Starting phenix.real_space_refine on Tue Mar 11 14:30:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i4g_35172/03_2025/8i4g_35172.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i4g_35172/03_2025/8i4g_35172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i4g_35172/03_2025/8i4g_35172.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i4g_35172/03_2025/8i4g_35172.map" model { file = "/net/cci-nas-00/data/ceres_data/8i4g_35172/03_2025/8i4g_35172.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i4g_35172/03_2025/8i4g_35172.cif" } resolution = 3.68 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= 0.001 sd= 0.029 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 25 5.16 5 C 3878 2.51 5 N 1005 2.21 5 O 1149 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6057 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 922 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "A" Number of atoms: 5135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5135 Classifications: {'peptide': 649} Link IDs: {'PTRANS': 34, 'TRANS': 614} Time building chain proxies: 3.97, per 1000 atoms: 0.66 Number of scatterers: 6057 At special positions: 0 Unit cell: (69.9, 94.132, 133.276, 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 25 16.00 O 1149 8.00 N 1005 7.00 C 3878 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 137 " - pdb=" SG CYS A 172 " distance=2.03 Simple disulfide: pdb=" SG CYS A 297 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 342 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 438 " distance=2.03 Simple disulfide: pdb=" SG CYS A 397 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 486 " - pdb=" SG CYS A 494 " distance=2.03 Simple disulfide: pdb=" SG CYS A 544 " - pdb=" SG CYS A 596 " distance=2.03 Simple disulfide: pdb=" SG CYS A 623 " - pdb=" SG CYS A 655 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 875.9 milliseconds 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1418 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 13 sheets defined 4.8% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 300 through 310 removed outlier: 3.965A pdb=" N GLU A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 348 Processing helix chain 'A' and resid 370 through 375 removed outlier: 3.994A pdb=" N VAL A 373 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 375 " --> pdb=" O SER A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'A' and resid 625 through 630 Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.619A pdb=" N VAL C 5 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP C 73 " --> pdb=" O THR C 78 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER C 71 " --> pdb=" O TYR C 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.773A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N MET C 34 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 37 through 39 removed outlier: 3.640A pdb=" N VAL A 70 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER A 68 " --> pdb=" O SER A 39 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 273 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N PHE A 73 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 56 through 63 removed outlier: 3.741A pdb=" N HIS A 57 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP A 61 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 63 " --> pdb=" O GLN A 277 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU A 282 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ALA A 294 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LYS A 284 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.782A pdb=" N GLY A 109 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS A 137 " --> pdb=" O SER A 122 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 132 through 133 removed outlier: 3.782A pdb=" N GLY A 109 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU A 147 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 96 through 100 removed outlier: 3.641A pdb=" N VAL A 96 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER A 100 " --> pdb=" O ARG A 196 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR A 214 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU A 197 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS A 212 " --> pdb=" O GLU A 197 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 199 " --> pdb=" O TYR A 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 319 through 320 removed outlier: 3.555A pdb=" N TYR A 618 " --> pdb=" O CYS A 655 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 362 through 364 removed outlier: 3.567A pdb=" N ALA A 403 " --> pdb=" O LYS A 362 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 362 through 364 removed outlier: 3.567A pdb=" N ALA A 403 " --> pdb=" O LYS A 362 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 367 through 368 removed outlier: 6.868A pdb=" N CYS A 367 " --> pdb=" O CYS A 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 458 through 460 removed outlier: 3.662A pdb=" N TYR A 459 " --> pdb=" O GLN A 499 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 544 through 547 removed outlier: 4.008A pdb=" N VAL A 545 " --> pdb=" O GLY A 556 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY A 556 " --> pdb=" O VAL A 545 " (cutoff:3.500A) 117 hydrogen bonds defined for protein. 270 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: 1.85 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1937 1.34 - 1.46: 1565 1.46 - 1.58: 2688 1.58 - 1.69: 0 1.69 - 1.81: 29 Bond restraints: 6219 Sorted by residual: bond pdb=" C GLN A 179 " pdb=" N PRO A 180 " ideal model delta sigma weight residual 1.332 1.361 -0.030 1.30e-02 5.92e+03 5.18e+00 bond pdb=" C PHE A 335 " pdb=" N PRO A 336 " ideal model delta sigma weight residual 1.328 1.351 -0.023 1.25e-02 6.40e+03 3.26e+00 bond pdb=" CA ILE A 203 " pdb=" CB ILE A 203 " ideal model delta sigma weight residual 1.528 1.541 -0.013 1.34e-02 5.57e+03 9.54e-01 bond pdb=" CA ILE A 125 " pdb=" CB ILE A 125 " ideal model delta sigma weight residual 1.527 1.539 -0.012 1.31e-02 5.83e+03 9.05e-01 bond pdb=" CA HIS A 631 " pdb=" C HIS A 631 " ideal model delta sigma weight residual 1.532 1.524 0.009 9.60e-03 1.09e+04 8.52e-01 ... (remaining 6214 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 7860 1.13 - 2.27: 480 2.27 - 3.40: 111 3.40 - 4.53: 13 4.53 - 5.66: 4 Bond angle restraints: 8468 Sorted by residual: angle pdb=" N VAL A 326 " pdb=" CA VAL A 326 " pdb=" C VAL A 326 " ideal model delta sigma weight residual 112.96 108.47 4.49 1.00e+00 1.00e+00 2.01e+01 angle pdb=" N THR A 308 " pdb=" CA THR A 308 " pdb=" C THR A 308 " ideal model delta sigma weight residual 114.39 110.19 4.20 1.45e+00 4.76e-01 8.40e+00 angle pdb=" C SER A 178 " pdb=" N GLN A 179 " pdb=" CA GLN A 179 " ideal model delta sigma weight residual 119.78 123.34 -3.56 1.24e+00 6.50e-01 8.26e+00 angle pdb=" N ARG C 67 " pdb=" CA ARG C 67 " pdb=" C ARG C 67 " ideal model delta sigma weight residual 114.56 111.01 3.55 1.27e+00 6.20e-01 7.80e+00 angle pdb=" N SER A 643 " pdb=" CA SER A 643 " pdb=" C SER A 643 " ideal model delta sigma weight residual 107.32 111.90 -4.58 1.65e+00 3.67e-01 7.72e+00 ... (remaining 8463 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.72: 3422 16.72 - 33.44: 171 33.44 - 50.15: 38 50.15 - 66.87: 10 66.87 - 83.59: 1 Dihedral angle restraints: 3642 sinusoidal: 1412 harmonic: 2230 Sorted by residual: dihedral pdb=" SG CYS A 137 " pdb=" CB CYS A 172 " pdb=" SG CYS A 172 " pdb=" CA CYS A 172 " ideal model delta sinusoidal sigma weight residual 79.00 23.14 55.86 1 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CB GLU A 102 " pdb=" CG GLU A 102 " pdb=" CD GLU A 102 " pdb=" OE1 GLU A 102 " ideal model delta sinusoidal sigma weight residual 0.00 -83.59 83.59 1 3.00e+01 1.11e-03 9.48e+00 dihedral pdb=" N TYR A 495 " pdb=" CA TYR A 495 " pdb=" CB TYR A 495 " pdb=" CG TYR A 495 " ideal model delta sinusoidal sigma weight residual 60.00 3.61 56.39 3 1.50e+01 4.44e-03 9.40e+00 ... (remaining 3639 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 538 0.025 - 0.050: 207 0.050 - 0.075: 91 0.075 - 0.100: 57 0.100 - 0.124: 28 Chirality restraints: 921 Sorted by residual: chirality pdb=" CB ILE A 416 " pdb=" CA ILE A 416 " pdb=" CG1 ILE A 416 " pdb=" CG2 ILE A 416 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA ILE A 209 " pdb=" N ILE A 209 " pdb=" C ILE A 209 " pdb=" CB ILE A 209 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA ILE A 216 " pdb=" N ILE A 216 " pdb=" C ILE A 216 " pdb=" CB ILE A 216 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.54e-01 ... (remaining 918 not shown) Planarity restraints: 1100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 605 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO A 606 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 606 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 606 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 342 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO A 343 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 343 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 343 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 532 " -0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO A 533 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 533 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 533 " -0.016 5.00e-02 4.00e+02 ... (remaining 1097 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1144 2.78 - 3.31: 5520 3.31 - 3.84: 10051 3.84 - 4.37: 11282 4.37 - 4.90: 19539 Nonbonded interactions: 47536 Sorted by model distance: nonbonded pdb=" OD1 ASN A 286 " pdb=" OG1 THR A 292 " model vdw 2.246 3.040 nonbonded pdb=" NH1 ARG A 42 " pdb=" OG SER A 227 " model vdw 2.258 3.120 nonbonded pdb=" O VAL A 136 " pdb=" OG1 THR A 173 " model vdw 2.278 3.040 nonbonded pdb=" OG1 THR A 256 " pdb=" OD1 ASP A 259 " model vdw 2.284 3.040 nonbonded pdb=" OG SER A 118 " pdb=" OE1 GLN A 140 " model vdw 2.285 3.040 ... (remaining 47531 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 group one per residue 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: 0.690 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.190 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 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 : 0.002 0.036 6219 Z= 0.152 Angle : 0.631 5.665 8468 Z= 0.405 Chirality : 0.040 0.124 921 Planarity : 0.003 0.030 1100 Dihedral : 10.191 83.589 2197 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 5.71 % Allowed : 9.62 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.78 (0.24), residues: 764 helix: -4.28 (0.42), residues: 40 sheet: -2.50 (0.33), residues: 174 loop : -3.60 (0.22), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 359 HIS 0.001 0.000 HIS A 525 PHE 0.007 0.001 PHE A 406 TYR 0.006 0.001 TYR A 271 ARG 0.002 0.000 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 237 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 18 LEU cc_start: 0.7431 (tp) cc_final: 0.7113 (tp) REVERT: C 31 TYR cc_start: 0.7516 (p90) cc_final: 0.7150 (p90) REVERT: C 77 ASN cc_start: 0.7701 (t0) cc_final: 0.7033 (t0) REVERT: C 83 MET cc_start: 0.6665 (mtt) cc_final: 0.6329 (mtt) REVERT: C 100 SER cc_start: 0.8672 (t) cc_final: 0.8044 (t) REVERT: A 40 PHE cc_start: 0.8285 (m-80) cc_final: 0.7997 (m-10) REVERT: A 60 GLN cc_start: 0.7379 (tm-30) cc_final: 0.6593 (tm-30) REVERT: A 72 TRP cc_start: 0.7879 (t60) cc_final: 0.7594 (t60) REVERT: A 89 VAL cc_start: 0.8032 (t) cc_final: 0.7814 (p) REVERT: A 105 ASN cc_start: 0.7580 (m-40) cc_final: 0.7091 (p0) REVERT: A 119 LYS cc_start: 0.7801 (tppt) cc_final: 0.7004 (tppt) REVERT: A 195 LEU cc_start: 0.8091 (tp) cc_final: 0.7838 (mp) REVERT: A 250 LEU cc_start: 0.7825 (tp) cc_final: 0.7346 (tp) REVERT: A 255 LEU cc_start: 0.4849 (OUTLIER) cc_final: 0.4544 (tp) REVERT: A 299 LEU cc_start: 0.7945 (tp) cc_final: 0.7721 (tp) REVERT: A 302 LEU cc_start: 0.7791 (tp) cc_final: 0.7425 (tt) REVERT: A 362 LYS cc_start: 0.7740 (tmtt) cc_final: 0.7149 (tmtt) REVERT: A 420 GLN cc_start: 0.7527 (mm110) cc_final: 0.7313 (mm110) REVERT: A 430 LYS cc_start: 0.8094 (mmmt) cc_final: 0.7837 (mmmt) REVERT: A 473 ASP cc_start: 0.8178 (t0) cc_final: 0.6691 (m-30) REVERT: A 495 TYR cc_start: 0.7874 (OUTLIER) cc_final: 0.6591 (p90) REVERT: A 516 VAL cc_start: 0.7378 (OUTLIER) cc_final: 0.7129 (p) REVERT: A 520 SER cc_start: 0.7335 (m) cc_final: 0.7022 (t) REVERT: A 523 LEU cc_start: 0.7889 (tp) cc_final: 0.7404 (tp) REVERT: A 525 HIS cc_start: 0.6133 (p-80) cc_final: 0.5862 (p-80) REVERT: A 534 LYS cc_start: 0.8497 (mmmm) cc_final: 0.8262 (mmtp) REVERT: A 535 LYS cc_start: 0.8136 (pptt) cc_final: 0.7639 (pptt) REVERT: A 580 ASP cc_start: 0.6577 (t70) cc_final: 0.5915 (t0) REVERT: A 592 ASP cc_start: 0.7649 (t70) cc_final: 0.7267 (t0) REVERT: A 593 ILE cc_start: 0.8225 (mt) cc_final: 0.7959 (mt) REVERT: A 594 THR cc_start: 0.8769 (p) cc_final: 0.8380 (m) REVERT: A 638 THR cc_start: 0.7661 (p) cc_final: 0.7429 (p) REVERT: A 670 ILE cc_start: 0.8518 (mt) cc_final: 0.8312 (tt) outliers start: 38 outliers final: 22 residues processed: 259 average time/residue: 0.1869 time to fit residues: 62.2641 Evaluate side-chains 232 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 484 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 667 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 0.0980 chunk 56 optimal weight: 0.0060 chunk 31 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 GLN A 420 GLN A 445 ASN A 548 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.163173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.142056 restraints weight = 10527.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.147079 restraints weight = 5644.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.150471 restraints weight = 3520.353| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6219 Z= 0.171 Angle : 0.597 11.531 8468 Z= 0.302 Chirality : 0.044 0.163 921 Planarity : 0.005 0.051 1100 Dihedral : 8.881 88.430 899 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 6.62 % Allowed : 15.64 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.15 (0.26), residues: 764 helix: -3.06 (0.85), residues: 28 sheet: -2.23 (0.33), residues: 196 loop : -3.17 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 639 HIS 0.002 0.000 HIS A 213 PHE 0.030 0.002 PHE A 568 TYR 0.019 0.001 TYR C 94 ARG 0.005 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 204 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 31 TYR cc_start: 0.7520 (p90) cc_final: 0.6977 (p90) REVERT: C 77 ASN cc_start: 0.8188 (t0) cc_final: 0.7610 (t0) REVERT: C 99 ARG cc_start: 0.7544 (ptt90) cc_final: 0.7322 (ppt170) REVERT: A 40 PHE cc_start: 0.8289 (m-80) cc_final: 0.8059 (m-10) REVERT: A 42 ARG cc_start: 0.7963 (ttm110) cc_final: 0.7728 (ttm110) REVERT: A 60 GLN cc_start: 0.7357 (tm-30) cc_final: 0.6529 (tm-30) REVERT: A 119 LYS cc_start: 0.7691 (tppt) cc_final: 0.6958 (tppt) REVERT: A 134 ILE cc_start: 0.7693 (mt) cc_final: 0.7275 (tt) REVERT: A 250 LEU cc_start: 0.7960 (tp) cc_final: 0.7517 (tp) REVERT: A 255 LEU cc_start: 0.4889 (OUTLIER) cc_final: 0.4565 (tp) REVERT: A 299 LEU cc_start: 0.8144 (tp) cc_final: 0.7850 (tp) REVERT: A 302 LEU cc_start: 0.7724 (tp) cc_final: 0.7379 (tt) REVERT: A 310 LYS cc_start: 0.8637 (mmtp) cc_final: 0.8432 (mmtt) REVERT: A 346 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7894 (mm-30) REVERT: A 362 LYS cc_start: 0.7625 (tmtt) cc_final: 0.7038 (tmtt) REVERT: A 430 LYS cc_start: 0.8017 (mmmt) cc_final: 0.7360 (mmmt) REVERT: A 434 ASP cc_start: 0.6902 (t0) cc_final: 0.6427 (t0) REVERT: A 466 LYS cc_start: 0.7954 (mmmm) cc_final: 0.7739 (mmmm) REVERT: A 472 ARG cc_start: 0.7801 (ttm170) cc_final: 0.7399 (ttm-80) REVERT: A 473 ASP cc_start: 0.8397 (t0) cc_final: 0.6579 (m-30) REVERT: A 495 TYR cc_start: 0.7915 (OUTLIER) cc_final: 0.6568 (p90) REVERT: A 518 VAL cc_start: 0.8563 (t) cc_final: 0.8277 (p) REVERT: A 520 SER cc_start: 0.7591 (m) cc_final: 0.7294 (t) REVERT: A 534 LYS cc_start: 0.8542 (mmmm) cc_final: 0.8321 (mmtp) REVERT: A 535 LYS cc_start: 0.8146 (pptt) cc_final: 0.7714 (pptt) REVERT: A 542 ASN cc_start: 0.8190 (m-40) cc_final: 0.7943 (m110) REVERT: A 543 LYS cc_start: 0.7581 (ttmt) cc_final: 0.7132 (ttmm) REVERT: A 580 ASP cc_start: 0.6905 (t70) cc_final: 0.6421 (t0) REVERT: A 593 ILE cc_start: 0.8595 (mt) cc_final: 0.8363 (mt) outliers start: 44 outliers final: 29 residues processed: 228 average time/residue: 0.1933 time to fit residues: 56.0860 Evaluate side-chains 218 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 484 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 667 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.149141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.128420 restraints weight = 10742.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.133097 restraints weight = 5798.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.136400 restraints weight = 3662.177| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6219 Z= 0.341 Angle : 0.713 12.652 8468 Z= 0.364 Chirality : 0.046 0.211 921 Planarity : 0.005 0.045 1100 Dihedral : 9.419 89.426 895 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 8.12 % Allowed : 16.54 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.00 (0.27), residues: 764 helix: -1.98 (1.24), residues: 22 sheet: -2.05 (0.33), residues: 198 loop : -3.16 (0.24), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 359 HIS 0.003 0.001 HIS A 525 PHE 0.027 0.002 PHE A 112 TYR 0.021 0.002 TYR A 642 ARG 0.005 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 214 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 18 LEU cc_start: 0.8153 (tp) cc_final: 0.7613 (tp) REVERT: C 27 PHE cc_start: 0.7939 (t80) cc_final: 0.7474 (t80) REVERT: C 29 PHE cc_start: 0.7453 (m-10) cc_final: 0.6987 (m-10) REVERT: C 31 TYR cc_start: 0.7631 (p90) cc_final: 0.7151 (p90) REVERT: C 77 ASN cc_start: 0.8517 (t0) cc_final: 0.7869 (t0) REVERT: C 83 MET cc_start: 0.6297 (OUTLIER) cc_final: 0.6082 (mpp) REVERT: A 40 PHE cc_start: 0.8452 (m-80) cc_final: 0.8080 (m-10) REVERT: A 41 THR cc_start: 0.7611 (p) cc_final: 0.7391 (t) REVERT: A 60 GLN cc_start: 0.7478 (tm-30) cc_final: 0.6640 (tm-30) REVERT: A 72 TRP cc_start: 0.8109 (t60) cc_final: 0.7740 (t60) REVERT: A 119 LYS cc_start: 0.7903 (tppt) cc_final: 0.7133 (tppt) REVERT: A 195 LEU cc_start: 0.8667 (tt) cc_final: 0.8422 (tt) REVERT: A 250 LEU cc_start: 0.8045 (tp) cc_final: 0.7602 (tp) REVERT: A 255 LEU cc_start: 0.5008 (OUTLIER) cc_final: 0.4558 (tp) REVERT: A 279 ARG cc_start: 0.7798 (mmm-85) cc_final: 0.7446 (mmt90) REVERT: A 299 LEU cc_start: 0.8152 (tp) cc_final: 0.7927 (tp) REVERT: A 305 THR cc_start: 0.8353 (m) cc_final: 0.8091 (p) REVERT: A 315 GLU cc_start: 0.6917 (mm-30) cc_final: 0.6384 (mm-30) REVERT: A 320 GLN cc_start: 0.7529 (mm-40) cc_final: 0.7150 (mm-40) REVERT: A 346 GLU cc_start: 0.8466 (mm-30) cc_final: 0.7811 (mm-30) REVERT: A 356 VAL cc_start: 0.8582 (OUTLIER) cc_final: 0.8328 (p) REVERT: A 361 ARG cc_start: 0.7739 (ttm170) cc_final: 0.6817 (ttm170) REVERT: A 429 TYR cc_start: 0.7862 (t80) cc_final: 0.7602 (t80) REVERT: A 430 LYS cc_start: 0.8265 (mmmt) cc_final: 0.7765 (mmmt) REVERT: A 467 LEU cc_start: 0.8036 (mm) cc_final: 0.7514 (mt) REVERT: A 472 ARG cc_start: 0.7881 (ttm170) cc_final: 0.7610 (ttm-80) REVERT: A 473 ASP cc_start: 0.8419 (t0) cc_final: 0.7207 (m-30) REVERT: A 495 TYR cc_start: 0.8271 (OUTLIER) cc_final: 0.6708 (p90) REVERT: A 520 SER cc_start: 0.8045 (m) cc_final: 0.7586 (p) REVERT: A 534 LYS cc_start: 0.8664 (mmmm) cc_final: 0.8302 (mmmm) REVERT: A 538 ASN cc_start: 0.7212 (t0) cc_final: 0.6953 (t0) REVERT: A 543 LYS cc_start: 0.7938 (ttmt) cc_final: 0.7550 (ttmm) REVERT: A 568 PHE cc_start: 0.7382 (t80) cc_final: 0.6884 (t80) REVERT: A 580 ASP cc_start: 0.7241 (t70) cc_final: 0.6368 (t0) REVERT: A 592 ASP cc_start: 0.7502 (t70) cc_final: 0.7130 (t0) REVERT: A 639 TRP cc_start: 0.6542 (OUTLIER) cc_final: 0.6190 (t60) outliers start: 54 outliers final: 34 residues processed: 238 average time/residue: 0.1888 time to fit residues: 58.1065 Evaluate side-chains 240 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 639 TRP Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 672 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 41 optimal weight: 0.0770 chunk 61 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN C 84 ASN A 69 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.151367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.130877 restraints weight = 10776.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.135636 restraints weight = 5811.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.138835 restraints weight = 3636.028| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6219 Z= 0.234 Angle : 0.666 11.778 8468 Z= 0.339 Chirality : 0.046 0.176 921 Planarity : 0.005 0.043 1100 Dihedral : 8.849 89.995 886 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer: Outliers : 7.97 % Allowed : 19.70 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.86 (0.27), residues: 764 helix: -1.77 (1.27), residues: 22 sheet: -1.88 (0.34), residues: 200 loop : -3.10 (0.24), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 359 HIS 0.003 0.001 HIS A 213 PHE 0.031 0.002 PHE A 649 TYR 0.016 0.001 TYR A 642 ARG 0.007 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 204 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 18 LEU cc_start: 0.8146 (tp) cc_final: 0.7643 (tp) REVERT: C 27 PHE cc_start: 0.7986 (t80) cc_final: 0.7595 (t80) REVERT: C 31 TYR cc_start: 0.7589 (p90) cc_final: 0.7168 (p90) REVERT: C 52 SER cc_start: 0.8357 (t) cc_final: 0.7684 (p) REVERT: C 77 ASN cc_start: 0.8400 (t0) cc_final: 0.7793 (t0) REVERT: C 93 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.6988 (tt) REVERT: A 41 THR cc_start: 0.7642 (p) cc_final: 0.7367 (t) REVERT: A 60 GLN cc_start: 0.7465 (tm-30) cc_final: 0.6596 (tm-30) REVERT: A 72 TRP cc_start: 0.8063 (t60) cc_final: 0.7710 (t60) REVERT: A 119 LYS cc_start: 0.7702 (tppt) cc_final: 0.6978 (tppt) REVERT: A 181 PHE cc_start: 0.6500 (OUTLIER) cc_final: 0.6151 (p90) REVERT: A 212 LYS cc_start: 0.8045 (tppt) cc_final: 0.7673 (tptp) REVERT: A 250 LEU cc_start: 0.8146 (tp) cc_final: 0.7656 (tp) REVERT: A 255 LEU cc_start: 0.4923 (OUTLIER) cc_final: 0.4560 (tp) REVERT: A 279 ARG cc_start: 0.7685 (mmm-85) cc_final: 0.7316 (mmt90) REVERT: A 302 LEU cc_start: 0.7986 (tp) cc_final: 0.7237 (tt) REVERT: A 315 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6175 (mm-30) REVERT: A 320 GLN cc_start: 0.7533 (mm-40) cc_final: 0.7181 (mm-40) REVERT: A 346 GLU cc_start: 0.8485 (mm-30) cc_final: 0.7855 (mm-30) REVERT: A 356 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8257 (p) REVERT: A 362 LYS cc_start: 0.7783 (tmtt) cc_final: 0.7170 (tmtt) REVERT: A 430 LYS cc_start: 0.8193 (mmmt) cc_final: 0.7703 (mmmt) REVERT: A 472 ARG cc_start: 0.7860 (ttm170) cc_final: 0.7598 (ttm-80) REVERT: A 473 ASP cc_start: 0.8381 (t0) cc_final: 0.7110 (m-30) REVERT: A 495 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.6599 (p90) REVERT: A 520 SER cc_start: 0.8063 (m) cc_final: 0.7574 (p) REVERT: A 534 LYS cc_start: 0.8632 (mmmm) cc_final: 0.8275 (mmmm) REVERT: A 538 ASN cc_start: 0.7266 (t0) cc_final: 0.6921 (t0) REVERT: A 539 LEU cc_start: 0.8468 (tp) cc_final: 0.8131 (tp) REVERT: A 543 LYS cc_start: 0.8007 (ttmt) cc_final: 0.7688 (ttmm) REVERT: A 568 PHE cc_start: 0.7342 (t80) cc_final: 0.7063 (t80) REVERT: A 580 ASP cc_start: 0.7163 (t70) cc_final: 0.6279 (t0) REVERT: A 592 ASP cc_start: 0.7463 (t70) cc_final: 0.7170 (t0) REVERT: A 639 TRP cc_start: 0.6401 (OUTLIER) cc_final: 0.6029 (t60) outliers start: 53 outliers final: 35 residues processed: 231 average time/residue: 0.1898 time to fit residues: 55.9617 Evaluate side-chains 234 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 193 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 569 GLN Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 639 TRP Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 672 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 0.0570 chunk 56 optimal weight: 3.9990 chunk 7 optimal weight: 0.0770 chunk 68 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 4 optimal weight: 0.0770 overall best weight: 0.3614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN A 127 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.154169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.132379 restraints weight = 10698.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.137456 restraints weight = 5731.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.140865 restraints weight = 3577.626| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6219 Z= 0.178 Angle : 0.643 12.016 8468 Z= 0.325 Chirality : 0.045 0.166 921 Planarity : 0.004 0.039 1100 Dihedral : 8.683 88.609 885 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 7.52 % Allowed : 22.26 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.57 (0.28), residues: 764 helix: -1.37 (1.38), residues: 22 sheet: -1.43 (0.36), residues: 195 loop : -3.01 (0.24), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 639 HIS 0.003 0.001 HIS A 525 PHE 0.038 0.002 PHE A 174 TYR 0.011 0.001 TYR A 618 ARG 0.006 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 202 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: C 18 LEU cc_start: 0.8063 (tp) cc_final: 0.7329 (tp) REVERT: C 27 PHE cc_start: 0.7987 (t80) cc_final: 0.7518 (t80) REVERT: C 31 TYR cc_start: 0.7631 (p90) cc_final: 0.7147 (p90) REVERT: C 52 SER cc_start: 0.8283 (t) cc_final: 0.7500 (p) REVERT: C 77 ASN cc_start: 0.8357 (t0) cc_final: 0.7621 (t0) REVERT: C 93 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.6857 (tt) REVERT: C 99 ARG cc_start: 0.7804 (ptt90) cc_final: 0.7418 (ppt170) REVERT: A 60 GLN cc_start: 0.7418 (tm-30) cc_final: 0.6543 (tm-30) REVERT: A 72 TRP cc_start: 0.8031 (t60) cc_final: 0.7689 (t60) REVERT: A 105 ASN cc_start: 0.7525 (m-40) cc_final: 0.6753 (p0) REVERT: A 119 LYS cc_start: 0.7679 (tppt) cc_final: 0.6917 (tppt) REVERT: A 175 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7861 (tm-30) REVERT: A 181 PHE cc_start: 0.6582 (OUTLIER) cc_final: 0.6138 (p90) REVERT: A 183 MET cc_start: 0.5780 (tmt) cc_final: 0.5155 (tmt) REVERT: A 201 LYS cc_start: 0.5547 (OUTLIER) cc_final: 0.5135 (ptpt) REVERT: A 212 LYS cc_start: 0.7968 (tppt) cc_final: 0.7574 (tptm) REVERT: A 250 LEU cc_start: 0.8112 (tp) cc_final: 0.7604 (tp) REVERT: A 255 LEU cc_start: 0.4874 (OUTLIER) cc_final: 0.4568 (tp) REVERT: A 279 ARG cc_start: 0.7650 (mmm-85) cc_final: 0.7288 (mmt90) REVERT: A 302 LEU cc_start: 0.7509 (tp) cc_final: 0.7156 (tt) REVERT: A 315 GLU cc_start: 0.6797 (mm-30) cc_final: 0.6361 (mm-30) REVERT: A 316 LYS cc_start: 0.6467 (mtmt) cc_final: 0.6132 (mtmt) REVERT: A 320 GLN cc_start: 0.7556 (mm-40) cc_final: 0.7160 (mm-40) REVERT: A 321 THR cc_start: 0.8004 (t) cc_final: 0.7587 (p) REVERT: A 325 ARG cc_start: 0.7340 (ptp-170) cc_final: 0.7061 (ptt180) REVERT: A 346 GLU cc_start: 0.8575 (mm-30) cc_final: 0.7962 (mm-30) REVERT: A 360 ASN cc_start: 0.8446 (m-40) cc_final: 0.7988 (p0) REVERT: A 362 LYS cc_start: 0.7748 (tmtt) cc_final: 0.7395 (tptp) REVERT: A 430 LYS cc_start: 0.8218 (mmmt) cc_final: 0.7641 (mmmt) REVERT: A 459 TYR cc_start: 0.7460 (p90) cc_final: 0.6813 (p90) REVERT: A 466 LYS cc_start: 0.7938 (mmmm) cc_final: 0.7665 (mmmm) REVERT: A 467 LEU cc_start: 0.7754 (mm) cc_final: 0.7264 (mp) REVERT: A 472 ARG cc_start: 0.7910 (ttm170) cc_final: 0.7600 (ttm-80) REVERT: A 473 ASP cc_start: 0.8381 (t0) cc_final: 0.7066 (m-30) REVERT: A 493 ASN cc_start: 0.7398 (m-40) cc_final: 0.7154 (m-40) REVERT: A 495 TYR cc_start: 0.8345 (OUTLIER) cc_final: 0.6774 (p90) REVERT: A 517 VAL cc_start: 0.7467 (t) cc_final: 0.7243 (m) REVERT: A 520 SER cc_start: 0.8085 (m) cc_final: 0.7490 (p) REVERT: A 534 LYS cc_start: 0.8599 (mmmm) cc_final: 0.8254 (mmmm) REVERT: A 538 ASN cc_start: 0.7278 (t0) cc_final: 0.6886 (t0) REVERT: A 568 PHE cc_start: 0.7327 (t80) cc_final: 0.7102 (t80) REVERT: A 580 ASP cc_start: 0.7164 (t70) cc_final: 0.6264 (t0) REVERT: A 667 GLU cc_start: 0.5050 (OUTLIER) cc_final: 0.4837 (pp20) REVERT: A 670 ILE cc_start: 0.8263 (mm) cc_final: 0.7979 (tp) outliers start: 50 outliers final: 32 residues processed: 223 average time/residue: 0.2064 time to fit residues: 58.0073 Evaluate side-chains 235 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 672 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 18 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 46 optimal weight: 0.0980 chunk 70 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.152773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.131465 restraints weight = 10461.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.136372 restraints weight = 5572.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.139671 restraints weight = 3462.965| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6219 Z= 0.215 Angle : 0.662 13.551 8468 Z= 0.333 Chirality : 0.045 0.181 921 Planarity : 0.004 0.038 1100 Dihedral : 8.659 89.199 884 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer: Outliers : 7.22 % Allowed : 22.71 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.47 (0.28), residues: 764 helix: -1.33 (1.39), residues: 22 sheet: -1.46 (0.34), residues: 211 loop : -2.92 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 359 HIS 0.003 0.001 HIS A 525 PHE 0.026 0.001 PHE A 174 TYR 0.016 0.001 TYR A 459 ARG 0.006 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 203 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 27 PHE cc_start: 0.8087 (t80) cc_final: 0.7682 (t80) REVERT: C 31 TYR cc_start: 0.7673 (p90) cc_final: 0.7144 (p90) REVERT: C 52 SER cc_start: 0.8257 (t) cc_final: 0.7486 (p) REVERT: C 77 ASN cc_start: 0.8435 (t0) cc_final: 0.7686 (t0) REVERT: C 93 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6741 (tt) REVERT: A 41 THR cc_start: 0.7620 (p) cc_final: 0.7311 (t) REVERT: A 60 GLN cc_start: 0.7436 (tm-30) cc_final: 0.6573 (tm-30) REVERT: A 72 TRP cc_start: 0.8064 (t60) cc_final: 0.7677 (t60) REVERT: A 119 LYS cc_start: 0.7752 (tppt) cc_final: 0.6985 (tppt) REVERT: A 181 PHE cc_start: 0.6736 (OUTLIER) cc_final: 0.6284 (p90) REVERT: A 183 MET cc_start: 0.5901 (tmt) cc_final: 0.5413 (tmt) REVERT: A 201 LYS cc_start: 0.5486 (OUTLIER) cc_final: 0.5087 (ptpt) REVERT: A 212 LYS cc_start: 0.8046 (tppt) cc_final: 0.7649 (tptp) REVERT: A 250 LEU cc_start: 0.8138 (tp) cc_final: 0.7618 (tp) REVERT: A 255 LEU cc_start: 0.4905 (OUTLIER) cc_final: 0.4554 (tp) REVERT: A 279 ARG cc_start: 0.7700 (mmm-85) cc_final: 0.7469 (mmt90) REVERT: A 291 ILE cc_start: 0.6489 (mm) cc_final: 0.6102 (mm) REVERT: A 302 LEU cc_start: 0.7498 (tp) cc_final: 0.7134 (tt) REVERT: A 316 LYS cc_start: 0.6292 (mtmt) cc_final: 0.5526 (mtpt) REVERT: A 319 TYR cc_start: 0.7337 (m-10) cc_final: 0.7017 (m-10) REVERT: A 320 GLN cc_start: 0.7588 (mm-40) cc_final: 0.7196 (mm-40) REVERT: A 325 ARG cc_start: 0.7439 (ptp-170) cc_final: 0.7132 (ptt180) REVERT: A 346 GLU cc_start: 0.8575 (mm-30) cc_final: 0.7978 (mm-30) REVERT: A 360 ASN cc_start: 0.8459 (m-40) cc_final: 0.8060 (p0) REVERT: A 362 LYS cc_start: 0.7684 (tmtt) cc_final: 0.7300 (tptp) REVERT: A 430 LYS cc_start: 0.8254 (mmmt) cc_final: 0.7585 (mmmt) REVERT: A 459 TYR cc_start: 0.7367 (p90) cc_final: 0.6659 (p90) REVERT: A 466 LYS cc_start: 0.7923 (mmmm) cc_final: 0.7645 (mmmm) REVERT: A 472 ARG cc_start: 0.7949 (ttm170) cc_final: 0.7611 (ttm-80) REVERT: A 473 ASP cc_start: 0.8458 (t0) cc_final: 0.7139 (m-30) REVERT: A 479 TYR cc_start: 0.7253 (t80) cc_final: 0.7038 (t80) REVERT: A 495 TYR cc_start: 0.8312 (OUTLIER) cc_final: 0.6593 (p90) REVERT: A 520 SER cc_start: 0.8041 (m) cc_final: 0.7579 (p) REVERT: A 534 LYS cc_start: 0.8598 (mmmm) cc_final: 0.8343 (mmtp) REVERT: A 538 ASN cc_start: 0.7269 (t0) cc_final: 0.6861 (t0) REVERT: A 568 PHE cc_start: 0.7479 (t80) cc_final: 0.7112 (t80) REVERT: A 580 ASP cc_start: 0.7045 (t70) cc_final: 0.6382 (t0) outliers start: 48 outliers final: 35 residues processed: 228 average time/residue: 0.2031 time to fit residues: 58.7846 Evaluate side-chains 232 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 349 ASN Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 672 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.150070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.128651 restraints weight = 10585.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.133542 restraints weight = 5662.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.136815 restraints weight = 3535.273| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6219 Z= 0.282 Angle : 0.715 11.376 8468 Z= 0.359 Chirality : 0.047 0.189 921 Planarity : 0.005 0.040 1100 Dihedral : 8.701 91.997 881 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.91 % Favored : 88.09 % Rotamer: Outliers : 6.62 % Allowed : 24.21 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.59 (0.28), residues: 764 helix: -2.10 (1.13), residues: 28 sheet: -1.32 (0.35), residues: 201 loop : -3.06 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 359 HIS 0.002 0.001 HIS A 525 PHE 0.025 0.002 PHE A 174 TYR 0.028 0.002 TYR A 459 ARG 0.008 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 PHE cc_start: 0.8138 (t80) cc_final: 0.7734 (t80) REVERT: C 31 TYR cc_start: 0.7698 (p90) cc_final: 0.7195 (p90) REVERT: C 52 SER cc_start: 0.8240 (t) cc_final: 0.7529 (p) REVERT: C 77 ASN cc_start: 0.8532 (t0) cc_final: 0.7777 (t0) REVERT: C 93 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6746 (tt) REVERT: A 41 THR cc_start: 0.7782 (p) cc_final: 0.7480 (t) REVERT: A 60 GLN cc_start: 0.7467 (tm-30) cc_final: 0.6605 (tm-30) REVERT: A 72 TRP cc_start: 0.8115 (t60) cc_final: 0.7627 (t60) REVERT: A 119 LYS cc_start: 0.7838 (tppt) cc_final: 0.7091 (tppt) REVERT: A 181 PHE cc_start: 0.6793 (OUTLIER) cc_final: 0.6365 (p90) REVERT: A 182 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.6891 (mt) REVERT: A 183 MET cc_start: 0.5954 (tmt) cc_final: 0.5624 (tmt) REVERT: A 250 LEU cc_start: 0.8152 (tp) cc_final: 0.7631 (tp) REVERT: A 302 LEU cc_start: 0.7638 (tp) cc_final: 0.7256 (tt) REVERT: A 319 TYR cc_start: 0.7381 (m-10) cc_final: 0.7083 (m-10) REVERT: A 320 GLN cc_start: 0.7576 (mm-40) cc_final: 0.7361 (mm-40) REVERT: A 325 ARG cc_start: 0.7590 (ptp-170) cc_final: 0.7346 (ptt180) REVERT: A 346 GLU cc_start: 0.8544 (mm-30) cc_final: 0.7938 (mm-30) REVERT: A 360 ASN cc_start: 0.8479 (m-40) cc_final: 0.8065 (p0) REVERT: A 362 LYS cc_start: 0.7713 (tmtt) cc_final: 0.7469 (tmtt) REVERT: A 401 VAL cc_start: 0.5998 (m) cc_final: 0.5640 (t) REVERT: A 430 LYS cc_start: 0.8251 (mmmt) cc_final: 0.7774 (mmmt) REVERT: A 459 TYR cc_start: 0.7350 (p90) cc_final: 0.6912 (p90) REVERT: A 472 ARG cc_start: 0.7993 (ttm170) cc_final: 0.7682 (ttm-80) REVERT: A 473 ASP cc_start: 0.8477 (t0) cc_final: 0.7300 (m-30) REVERT: A 520 SER cc_start: 0.8171 (m) cc_final: 0.7719 (p) REVERT: A 538 ASN cc_start: 0.7330 (t0) cc_final: 0.7004 (t0) REVERT: A 568 PHE cc_start: 0.7522 (t80) cc_final: 0.7123 (t80) REVERT: A 580 ASP cc_start: 0.7064 (t70) cc_final: 0.6366 (t0) outliers start: 44 outliers final: 32 residues processed: 225 average time/residue: 0.1990 time to fit residues: 56.9841 Evaluate side-chains 235 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 672 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 54 optimal weight: 0.0980 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 24 optimal weight: 0.0970 chunk 45 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 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 = 0.3996 r_free = 0.3996 target = 0.151410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.129851 restraints weight = 10577.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.134739 restraints weight = 5712.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.138040 restraints weight = 3589.797| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6219 Z= 0.223 Angle : 0.741 14.087 8468 Z= 0.365 Chirality : 0.047 0.199 921 Planarity : 0.004 0.040 1100 Dihedral : 8.382 92.399 875 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer: Outliers : 6.02 % Allowed : 25.26 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.39 (0.28), residues: 764 helix: -2.07 (1.13), residues: 28 sheet: -1.08 (0.35), residues: 193 loop : -2.95 (0.24), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 359 HIS 0.002 0.001 HIS A 525 PHE 0.033 0.002 PHE A 174 TYR 0.028 0.002 TYR A 459 ARG 0.007 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 201 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 27 PHE cc_start: 0.8121 (t80) cc_final: 0.7739 (t80) REVERT: C 52 SER cc_start: 0.8227 (t) cc_final: 0.7471 (p) REVERT: C 77 ASN cc_start: 0.8490 (t0) cc_final: 0.7707 (t0) REVERT: C 93 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6771 (tt) REVERT: C 99 ARG cc_start: 0.7977 (ptt90) cc_final: 0.7421 (ppt170) REVERT: A 41 THR cc_start: 0.7708 (p) cc_final: 0.7393 (t) REVERT: A 60 GLN cc_start: 0.7412 (tm-30) cc_final: 0.6562 (tm-30) REVERT: A 72 TRP cc_start: 0.8051 (t60) cc_final: 0.7595 (t60) REVERT: A 108 ARG cc_start: 0.7699 (mtm180) cc_final: 0.7307 (mtp180) REVERT: A 119 LYS cc_start: 0.7772 (tppt) cc_final: 0.6984 (tppt) REVERT: A 181 PHE cc_start: 0.6790 (OUTLIER) cc_final: 0.6343 (p90) REVERT: A 182 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6815 (mt) REVERT: A 183 MET cc_start: 0.6095 (tmt) cc_final: 0.5657 (tmt) REVERT: A 250 LEU cc_start: 0.8116 (tp) cc_final: 0.7595 (tp) REVERT: A 302 LEU cc_start: 0.7503 (tp) cc_final: 0.7137 (tt) REVERT: A 319 TYR cc_start: 0.7337 (m-10) cc_final: 0.7039 (m-10) REVERT: A 346 GLU cc_start: 0.8530 (mm-30) cc_final: 0.7925 (mm-30) REVERT: A 360 ASN cc_start: 0.8476 (m-40) cc_final: 0.8091 (p0) REVERT: A 430 LYS cc_start: 0.8107 (mmmt) cc_final: 0.7589 (mmmt) REVERT: A 434 ASP cc_start: 0.7104 (t0) cc_final: 0.6788 (t0) REVERT: A 464 LYS cc_start: 0.7824 (mmtt) cc_final: 0.7551 (mmtm) REVERT: A 472 ARG cc_start: 0.7970 (ttm170) cc_final: 0.7633 (ttm-80) REVERT: A 473 ASP cc_start: 0.8453 (t0) cc_final: 0.6950 (m-30) REVERT: A 518 VAL cc_start: 0.8398 (t) cc_final: 0.8121 (p) REVERT: A 520 SER cc_start: 0.8159 (m) cc_final: 0.7563 (p) REVERT: A 538 ASN cc_start: 0.7357 (t0) cc_final: 0.7006 (t0) REVERT: A 546 ASN cc_start: 0.7583 (m-40) cc_final: 0.6871 (p0) REVERT: A 568 PHE cc_start: 0.7465 (t80) cc_final: 0.7096 (t80) REVERT: A 580 ASP cc_start: 0.7059 (t70) cc_final: 0.6371 (t0) outliers start: 40 outliers final: 33 residues processed: 218 average time/residue: 0.1934 time to fit residues: 53.9593 Evaluate side-chains 234 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 198 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 386 TYR Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 672 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 5 optimal weight: 0.0980 chunk 1 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 2 optimal weight: 0.1980 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** 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 = 0.4008 r_free = 0.4008 target = 0.152480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.130601 restraints weight = 10649.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.135549 restraints weight = 5762.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.138882 restraints weight = 3628.017| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6219 Z= 0.213 Angle : 0.743 14.382 8468 Z= 0.367 Chirality : 0.046 0.212 921 Planarity : 0.004 0.039 1100 Dihedral : 8.323 92.731 875 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % Rotamer: Outliers : 5.26 % Allowed : 26.62 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.26 (0.28), residues: 764 helix: -2.02 (1.13), residues: 28 sheet: -0.97 (0.35), residues: 197 loop : -2.86 (0.24), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 359 HIS 0.002 0.001 HIS A 525 PHE 0.028 0.002 PHE A 174 TYR 0.036 0.001 TYR A 459 ARG 0.003 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 PHE cc_start: 0.8103 (t80) cc_final: 0.7715 (t80) REVERT: C 31 TYR cc_start: 0.7664 (p90) cc_final: 0.7128 (p90) REVERT: C 52 SER cc_start: 0.8167 (t) cc_final: 0.7408 (p) REVERT: C 72 ARG cc_start: 0.7698 (tpp80) cc_final: 0.7443 (tpp80) REVERT: C 77 ASN cc_start: 0.8443 (t0) cc_final: 0.7628 (t0) REVERT: C 81 LEU cc_start: 0.5798 (mt) cc_final: 0.5595 (mt) REVERT: C 93 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6743 (tt) REVERT: C 99 ARG cc_start: 0.7880 (ptt90) cc_final: 0.7420 (ppt170) REVERT: A 41 THR cc_start: 0.7695 (p) cc_final: 0.7394 (t) REVERT: A 60 GLN cc_start: 0.7383 (tm-30) cc_final: 0.6531 (tm-30) REVERT: A 72 TRP cc_start: 0.8044 (t60) cc_final: 0.7616 (t60) REVERT: A 108 ARG cc_start: 0.7743 (mtm180) cc_final: 0.7367 (mtp180) REVERT: A 119 LYS cc_start: 0.7724 (tppt) cc_final: 0.6973 (tppt) REVERT: A 181 PHE cc_start: 0.6843 (OUTLIER) cc_final: 0.6392 (p90) REVERT: A 182 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6809 (mt) REVERT: A 183 MET cc_start: 0.6007 (tmt) cc_final: 0.5585 (tmt) REVERT: A 250 LEU cc_start: 0.8027 (tp) cc_final: 0.7468 (tp) REVERT: A 255 LEU cc_start: 0.5082 (tp) cc_final: 0.4624 (tt) REVERT: A 302 LEU cc_start: 0.7473 (tp) cc_final: 0.7102 (tt) REVERT: A 319 TYR cc_start: 0.7305 (m-10) cc_final: 0.7037 (m-10) REVERT: A 346 GLU cc_start: 0.8504 (mm-30) cc_final: 0.7898 (mm-30) REVERT: A 360 ASN cc_start: 0.8488 (m-40) cc_final: 0.8089 (p0) REVERT: A 361 ARG cc_start: 0.7817 (ttm170) cc_final: 0.7251 (ttm170) REVERT: A 430 LYS cc_start: 0.8073 (mmmt) cc_final: 0.7804 (mmmt) REVERT: A 434 ASP cc_start: 0.7073 (t0) cc_final: 0.6768 (t0) REVERT: A 464 LYS cc_start: 0.7892 (mmtt) cc_final: 0.7629 (mmtm) REVERT: A 472 ARG cc_start: 0.7933 (ttm170) cc_final: 0.7601 (ttm-80) REVERT: A 473 ASP cc_start: 0.8445 (t0) cc_final: 0.6914 (m-30) REVERT: A 518 VAL cc_start: 0.8392 (t) cc_final: 0.8042 (p) REVERT: A 520 SER cc_start: 0.8235 (m) cc_final: 0.7462 (p) REVERT: A 538 ASN cc_start: 0.7420 (t0) cc_final: 0.7055 (t0) REVERT: A 568 PHE cc_start: 0.7484 (t80) cc_final: 0.7187 (t80) REVERT: A 580 ASP cc_start: 0.7053 (t70) cc_final: 0.6373 (t0) outliers start: 35 outliers final: 28 residues processed: 216 average time/residue: 0.2022 time to fit residues: 56.4191 Evaluate side-chains 224 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 672 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 44 optimal weight: 0.6980 chunk 33 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 202 ASN ** 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 = 0.4003 r_free = 0.4003 target = 0.152024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.130247 restraints weight = 10673.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.135196 restraints weight = 5757.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.138466 restraints weight = 3615.349| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6219 Z= 0.221 Angle : 0.737 14.132 8468 Z= 0.365 Chirality : 0.047 0.208 921 Planarity : 0.004 0.041 1100 Dihedral : 8.226 93.599 873 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 5.11 % Allowed : 27.07 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.16 (0.28), residues: 764 helix: -2.00 (1.13), residues: 28 sheet: -0.86 (0.36), residues: 197 loop : -2.81 (0.24), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 359 HIS 0.003 0.001 HIS A 57 PHE 0.034 0.002 PHE A 174 TYR 0.035 0.001 TYR A 459 ARG 0.005 0.000 ARG A 325 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 27 PHE cc_start: 0.8136 (t80) cc_final: 0.7775 (t80) REVERT: C 29 PHE cc_start: 0.7355 (m-10) cc_final: 0.6915 (m-10) REVERT: C 52 SER cc_start: 0.8113 (t) cc_final: 0.7388 (p) REVERT: C 72 ARG cc_start: 0.7669 (tpp80) cc_final: 0.7415 (tpp80) REVERT: C 77 ASN cc_start: 0.8472 (t0) cc_final: 0.7750 (t0) REVERT: C 93 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6794 (tt) REVERT: C 99 ARG cc_start: 0.7899 (ptt90) cc_final: 0.7412 (ppt170) REVERT: A 41 THR cc_start: 0.7718 (p) cc_final: 0.7429 (t) REVERT: A 60 GLN cc_start: 0.7356 (tm-30) cc_final: 0.6504 (tm-30) REVERT: A 72 TRP cc_start: 0.8056 (t60) cc_final: 0.7586 (t60) REVERT: A 108 ARG cc_start: 0.7763 (mtm180) cc_final: 0.7554 (mtm110) REVERT: A 119 LYS cc_start: 0.7704 (tppt) cc_final: 0.6978 (tppt) REVERT: A 181 PHE cc_start: 0.6838 (OUTLIER) cc_final: 0.6437 (p90) REVERT: A 182 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6701 (mt) REVERT: A 183 MET cc_start: 0.5998 (tmt) cc_final: 0.5585 (tmt) REVERT: A 250 LEU cc_start: 0.7996 (tp) cc_final: 0.7458 (tp) REVERT: A 255 LEU cc_start: 0.5125 (tp) cc_final: 0.4748 (tt) REVERT: A 302 LEU cc_start: 0.7491 (tp) cc_final: 0.7108 (tt) REVERT: A 319 TYR cc_start: 0.7267 (m-10) cc_final: 0.7026 (m-10) REVERT: A 321 THR cc_start: 0.8157 (t) cc_final: 0.7793 (p) REVERT: A 346 GLU cc_start: 0.8493 (mm-30) cc_final: 0.7975 (mm-30) REVERT: A 360 ASN cc_start: 0.8468 (m-40) cc_final: 0.8113 (p0) REVERT: A 429 TYR cc_start: 0.7705 (t80) cc_final: 0.7285 (t80) REVERT: A 430 LYS cc_start: 0.8069 (mmmt) cc_final: 0.7800 (mmmt) REVERT: A 434 ASP cc_start: 0.7047 (t0) cc_final: 0.6756 (t0) REVERT: A 472 ARG cc_start: 0.7940 (ttm170) cc_final: 0.7620 (ttm-80) REVERT: A 473 ASP cc_start: 0.8466 (t0) cc_final: 0.7242 (m-30) REVERT: A 518 VAL cc_start: 0.8315 (t) cc_final: 0.7926 (p) REVERT: A 520 SER cc_start: 0.8246 (m) cc_final: 0.7505 (p) REVERT: A 538 ASN cc_start: 0.7376 (t0) cc_final: 0.7059 (t0) REVERT: A 568 PHE cc_start: 0.7398 (t80) cc_final: 0.6928 (t80) REVERT: A 580 ASP cc_start: 0.7056 (t70) cc_final: 0.6360 (t0) REVERT: A 681 GLN cc_start: 0.7850 (mp10) cc_final: 0.7590 (mp10) outliers start: 34 outliers final: 28 residues processed: 207 average time/residue: 0.1933 time to fit residues: 51.6220 Evaluate side-chains 222 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 484 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 569 GLN Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 672 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 15 optimal weight: 3.9990 chunk 5 optimal weight: 0.0060 chunk 69 optimal weight: 0.8980 chunk 22 optimal weight: 0.1980 chunk 48 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 40 optimal weight: 0.0770 chunk 57 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 overall best weight: 0.3154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN ** A 202 ASN ** 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 = 0.4029 r_free = 0.4029 target = 0.154319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.132416 restraints weight = 10777.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.137473 restraints weight = 5801.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.140847 restraints weight = 3620.477| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6219 Z= 0.189 Angle : 0.730 13.369 8468 Z= 0.359 Chirality : 0.046 0.215 921 Planarity : 0.004 0.040 1100 Dihedral : 7.943 92.222 871 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 3.91 % Allowed : 28.12 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.98 (0.29), residues: 764 helix: -0.07 (1.84), residues: 16 sheet: -0.95 (0.35), residues: 212 loop : -2.69 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 359 HIS 0.002 0.001 HIS A 57 PHE 0.033 0.002 PHE A 174 TYR 0.030 0.001 TYR A 459 ARG 0.002 0.000 ARG A 325 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2469.78 seconds wall clock time: 43 minutes 12.78 seconds (2592.78 seconds total)