27296 ( 912) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 87 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: B 37 TYR cc_start: 0.8618 (m-10) cc_final: 0.7950 (p90) REVERT: B 87 ASP cc_start: 0.8735 (t0) cc_final: 0.8076 (t0) REVERT: B 148 TYR cc_start: 0.7259 (OUTLIER) cc_final: 0.6308 (m-80) REVERT: B 330 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7140 (pp) REVERT: B 400 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7355 (mp0) REVERT: A 5 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.8048 (mp) REVERT: A 41 LYS cc_start: 0.5782 (OUTLIER) cc_final: 0.5197 (mtmm) REVERT: A 54 ARG cc_start: 0.7839 (mtm110) cc_final: 0.7445 (ptp-110) REVERT: A 87 GLN cc_start: 0.9050 (tm-30) cc_final: 0.8696 (tm-30) REVERT: A 212 ASN cc_start: 0.8859 (t0) cc_final: 0.8285 (t0) REVERT: A 267 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8183 (mm-40) REVERT: A 398 GLU cc_start: 0.8817 (mp0) cc_final: 0.7834 (tm-30) outliers start: 34 outliers final: 15 residues processed: 108 average time/residue: 0.4418 time to fit residues: 51.4116 Evaluate side-chains 102 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 417 SER Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 423 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 54 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 1 optimal weight: 0.0980 chunk 52 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** 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 = 0.3849 r_free = 0.3849 target = 0.120304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.091379 restraints weight = 12512.657| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 3.39 r_work: 0.3258 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7466 Z= 0.131 Angle : 0.590 8.144 10090 Z= 0.303 Chirality : 0.042 0.293 1076 Planarity : 0.004 0.061 1288 Dihedral : 4.834 43.424 959 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.05 % Allowed : 25.03 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.28), residues: 886 helix: 1.14 (0.28), residues: 325 sheet: -0.63 (0.39), residues: 166 loop : -0.14 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 263 TYR 0.018 0.001 TYR B 48 PHE 0.017 0.001 PHE A 259 TRP 0.018 0.001 TRP B 370 HIS 0.007 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 7466) covalent geometry : angle 0.58991 (10090) hydrogen bonds : bond 0.04051 ( 332) hydrogen bonds : angle 5.08966 ( 912) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.8642 (m-10) cc_final: 0.7930 (p90) REVERT: B 87 ASP cc_start: 0.8708 (t0) cc_final: 0.8049 (t0) REVERT: B 148 TYR cc_start: 0.7231 (OUTLIER) cc_final: 0.6309 (m-80) REVERT: B 330 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7023 (pp) REVERT: B 400 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7254 (mp0) REVERT: A 5 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7973 (mp) REVERT: A 41 LYS cc_start: 0.5626 (OUTLIER) cc_final: 0.5108 (mtmm) REVERT: A 54 ARG cc_start: 0.7812 (mtm110) cc_final: 0.7405 (ptp-110) REVERT: A 87 GLN cc_start: 0.9024 (tm-30) cc_final: 0.8679 (tm-30) REVERT: A 212 ASN cc_start: 0.8894 (t0) cc_final: 0.8312 (t0) outliers start: 24 outliers final: 13 residues processed: 107 average time/residue: 0.4469 time to fit residues: 51.3433 Evaluate side-chains 100 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 423 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 71 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 0.0060 chunk 26 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 GLN A 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.119839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.090852 restraints weight = 12511.475| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.39 r_work: 0.3243 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7466 Z= 0.143 Angle : 0.605 9.291 10090 Z= 0.308 Chirality : 0.043 0.282 1076 Planarity : 0.004 0.057 1288 Dihedral : 4.790 44.078 959 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.30 % Allowed : 25.29 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.28 (0.28), residues: 886 helix: 1.25 (0.28), residues: 319 sheet: -0.61 (0.39), residues: 171 loop : -0.20 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 263 TYR 0.013 0.001 TYR A 293 PHE 0.022 0.002 PHE A 223 TRP 0.014 0.001 TRP B 370 HIS 0.007 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 7466) covalent geometry : angle 0.60464 (10090) hydrogen bonds : bond 0.04073 ( 332) hydrogen bonds : angle 5.06607 ( 912) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.8665 (m-10) cc_final: 0.7949 (p90) REVERT: B 148 TYR cc_start: 0.7204 (OUTLIER) cc_final: 0.6283 (m-80) REVERT: B 330 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7033 (pp) REVERT: B 400 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7257 (mp0) REVERT: B 497 LYS cc_start: 0.9241 (tppt) cc_final: 0.8897 (tmmt) REVERT: B 503 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.7923 (m-80) REVERT: A 5 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7992 (mp) REVERT: A 41 LYS cc_start: 0.5586 (OUTLIER) cc_final: 0.5053 (mtmm) REVERT: A 54 ARG cc_start: 0.7811 (mtm110) cc_final: 0.7391 (ptp-110) REVERT: A 87 GLN cc_start: 0.9053 (tm-30) cc_final: 0.8763 (tm-30) REVERT: A 184 GLU cc_start: 0.8228 (pt0) cc_final: 0.7870 (pp20) REVERT: A 212 ASN cc_start: 0.8898 (t0) cc_final: 0.8317 (t0) outliers start: 26 outliers final: 12 residues processed: 103 average time/residue: 0.4136 time to fit residues: 45.9660 Evaluate side-chains 99 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 503 PHE Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 423 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 40 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.120180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.091240 restraints weight = 12366.704| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 3.38 r_work: 0.3261 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7466 Z= 0.148 Angle : 0.625 9.787 10090 Z= 0.318 Chirality : 0.043 0.280 1076 Planarity : 0.004 0.054 1288 Dihedral : 4.702 44.479 957 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.54 % Allowed : 26.43 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.35 (0.29), residues: 886 helix: 1.36 (0.28), residues: 318 sheet: -0.60 (0.39), residues: 171 loop : -0.19 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 209 TYR 0.012 0.001 TYR A 293 PHE 0.023 0.001 PHE A 259 TRP 0.014 0.001 TRP B 370 HIS 0.007 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 7466) covalent geometry : angle 0.62547 (10090) hydrogen bonds : bond 0.04104 ( 332) hydrogen bonds : angle 5.05177 ( 912) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.8660 (m-10) cc_final: 0.7955 (p90) REVERT: B 87 ASP cc_start: 0.8725 (t0) cc_final: 0.8315 (p0) REVERT: B 148 TYR cc_start: 0.7185 (OUTLIER) cc_final: 0.6263 (m-80) REVERT: B 330 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7103 (pp) REVERT: B 400 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7290 (mp0) REVERT: B 497 LYS cc_start: 0.9237 (tppt) cc_final: 0.8903 (tmmt) REVERT: A 5 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7995 (mp) REVERT: A 41 LYS cc_start: 0.5612 (OUTLIER) cc_final: 0.5100 (mtmm) REVERT: A 54 ARG cc_start: 0.7807 (mtm110) cc_final: 0.7366 (ptp-110) REVERT: A 86 LYS cc_start: 0.8817 (tppp) cc_final: 0.8410 (mptt) REVERT: A 87 GLN cc_start: 0.9102 (tm-30) cc_final: 0.8729 (tm-30) REVERT: A 184 GLU cc_start: 0.8228 (pt0) cc_final: 0.7882 (pp20) REVERT: A 212 ASN cc_start: 0.8924 (t0) cc_final: 0.8330 (t0) REVERT: A 223 PHE cc_start: 0.6101 (m-80) cc_final: 0.5898 (m-80) outliers start: 20 outliers final: 12 residues processed: 99 average time/residue: 0.4448 time to fit residues: 47.2364 Evaluate side-chains 103 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 423 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 57 optimal weight: 0.3980 chunk 21 optimal weight: 0.1980 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** 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 = 0.3852 r_free = 0.3852 target = 0.120606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.091803 restraints weight = 12521.052| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 3.38 r_work: 0.3265 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7466 Z= 0.138 Angle : 0.637 9.713 10090 Z= 0.322 Chirality : 0.042 0.275 1076 Planarity : 0.004 0.050 1288 Dihedral : 4.644 44.710 957 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.03 % Allowed : 27.06 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.29), residues: 886 helix: 1.43 (0.28), residues: 318 sheet: -0.55 (0.40), residues: 169 loop : -0.17 (0.33), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 209 TYR 0.027 0.001 TYR B 48 PHE 0.016 0.001 PHE A 255 TRP 0.015 0.001 TRP B 370 HIS 0.006 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 7466) covalent geometry : angle 0.63748 (10090) hydrogen bonds : bond 0.03937 ( 332) hydrogen bonds : angle 5.03807 ( 912) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: B 37 TYR cc_start: 0.8655 (m-10) cc_final: 0.7940 (p90) REVERT: B 87 ASP cc_start: 0.8707 (t0) cc_final: 0.8289 (p0) REVERT: B 148 TYR cc_start: 0.7163 (OUTLIER) cc_final: 0.6238 (m-80) REVERT: B 330 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7067 (pp) REVERT: B 400 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7242 (mp0) REVERT: B 497 LYS cc_start: 0.9221 (tppt) cc_final: 0.8891 (tmmt) REVERT: A 5 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7943 (mp) REVERT: A 41 LYS cc_start: 0.5624 (OUTLIER) cc_final: 0.5219 (mtmm) REVERT: A 54 ARG cc_start: 0.7782 (mtm110) cc_final: 0.7428 (mtm110) REVERT: A 86 LYS cc_start: 0.8800 (tppp) cc_final: 0.8345 (mptt) REVERT: A 87 GLN cc_start: 0.9189 (tm-30) cc_final: 0.8842 (tm-30) REVERT: A 184 GLU cc_start: 0.8161 (pt0) cc_final: 0.7826 (pp20) REVERT: A 194 MET cc_start: 0.7254 (ttp) cc_final: 0.6442 (pp-130) REVERT: A 212 ASN cc_start: 0.8918 (t0) cc_final: 0.8324 (t0) outliers start: 16 outliers final: 12 residues processed: 106 average time/residue: 0.4302 time to fit residues: 49.1981 Evaluate side-chains 105 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 423 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 56 optimal weight: 0.0010 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 0.0070 chunk 17 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.121124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.092173 restraints weight = 12527.905| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 3.41 r_work: 0.3271 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7466 Z= 0.135 Angle : 0.639 9.984 10090 Z= 0.322 Chirality : 0.042 0.271 1076 Planarity : 0.004 0.048 1288 Dihedral : 4.604 44.832 957 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.41 % Allowed : 27.32 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.46 (0.29), residues: 886 helix: 1.58 (0.28), residues: 312 sheet: -0.66 (0.39), residues: 177 loop : -0.15 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 209 TYR 0.012 0.001 TYR A 293 PHE 0.025 0.001 PHE A 259 TRP 0.014 0.002 TRP B 370 HIS 0.006 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 7466) covalent geometry : angle 0.63892 (10090) hydrogen bonds : bond 0.03917 ( 332) hydrogen bonds : angle 5.02791 ( 912) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2667.01 seconds wall clock time: 46 minutes 21.57 seconds (2781.57 seconds total)