Starting phenix.real_space_refine on Sun May 11 02:47:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qlo_18486/05_2025/8qlo_18486.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qlo_18486/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qlo_18486/05_2025/8qlo_18486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qlo_18486/05_2025/8qlo_18486.map" model { file = "/net/cci-nas-00/data/ceres_data/8qlo_18486/05_2025/8qlo_18486.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qlo_18486/05_2025/8qlo_18486.cif" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.88, per 1000 atoms: 0.67 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: 1.63 Conformation dependent library (CDL) restraints added in 982.0 milliseconds 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: 0.96 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: 2.49 Time building geometry restraints manager: 1.94 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: 0.000 Normalize map: mean=0, sd=1: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.160 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.970 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (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 TRP 0.022 0.002 TRP B 370 HIS 0.003 0.001 HIS B 326 PHE 0.022 0.002 PHE B 373 TYR 0.021 0.002 TYR B 472 ARG 0.008 0.001 ARG A 209 Details of bonding type rmsd hydrogen bonds : bond 0.17684 ( 332) hydrogen bonds : angle 7.99214 ( 912) covalent geometry : bond 0.00895 ( 7466) covalent geometry : angle 1.17977 (10090) *********************** 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 : 0.993 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: 1.2208 time to fit residues: 203.7275 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 : 0.812 ------------------------------------------------------------------------------- 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 74 optimal weight: 2.9990 chunk 66 optimal weight: 0.0170 chunk 37 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 234 ASN A 434 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.124034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.095228 restraints weight = 12130.694| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 3.34 r_work: 0.3324 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1920 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= 0.142 Angle : 0.602 7.362 10090 Z= 0.313 Chirality : 0.043 0.226 1076 Planarity : 0.004 0.038 1288 Dihedral : 5.496 50.416 971 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.18 % Allowed : 19.57 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.28), residues: 886 helix: 0.85 (0.28), residues: 325 sheet: -0.86 (0.40), residues: 163 loop : -0.57 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 370 HIS 0.002 0.001 HIS A 9 PHE 0.016 0.002 PHE A 259 TYR 0.012 0.001 TYR B 262 ARG 0.006 0.001 ARG A 209 Details of bonding type rmsd hydrogen bonds : bond 0.04689 ( 332) hydrogen bonds : angle 5.50789 ( 912) covalent geometry : bond 0.00316 ( 7466) covalent geometry : angle 0.60213 (10090) *********************** 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 127 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.8509 (m-10) cc_final: 0.7852 (p90) REVERT: B 87 ASP cc_start: 0.8571 (t0) cc_final: 0.7930 (t70) REVERT: B 135 LYS cc_start: 0.7537 (mttt) cc_final: 0.7222 (pptt) REVERT: B 148 TYR cc_start: 0.6758 (OUTLIER) cc_final: 0.6141 (m-80) REVERT: B 400 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6638 (mp0) REVERT: A 41 LYS cc_start: 0.5632 (OUTLIER) cc_final: 0.5382 (ptmm) REVERT: A 54 ARG cc_start: 0.7999 (mtm110) cc_final: 0.7723 (ptp-110) REVERT: A 77 GLU cc_start: 0.7372 (mp0) cc_final: 0.7053 (mp0) REVERT: A 88 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8412 (mm) REVERT: A 91 ASP cc_start: 0.8669 (m-30) cc_final: 0.8245 (t0) REVERT: A 345 LYS cc_start: 0.8333 (mptt) cc_final: 0.8026 (mmtm) REVERT: A 398 GLU cc_start: 0.8725 (mp0) cc_final: 0.8016 (tm-30) outliers start: 25 outliers final: 7 residues processed: 118 average time/residue: 1.0184 time to fit residues: 128.2178 Evaluate side-chains 96 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 148 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 58 ILE 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 423 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 60 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.121999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.093013 restraints weight = 12393.534| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 3.39 r_work: 0.3279 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7466 Z= 0.145 Angle : 0.565 6.442 10090 Z= 0.293 Chirality : 0.042 0.232 1076 Planarity : 0.004 0.039 1288 Dihedral : 4.723 36.386 960 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.18 % Allowed : 20.33 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.28), residues: 886 helix: 1.19 (0.28), residues: 325 sheet: -0.90 (0.39), residues: 163 loop : -0.35 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 370 HIS 0.003 0.001 HIS A 9 PHE 0.013 0.001 PHE A 158 TYR 0.013 0.001 TYR B 285 ARG 0.016 0.001 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.04382 ( 332) hydrogen bonds : angle 5.21237 ( 912) covalent geometry : bond 0.00332 ( 7466) covalent geometry : angle 0.56494 (10090) *********************** 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 118 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.8558 (m-10) cc_final: 0.7857 (p90) REVERT: B 87 ASP cc_start: 0.8639 (t0) cc_final: 0.8018 (t70) REVERT: B 135 LYS cc_start: 0.7675 (mttt) cc_final: 0.7130 (pptt) REVERT: B 400 GLU cc_start: 0.7323 (mt-10) cc_final: 0.6784 (mp0) REVERT: B 471 ILE cc_start: 0.8300 (mt) cc_final: 0.7965 (mp) REVERT: A 41 LYS cc_start: 0.5682 (OUTLIER) cc_final: 0.5407 (ptmm) REVERT: A 54 ARG cc_start: 0.7940 (mtm110) cc_final: 0.7653 (ptp-110) REVERT: A 77 GLU cc_start: 0.7437 (mp0) cc_final: 0.6925 (mm-30) REVERT: A 88 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8371 (mm) REVERT: A 101 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8173 (mt-10) REVERT: A 345 LYS cc_start: 0.8387 (mptt) cc_final: 0.7975 (mmtm) REVERT: A 398 GLU cc_start: 0.8742 (mp0) cc_final: 0.7941 (tm-30) outliers start: 25 outliers final: 11 residues processed: 108 average time/residue: 1.0100 time to fit residues: 116.6484 Evaluate side-chains 99 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 151 CYS Chi-restraints excluded: chain B residue 330 LEU 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 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 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 63 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 37 optimal weight: 0.4980 chunk 73 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.120849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.091804 restraints weight = 12433.683| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 3.37 r_work: 0.3267 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7466 Z= 0.156 Angle : 0.561 6.444 10090 Z= 0.289 Chirality : 0.042 0.241 1076 Planarity : 0.004 0.037 1288 Dihedral : 4.715 39.514 959 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.94 % Allowed : 20.46 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.28), residues: 886 helix: 1.34 (0.28), residues: 324 sheet: -0.80 (0.38), residues: 165 loop : -0.30 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 370 HIS 0.003 0.001 HIS A 9 PHE 0.013 0.001 PHE A 158 TYR 0.012 0.001 TYR B 285 ARG 0.008 0.001 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.04304 ( 332) hydrogen bonds : angle 5.12353 ( 912) covalent geometry : bond 0.00358 ( 7466) covalent geometry : angle 0.56141 (10090) *********************** 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 128 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.794 Fit side-chains REVERT: B 37 TYR cc_start: 0.8578 (m-10) cc_final: 0.7891 (p90) REVERT: B 87 ASP cc_start: 0.8707 (t0) cc_final: 0.8090 (t70) REVERT: B 148 TYR cc_start: 0.6996 (OUTLIER) cc_final: 0.6247 (m-80) REVERT: B 400 GLU cc_start: 0.7625 (mt-10) cc_final: 0.6970 (mp0) REVERT: B 471 ILE cc_start: 0.8386 (mt) cc_final: 0.8064 (mp) REVERT: A 5 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7608 (mp) REVERT: A 41 LYS cc_start: 0.5693 (OUTLIER) cc_final: 0.4938 (mtmm) REVERT: A 54 ARG cc_start: 0.7963 (mtm110) cc_final: 0.7613 (ptp-110) REVERT: A 77 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6930 (mm-30) REVERT: A 88 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8372 (mm) REVERT: A 224 MET cc_start: 0.7835 (ptm) cc_final: 0.7495 (pp-130) REVERT: A 226 GLN cc_start: 0.8067 (mt0) cc_final: 0.7849 (mt0) REVERT: A 263 ARG cc_start: 0.7931 (ttp80) cc_final: 0.7166 (ttp80) REVERT: A 267 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7856 (mp10) REVERT: A 345 LYS cc_start: 0.8453 (mptt) cc_final: 0.7990 (mmtm) REVERT: A 398 GLU cc_start: 0.8745 (mp0) cc_final: 0.7957 (tm-30) outliers start: 31 outliers final: 13 residues processed: 116 average time/residue: 1.0035 time to fit residues: 124.3627 Evaluate side-chains 101 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 77 GLU 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 247 LEU 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 34 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 56 optimal weight: 0.0980 chunk 33 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 64 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.119719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.090763 restraints weight = 12378.054| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 3.36 r_work: 0.3238 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7466 Z= 0.170 Angle : 0.570 7.054 10090 Z= 0.294 Chirality : 0.043 0.239 1076 Planarity : 0.004 0.036 1288 Dihedral : 4.682 40.719 957 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.19 % Allowed : 21.35 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.28), residues: 886 helix: 1.29 (0.28), residues: 324 sheet: -0.64 (0.39), residues: 165 loop : -0.23 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 370 HIS 0.009 0.001 HIS B 59 PHE 0.016 0.002 PHE A 223 TYR 0.012 0.001 TYR B 285 ARG 0.006 0.001 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.04323 ( 332) hydrogen bonds : angle 5.10638 ( 912) covalent geometry : bond 0.00397 ( 7466) covalent geometry : angle 0.57035 (10090) *********************** 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 119 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 86 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: B 37 TYR cc_start: 0.8595 (m-10) cc_final: 0.7906 (p90) REVERT: B 87 ASP cc_start: 0.8719 (t0) cc_final: 0.8105 (t70) REVERT: B 148 TYR cc_start: 0.7063 (OUTLIER) cc_final: 0.6263 (m-80) REVERT: B 400 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7038 (mp0) REVERT: B 471 ILE cc_start: 0.8366 (mt) cc_final: 0.8030 (mp) REVERT: A 5 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7671 (mp) REVERT: A 54 ARG cc_start: 0.7897 (mtm110) cc_final: 0.7544 (ptp-110) REVERT: A 77 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6918 (mm-30) REVERT: A 88 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8419 (mm) REVERT: A 212 ASN cc_start: 0.8850 (t0) cc_final: 0.8315 (t0) REVERT: A 267 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8166 (mm-40) REVERT: A 398 GLU cc_start: 0.8736 (mp0) cc_final: 0.7922 (tm-30) outliers start: 33 outliers final: 15 residues processed: 107 average time/residue: 0.8758 time to fit residues: 101.0047 Evaluate side-chains 100 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 3 ASN Chi-restraints excluded: chain A residue 5 ILE 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 123 SER Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 267 GLN 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 12 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 49 optimal weight: 0.2980 chunk 6 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.120915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.092044 restraints weight = 12317.765| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 3.36 r_work: 0.3261 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7466 Z= 0.140 Angle : 0.563 7.474 10090 Z= 0.287 Chirality : 0.042 0.249 1076 Planarity : 0.004 0.066 1288 Dihedral : 4.629 40.786 957 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.57 % Allowed : 22.11 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.28), residues: 886 helix: 1.45 (0.28), residues: 324 sheet: -0.54 (0.40), residues: 163 loop : -0.12 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 370 HIS 0.008 0.001 HIS B 59 PHE 0.016 0.001 PHE A 259 TYR 0.011 0.001 TYR A 293 ARG 0.016 0.001 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.04080 ( 332) hydrogen bonds : angle 4.97413 ( 912) covalent geometry : bond 0.00325 ( 7466) covalent geometry : angle 0.56305 (10090) *********************** 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 126 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 90 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.8609 (m-10) cc_final: 0.7908 (p90) REVERT: B 87 ASP cc_start: 0.8738 (t0) cc_final: 0.8118 (t70) REVERT: B 148 TYR cc_start: 0.7028 (OUTLIER) cc_final: 0.6224 (m-80) REVERT: B 400 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7079 (mp0) REVERT: A 5 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7756 (mp) REVERT: A 41 LYS cc_start: 0.5608 (OUTLIER) cc_final: 0.4959 (mtmm) REVERT: A 54 ARG cc_start: 0.7849 (mtm110) cc_final: 0.7472 (ptp-110) REVERT: A 77 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6945 (mm-30) REVERT: A 88 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8410 (mm) REVERT: A 212 ASN cc_start: 0.8854 (t0) cc_final: 0.8308 (t0) REVERT: A 267 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.8141 (mm-40) REVERT: A 398 GLU cc_start: 0.8743 (mp0) cc_final: 0.7922 (tm-30) outliers start: 36 outliers final: 16 residues processed: 114 average time/residue: 0.8710 time to fit residues: 107.0926 Evaluate side-chains 103 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 3 ASN 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 77 GLU 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 247 LEU 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 43 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 69 optimal weight: 0.0670 chunk 80 optimal weight: 0.9980 chunk 37 optimal weight: 0.0980 chunk 11 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.5920 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.121319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.092708 restraints weight = 12269.937| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.36 r_work: 0.3275 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7466 Z= 0.129 Angle : 0.567 8.111 10090 Z= 0.289 Chirality : 0.042 0.248 1076 Planarity : 0.004 0.062 1288 Dihedral : 4.605 41.053 957 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.68 % Allowed : 23.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.29), residues: 886 helix: 1.44 (0.28), residues: 324 sheet: -0.50 (0.40), residues: 163 loop : -0.09 (0.33), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 370 HIS 0.008 0.001 HIS B 59 PHE 0.021 0.001 PHE A 223 TYR 0.012 0.001 TYR A 293 ARG 0.011 0.001 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 332) hydrogen bonds : angle 4.95186 ( 912) covalent geometry : bond 0.00297 ( 7466) covalent geometry : angle 0.56722 (10090) *********************** 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 124 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.8593 (m-10) cc_final: 0.7913 (p90) REVERT: B 87 ASP cc_start: 0.8732 (t0) cc_final: 0.8120 (t70) REVERT: B 148 TYR cc_start: 0.7092 (OUTLIER) cc_final: 0.6253 (m-80) REVERT: B 400 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7095 (mp0) REVERT: A 5 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7778 (mp) REVERT: A 41 LYS cc_start: 0.5718 (OUTLIER) cc_final: 0.5136 (mtmm) REVERT: A 54 ARG cc_start: 0.7801 (mtm110) cc_final: 0.7400 (ptp-110) REVERT: A 77 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.6962 (mm-30) REVERT: A 88 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8371 (mm) REVERT: A 184 GLU cc_start: 0.7959 (tt0) cc_final: 0.7476 (tm-30) REVERT: A 212 ASN cc_start: 0.8854 (t0) cc_final: 0.8306 (t0) REVERT: A 349 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6834 (pm20) REVERT: A 398 GLU cc_start: 0.8741 (mp0) cc_final: 0.7921 (tm-30) outliers start: 29 outliers final: 18 residues processed: 112 average time/residue: 0.8665 time to fit residues: 104.9457 Evaluate side-chains 106 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 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 3 ASN 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 75 LEU Chi-restraints excluded: chain A residue 77 GLU 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 349 GLU 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 55 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 9 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.120922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.092201 restraints weight = 12414.645| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 3.38 r_work: 0.3262 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3123 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= 0.144 Angle : 0.579 8.344 10090 Z= 0.296 Chirality : 0.042 0.250 1076 Planarity : 0.004 0.057 1288 Dihedral : 4.631 41.812 957 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.07 % Allowed : 23.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.29), residues: 886 helix: 1.46 (0.29), residues: 323 sheet: -0.51 (0.40), residues: 169 loop : -0.07 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 33 HIS 0.007 0.001 HIS B 59 PHE 0.018 0.001 PHE A 259 TYR 0.011 0.001 TYR A 293 ARG 0.010 0.001 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 332) hydrogen bonds : angle 4.94431 ( 912) covalent geometry : bond 0.00335 ( 7466) covalent geometry : angle 0.57905 (10090) *********************** 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 122 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 90 time to evaluate : 0.799 Fit side-chains REVERT: B 37 TYR cc_start: 0.8607 (m-10) cc_final: 0.7947 (p90) REVERT: B 87 ASP cc_start: 0.8768 (t0) cc_final: 0.8142 (t70) REVERT: B 148 TYR cc_start: 0.7199 (OUTLIER) cc_final: 0.6306 (m-80) REVERT: B 330 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7085 (pp) REVERT: B 400 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7188 (mp0) REVERT: B 503 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.7946 (m-80) REVERT: A 5 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7836 (mp) REVERT: A 41 LYS cc_start: 0.5676 (OUTLIER) cc_final: 0.5129 (mtmm) REVERT: A 54 ARG cc_start: 0.7814 (mtm110) cc_final: 0.7410 (ptp-110) REVERT: A 77 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6982 (mm-30) REVERT: A 86 LYS cc_start: 0.9004 (tptp) cc_final: 0.8789 (tppp) REVERT: A 88 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8311 (mm) REVERT: A 267 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8168 (mm-40) REVERT: A 349 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6856 (pm20) REVERT: A 398 GLU cc_start: 0.8743 (mp0) cc_final: 0.7822 (tm-30) outliers start: 32 outliers final: 15 residues processed: 111 average time/residue: 0.8833 time to fit residues: 105.5448 Evaluate side-chains 112 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 151 CYS Chi-restraints excluded: chain B residue 330 LEU 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 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 61 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 77 GLU 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 247 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 349 GLU 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 3 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 371 ASN A 9 HIS A 129 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.120687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.091775 restraints weight = 12518.787| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.40 r_work: 0.3260 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7466 Z= 0.148 Angle : 0.602 9.576 10090 Z= 0.307 Chirality : 0.043 0.235 1076 Planarity : 0.004 0.054 1288 Dihedral : 4.664 42.567 957 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.68 % Allowed : 24.02 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.29), residues: 886 helix: 1.53 (0.28), residues: 317 sheet: -0.52 (0.40), residues: 169 loop : -0.09 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 33 HIS 0.008 0.001 HIS B 59 PHE 0.023 0.002 PHE A 259 TYR 0.019 0.001 TYR B 48 ARG 0.004 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.04036 ( 332) hydrogen bonds : angle 4.96542 ( 912) covalent geometry : bond 0.00346 ( 7466) covalent geometry : angle 0.60232 (10090) *********************** 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 117 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: B 37 TYR cc_start: 0.8631 (m-10) cc_final: 0.7944 (p90) REVERT: B 87 ASP cc_start: 0.8774 (t0) cc_final: 0.8185 (t70) REVERT: B 148 TYR cc_start: 0.7242 (OUTLIER) cc_final: 0.6318 (m-80) REVERT: B 330 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7090 (pp) REVERT: B 400 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7189 (mp0) REVERT: B 497 LYS cc_start: 0.9238 (tppt) cc_final: 0.8879 (tmmt) REVERT: A 5 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7885 (mp) REVERT: A 41 LYS cc_start: 0.5636 (OUTLIER) cc_final: 0.5127 (mtmm) REVERT: A 54 ARG cc_start: 0.7806 (mtm110) cc_final: 0.7397 (ptp-110) REVERT: A 77 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6996 (mm-30) REVERT: A 87 GLN cc_start: 0.9163 (tm-30) cc_final: 0.8856 (tm-30) REVERT: A 267 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8175 (mm-40) REVERT: A 349 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.6864 (pm20) REVERT: A 398 GLU cc_start: 0.8807 (mp0) cc_final: 0.7775 (tm-30) outliers start: 29 outliers final: 14 residues processed: 106 average time/residue: 1.0247 time to fit residues: 118.2476 Evaluate side-chains 106 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 151 CYS 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 75 LEU Chi-restraints excluded: chain A residue 77 GLU 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 267 GLN Chi-restraints excluded: chain A residue 349 GLU 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 24 optimal weight: 0.7980 chunk 49 optimal weight: 0.3980 chunk 26 optimal weight: 0.0060 chunk 83 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 85 optimal weight: 0.0670 chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 76 optimal weight: 0.4980 overall best weight: 0.3534 ------------------------------------------------------------------------------- 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 9 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.123311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.094321 restraints weight = 12604.688| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.46 r_work: 0.3306 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3371 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= 0.118 Angle : 0.587 9.684 10090 Z= 0.297 Chirality : 0.042 0.234 1076 Planarity : 0.004 0.046 1288 Dihedral : 4.566 42.609 957 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.54 % Allowed : 25.92 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.29), residues: 886 helix: 1.64 (0.28), residues: 317 sheet: -0.61 (0.39), residues: 172 loop : -0.01 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 33 HIS 0.007 0.001 HIS A 9 PHE 0.011 0.001 PHE A 176 TYR 0.012 0.001 TYR A 293 ARG 0.004 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 332) hydrogen bonds : angle 4.89148 ( 912) covalent geometry : bond 0.00273 ( 7466) covalent geometry : angle 0.58689 (10090) ********************** 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: 20 poor density : 93 time to evaluate : 0.804 Fit side-chains revert: symmetry clash REVERT: B 37 TYR cc_start: 0.8618 (m-10) cc_final: 0.7939 (p90) REVERT: B 87 ASP cc_start: 0.8747 (t0) cc_final: 0.8119 (t70) REVERT: B 148 TYR cc_start: 0.7140 (OUTLIER) cc_final: 0.6291 (m-80) REVERT: B 330 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7087 (pp) REVERT: B 400 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7170 (mp0) REVERT: B 497 LYS cc_start: 0.9219 (tppt) cc_final: 0.8885 (tmmt) REVERT: A 41 LYS cc_start: 0.5633 (OUTLIER) cc_final: 0.5166 (mtmm) REVERT: A 54 ARG cc_start: 0.7750 (mtm110) cc_final: 0.7387 (mtm110) REVERT: A 77 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7017 (mm-30) REVERT: A 87 GLN cc_start: 0.9131 (tm-30) cc_final: 0.8801 (tm-30) REVERT: A 224 MET cc_start: 0.6992 (pmm) cc_final: 0.6544 (mpt) REVERT: A 349 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.6912 (pm20) outliers start: 20 outliers final: 12 residues processed: 104 average time/residue: 0.8702 time to fit residues: 97.7097 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 : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 476 VAL 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 75 LEU Chi-restraints excluded: chain A residue 77 GLU 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 349 GLU 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 41 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 51 optimal weight: 0.0970 chunk 5 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.122204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.093290 restraints weight = 12392.508| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.41 r_work: 0.3290 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7466 Z= 0.136 Angle : 0.620 9.628 10090 Z= 0.310 Chirality : 0.043 0.229 1076 Planarity : 0.004 0.043 1288 Dihedral : 4.568 43.177 957 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.67 % Allowed : 26.18 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.29), residues: 886 helix: 1.70 (0.28), residues: 312 sheet: -0.61 (0.39), residues: 172 loop : -0.03 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 33 HIS 0.007 0.001 HIS A 9 PHE 0.022 0.001 PHE A 259 TYR 0.030 0.001 TYR B 48 ARG 0.004 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 332) hydrogen bonds : angle 4.92092 ( 912) covalent geometry : bond 0.00321 ( 7466) covalent geometry : angle 0.61975 (10090) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6042.24 seconds wall clock time: 104 minutes 50.40 seconds (6290.40 seconds total)