Starting phenix.real_space_refine on Sat May 10 11:16:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i4g_35172/05_2025/8i4g_35172.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i4g_35172/05_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_35172/05_2025/8i4g_35172.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i4g_35172/05_2025/8i4g_35172.map" model { file = "/net/cci-nas-00/data/ceres_data/8i4g_35172/05_2025/8i4g_35172.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i4g_35172/05_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-5687/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: 4.07, per 1000 atoms: 0.67 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: 1.35 Conformation dependent library (CDL) restraints added in 821.3 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: 0.83 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: 2.02 Time building geometry restraints manager: 1.58 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: 0.700 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.380 Find NCS groups from input model: 0.070 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:2.520 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 6228 Z= 0.147 Angle : 0.631 5.665 8486 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 Details of bonding type rmsd hydrogen bonds : bond 0.30077 ( 103) hydrogen bonds : angle 11.61967 ( 270) SS BOND : bond 0.00146 ( 9) SS BOND : angle 0.64596 ( 18) covalent geometry : bond 0.00232 ( 6219) covalent geometry : angle 0.63067 ( 8468) *********************** 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 : 0.836 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: 0.2224 time to fit residues: 75.9845 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 : 0.609 ------------------------------------------------------------------------------- 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: 0.2980 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: 0.3796 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.162387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.141209 restraints weight = 10563.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.146196 restraints weight = 5643.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.149578 restraints weight = 3529.928| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6228 Z= 0.122 Angle : 0.608 11.888 8486 Z= 0.305 Chirality : 0.044 0.169 921 Planarity : 0.004 0.044 1100 Dihedral : 8.945 88.562 899 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 6.77 % Allowed : 15.79 % Favored : 77.44 % 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: -4.14 (0.26), residues: 764 helix: -3.16 (0.83), residues: 28 sheet: -2.25 (0.33), residues: 195 loop : -3.15 (0.23), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 110 HIS 0.002 0.001 HIS A 213 PHE 0.029 0.002 PHE A 568 TYR 0.020 0.001 TYR C 94 ARG 0.005 0.001 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03199 ( 103) hydrogen bonds : angle 6.71750 ( 270) SS BOND : bond 0.00387 ( 9) SS BOND : angle 2.09205 ( 18) covalent geometry : bond 0.00271 ( 6219) covalent geometry : angle 0.60130 ( 8468) *********************** 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 247 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 202 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 31 TYR cc_start: 0.7537 (p90) cc_final: 0.6979 (p90) REVERT: C 77 ASN cc_start: 0.8218 (t0) cc_final: 0.7647 (t0) REVERT: A 40 PHE cc_start: 0.8299 (m-80) cc_final: 0.8053 (m-10) REVERT: A 42 ARG cc_start: 0.7980 (ttm110) cc_final: 0.7553 (ttm110) REVERT: A 60 GLN cc_start: 0.7344 (tm-30) cc_final: 0.6532 (tm-30) REVERT: A 119 LYS cc_start: 0.7689 (tppt) cc_final: 0.6885 (tppt) REVERT: A 134 ILE cc_start: 0.7685 (mt) cc_final: 0.7323 (tt) REVERT: A 250 LEU cc_start: 0.8002 (tp) cc_final: 0.7541 (tp) REVERT: A 255 LEU cc_start: 0.4948 (OUTLIER) cc_final: 0.4624 (tp) REVERT: A 299 LEU cc_start: 0.8161 (tp) cc_final: 0.7871 (tp) REVERT: A 302 LEU cc_start: 0.7760 (tp) cc_final: 0.7430 (tt) REVERT: A 320 GLN cc_start: 0.7458 (mm-40) cc_final: 0.7251 (mm-40) REVERT: A 346 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7897 (mm-30) REVERT: A 362 LYS cc_start: 0.7586 (tmtt) cc_final: 0.6980 (tmtt) REVERT: A 398 PHE cc_start: 0.8213 (m-10) cc_final: 0.7995 (m-10) REVERT: A 430 LYS cc_start: 0.7994 (mmmt) cc_final: 0.7308 (mmmt) REVERT: A 434 ASP cc_start: 0.6917 (t0) cc_final: 0.6442 (t0) REVERT: A 472 ARG cc_start: 0.7808 (ttm170) cc_final: 0.7559 (ttm-80) REVERT: A 473 ASP cc_start: 0.8421 (t0) cc_final: 0.6644 (m-30) REVERT: A 495 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.6568 (p90) REVERT: A 518 VAL cc_start: 0.8556 (t) cc_final: 0.8286 (p) REVERT: A 520 SER cc_start: 0.7562 (m) cc_final: 0.7269 (t) REVERT: A 534 LYS cc_start: 0.8542 (mmmm) cc_final: 0.8320 (mmtp) REVERT: A 535 LYS cc_start: 0.8149 (pptt) cc_final: 0.7716 (pptt) REVERT: A 542 ASN cc_start: 0.8190 (m-40) cc_final: 0.7967 (m110) REVERT: A 543 LYS cc_start: 0.7610 (ttmt) cc_final: 0.7150 (ttmm) REVERT: A 580 ASP cc_start: 0.6956 (t70) cc_final: 0.6443 (t0) REVERT: A 593 ILE cc_start: 0.8615 (mt) cc_final: 0.8390 (mt) REVERT: A 598 PHE cc_start: 0.7091 (t80) cc_final: 0.6796 (t80) outliers start: 45 outliers final: 30 residues processed: 227 average time/residue: 0.1814 time to fit residues: 52.9746 Evaluate side-chains 220 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain A residue 44 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 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 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 Chi-restraints excluded: chain A residue 672 ILE 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: 6.9990 chunk 47 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 0.0000 chunk 16 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.6786 ------------------------------------------------------------------------------- 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 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.155632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.134698 restraints weight = 10692.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.139599 restraints weight = 5748.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.142870 restraints weight = 3612.886| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6228 Z= 0.143 Angle : 0.621 11.165 8486 Z= 0.312 Chirality : 0.044 0.178 921 Planarity : 0.004 0.041 1100 Dihedral : 8.770 86.794 894 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 7.67 % Allowed : 17.59 % Favored : 74.74 % 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: -3.77 (0.27), residues: 764 helix: -2.01 (1.23), residues: 22 sheet: -1.83 (0.34), residues: 197 loop : -3.01 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 359 HIS 0.002 0.001 HIS A 213 PHE 0.027 0.002 PHE A 496 TYR 0.013 0.002 TYR A 97 ARG 0.004 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03144 ( 103) hydrogen bonds : angle 6.09229 ( 270) SS BOND : bond 0.00479 ( 9) SS BOND : angle 2.30905 ( 18) covalent geometry : bond 0.00315 ( 6219) covalent geometry : angle 0.61276 ( 8468) *********************** 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 251 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 200 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 31 TYR cc_start: 0.7514 (p90) cc_final: 0.7015 (p90) REVERT: C 77 ASN cc_start: 0.8330 (t0) cc_final: 0.7698 (t0) REVERT: A 40 PHE cc_start: 0.8332 (m-80) cc_final: 0.8036 (m-10) REVERT: A 60 GLN cc_start: 0.7360 (tm-30) cc_final: 0.6498 (tm-30) REVERT: A 72 TRP cc_start: 0.8003 (t60) cc_final: 0.7713 (t60) REVERT: A 119 LYS cc_start: 0.7703 (tppt) cc_final: 0.7031 (tppt) REVERT: A 250 LEU cc_start: 0.8071 (tp) cc_final: 0.7596 (tp) REVERT: A 255 LEU cc_start: 0.4743 (OUTLIER) cc_final: 0.4377 (tp) REVERT: A 299 LEU cc_start: 0.8164 (tp) cc_final: 0.7930 (tp) REVERT: A 302 LEU cc_start: 0.7844 (tp) cc_final: 0.7144 (tt) REVERT: A 305 THR cc_start: 0.8320 (m) cc_final: 0.8092 (p) REVERT: A 319 TYR cc_start: 0.7281 (m-10) cc_final: 0.6977 (m-10) REVERT: A 320 GLN cc_start: 0.7499 (mm-40) cc_final: 0.7228 (mm-40) REVERT: A 346 GLU cc_start: 0.8432 (mm-30) cc_final: 0.7775 (mm-30) REVERT: A 362 LYS cc_start: 0.7683 (tmtt) cc_final: 0.7063 (tmtt) REVERT: A 430 LYS cc_start: 0.8086 (mmmt) cc_final: 0.7409 (mmmt) REVERT: A 472 ARG cc_start: 0.7806 (ttm170) cc_final: 0.7574 (ttm-80) REVERT: A 473 ASP cc_start: 0.8400 (t0) cc_final: 0.7021 (m-30) REVERT: A 495 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.6618 (p90) REVERT: A 520 SER cc_start: 0.7854 (m) cc_final: 0.7158 (p) REVERT: A 523 LEU cc_start: 0.7992 (tp) cc_final: 0.7788 (tp) REVERT: A 534 LYS cc_start: 0.8628 (mmmm) cc_final: 0.8355 (mmtp) REVERT: A 568 PHE cc_start: 0.7253 (t80) cc_final: 0.6876 (t80) REVERT: A 580 ASP cc_start: 0.7119 (t70) cc_final: 0.6381 (t0) REVERT: A 592 ASP cc_start: 0.7557 (t70) cc_final: 0.7237 (t0) REVERT: A 593 ILE cc_start: 0.8678 (mt) cc_final: 0.8468 (mt) REVERT: A 598 PHE cc_start: 0.7522 (t80) cc_final: 0.7299 (t80) outliers start: 51 outliers final: 30 residues processed: 224 average time/residue: 0.1859 time to fit residues: 53.3479 Evaluate side-chains 222 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 VAL 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 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 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 333 VAL 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 41 optimal weight: 0.1980 chunk 61 optimal weight: 0.0980 chunk 42 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN A 548 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.150556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.130160 restraints weight = 10850.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.134992 restraints weight = 5771.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.138245 restraints weight = 3584.214| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6228 Z= 0.192 Angle : 0.685 12.714 8486 Z= 0.349 Chirality : 0.046 0.181 921 Planarity : 0.005 0.048 1100 Dihedral : 8.717 88.655 887 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.83 % Favored : 87.17 % Rotamer: Outliers : 7.22 % Allowed : 19.25 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.80 (0.27), residues: 764 helix: -1.68 (1.28), residues: 22 sheet: -1.91 (0.33), residues: 205 loop : -3.03 (0.24), residues: 537 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 0.028 0.002 PHE A 174 TYR 0.019 0.002 TYR A 642 ARG 0.005 0.001 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03202 ( 103) hydrogen bonds : angle 5.73475 ( 270) SS BOND : bond 0.00322 ( 9) SS BOND : angle 2.20430 ( 18) covalent geometry : bond 0.00409 ( 6219) covalent geometry : angle 0.67853 ( 8468) *********************** 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 253 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 205 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 18 LEU cc_start: 0.8146 (tp) cc_final: 0.7299 (tp) REVERT: C 27 PHE cc_start: 0.8069 (t80) cc_final: 0.7654 (t80) REVERT: C 31 TYR cc_start: 0.7644 (p90) cc_final: 0.7176 (p90) REVERT: C 34 MET cc_start: 0.6297 (mtp) cc_final: 0.6011 (mtp) REVERT: C 52 SER cc_start: 0.8312 (t) cc_final: 0.7613 (p) REVERT: C 77 ASN cc_start: 0.8536 (t0) cc_final: 0.7980 (t0) REVERT: A 41 THR cc_start: 0.7702 (p) cc_final: 0.7434 (t) REVERT: A 60 GLN cc_start: 0.7458 (tm-30) cc_final: 0.6572 (tm-30) REVERT: A 72 TRP cc_start: 0.8098 (t60) cc_final: 0.7708 (t60) REVERT: A 119 LYS cc_start: 0.7774 (tppt) cc_final: 0.7064 (tppt) REVERT: A 159 MET cc_start: 0.2007 (ppp) cc_final: 0.1786 (ppp) REVERT: A 250 LEU cc_start: 0.8110 (tp) cc_final: 0.7635 (tp) REVERT: A 255 LEU cc_start: 0.4885 (OUTLIER) cc_final: 0.4499 (tp) REVERT: A 305 THR cc_start: 0.8342 (m) cc_final: 0.8122 (p) REVERT: A 320 GLN cc_start: 0.7550 (mm-40) cc_final: 0.7302 (mm-40) REVERT: A 346 GLU cc_start: 0.8504 (mm-30) cc_final: 0.7893 (mm-30) REVERT: A 356 VAL cc_start: 0.8548 (OUTLIER) cc_final: 0.8259 (p) REVERT: A 362 LYS cc_start: 0.7698 (tmtt) cc_final: 0.7023 (tmtt) REVERT: A 430 LYS cc_start: 0.8204 (mmmt) cc_final: 0.7741 (mmmt) REVERT: A 459 TYR cc_start: 0.7390 (p90) cc_final: 0.7035 (p90) REVERT: A 472 ARG cc_start: 0.7945 (ttm170) cc_final: 0.7594 (ttm-80) REVERT: A 473 ASP cc_start: 0.8471 (t0) cc_final: 0.7180 (m-30) REVERT: A 493 ASN cc_start: 0.7380 (m-40) cc_final: 0.7135 (m-40) REVERT: A 495 TYR cc_start: 0.8320 (OUTLIER) cc_final: 0.6767 (p90) REVERT: A 520 SER cc_start: 0.8032 (m) cc_final: 0.7563 (p) REVERT: A 523 LEU cc_start: 0.8034 (tp) cc_final: 0.7815 (tp) REVERT: A 534 LYS cc_start: 0.8636 (mmmm) cc_final: 0.8290 (mmmm) REVERT: A 538 ASN cc_start: 0.7205 (t0) cc_final: 0.6900 (t0) REVERT: A 543 LYS cc_start: 0.7961 (ttmt) cc_final: 0.7486 (ttmm) REVERT: A 568 PHE cc_start: 0.7377 (t80) cc_final: 0.6963 (t80) REVERT: A 580 ASP cc_start: 0.7260 (t70) cc_final: 0.6451 (t0) REVERT: A 592 ASP cc_start: 0.7523 (t70) cc_final: 0.7191 (t0) REVERT: A 639 TRP cc_start: 0.6572 (OUTLIER) cc_final: 0.6221 (t60) outliers start: 48 outliers final: 32 residues processed: 230 average time/residue: 0.1844 time to fit residues: 54.2219 Evaluate side-chains 232 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 196 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 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 318 ILE 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 446 LYS 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 0.0470 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 7 optimal weight: 0.2980 chunk 68 optimal weight: 0.3980 chunk 57 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 0.0170 chunk 4 optimal weight: 0.3980 overall best weight: 0.2316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN A 69 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 = 0.4043 r_free = 0.4043 target = 0.155017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.133824 restraints weight = 10535.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.138792 restraints weight = 5563.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.142138 restraints weight = 3441.778| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6228 Z= 0.116 Angle : 0.649 11.512 8486 Z= 0.328 Chirality : 0.045 0.168 921 Planarity : 0.004 0.040 1100 Dihedral : 8.357 86.433 883 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 6.47 % Allowed : 22.71 % Favored : 70.83 % 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: -3.55 (0.28), residues: 764 helix: -1.49 (1.34), residues: 22 sheet: -1.48 (0.36), residues: 190 loop : -2.96 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 639 HIS 0.003 0.001 HIS A 525 PHE 0.025 0.001 PHE A 649 TYR 0.016 0.001 TYR A 319 ARG 0.006 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.02798 ( 103) hydrogen bonds : angle 5.44204 ( 270) SS BOND : bond 0.00151 ( 9) SS BOND : angle 2.12712 ( 18) covalent geometry : bond 0.00268 ( 6219) covalent geometry : angle 0.64242 ( 8468) *********************** 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 246 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 18 LEU cc_start: 0.7884 (tp) cc_final: 0.7506 (tp) REVERT: C 27 PHE cc_start: 0.8052 (t80) cc_final: 0.7534 (t80) REVERT: C 31 TYR cc_start: 0.7681 (p90) cc_final: 0.7200 (p90) REVERT: C 52 SER cc_start: 0.8258 (t) cc_final: 0.7474 (p) REVERT: C 77 ASN cc_start: 0.8506 (t0) cc_final: 0.7818 (t0) REVERT: C 83 MET cc_start: 0.6404 (OUTLIER) cc_final: 0.6135 (mtm) REVERT: C 93 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6693 (tt) REVERT: A 41 THR cc_start: 0.7579 (p) cc_final: 0.7255 (t) REVERT: A 44 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.8233 (t) REVERT: A 60 GLN cc_start: 0.7459 (tm-30) cc_final: 0.6562 (tm-30) REVERT: A 72 TRP cc_start: 0.8017 (t60) cc_final: 0.7634 (t60) REVERT: A 119 LYS cc_start: 0.7727 (tppt) cc_final: 0.6962 (tppt) REVERT: A 159 MET cc_start: 0.2030 (OUTLIER) cc_final: 0.1827 (ppp) REVERT: A 183 MET cc_start: 0.6047 (tmt) cc_final: 0.5732 (tmt) REVERT: A 201 LYS cc_start: 0.5442 (OUTLIER) cc_final: 0.4971 (ptpt) REVERT: A 250 LEU cc_start: 0.8042 (tp) cc_final: 0.7528 (tp) REVERT: A 255 LEU cc_start: 0.4719 (OUTLIER) cc_final: 0.4487 (tp) REVERT: A 302 LEU cc_start: 0.7660 (tp) cc_final: 0.7313 (tt) REVERT: A 316 LYS cc_start: 0.6489 (mtmt) cc_final: 0.5733 (mtpt) REVERT: A 319 TYR cc_start: 0.7373 (m-10) cc_final: 0.7085 (m-10) REVERT: A 320 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7213 (mm-40) REVERT: A 346 GLU cc_start: 0.8549 (mm-30) cc_final: 0.7952 (mm-30) REVERT: A 356 VAL cc_start: 0.8484 (OUTLIER) cc_final: 0.8176 (p) REVERT: A 362 LYS cc_start: 0.7646 (tmtt) cc_final: 0.7263 (tptp) REVERT: A 430 LYS cc_start: 0.8089 (mmmt) cc_final: 0.7451 (mmmt) REVERT: A 459 TYR cc_start: 0.7231 (p90) cc_final: 0.6405 (p90) REVERT: A 472 ARG cc_start: 0.7948 (ttm170) cc_final: 0.7551 (ttm-80) REVERT: A 473 ASP cc_start: 0.8422 (t0) cc_final: 0.6807 (m-30) REVERT: A 495 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.6731 (p90) REVERT: A 499 GLN cc_start: 0.6840 (tm-30) cc_final: 0.6590 (tm-30) REVERT: A 520 SER cc_start: 0.7914 (m) cc_final: 0.7270 (p) REVERT: A 523 LEU cc_start: 0.8057 (tp) cc_final: 0.7845 (tp) REVERT: A 534 LYS cc_start: 0.8571 (mmmm) cc_final: 0.8304 (mmtp) REVERT: A 538 ASN cc_start: 0.7184 (t0) cc_final: 0.6858 (t0) REVERT: A 568 PHE cc_start: 0.7426 (t80) cc_final: 0.7035 (t80) REVERT: A 580 ASP cc_start: 0.7189 (t70) cc_final: 0.6342 (t0) REVERT: A 592 ASP cc_start: 0.7610 (t70) cc_final: 0.7385 (t0) REVERT: A 639 TRP cc_start: 0.6368 (OUTLIER) cc_final: 0.5978 (t60) outliers start: 43 outliers final: 25 residues processed: 223 average time/residue: 0.2006 time to fit residues: 56.5337 Evaluate side-chains 229 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain A residue 44 VAL 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 159 MET 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 356 VAL 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 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 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 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: 0.0370 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- 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 A 609 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.150001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.128191 restraints weight = 10648.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.133185 restraints weight = 5777.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.136550 restraints weight = 3637.066| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6228 Z= 0.215 Angle : 0.737 13.471 8486 Z= 0.374 Chirality : 0.047 0.173 921 Planarity : 0.005 0.042 1100 Dihedral : 8.583 89.524 881 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer: Outliers : 6.32 % Allowed : 23.61 % 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: -3.61 (0.28), residues: 764 helix: -2.24 (1.02), residues: 28 sheet: -1.71 (0.33), residues: 218 loop : -2.91 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 359 HIS 0.003 0.001 HIS A 525 PHE 0.028 0.002 PHE A 174 TYR 0.021 0.002 TYR A 642 ARG 0.008 0.001 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03299 ( 103) hydrogen bonds : angle 5.64694 ( 270) SS BOND : bond 0.00285 ( 9) SS BOND : angle 2.37767 ( 18) covalent geometry : bond 0.00471 ( 6219) covalent geometry : angle 0.72968 ( 8468) *********************** 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 249 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 207 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 18 LEU cc_start: 0.8347 (tp) cc_final: 0.7626 (tp) REVERT: C 27 PHE cc_start: 0.8203 (t80) cc_final: 0.7840 (t80) REVERT: C 29 PHE cc_start: 0.7429 (m-10) cc_final: 0.7109 (m-10) REVERT: C 31 TYR cc_start: 0.7665 (p90) cc_final: 0.7169 (p90) REVERT: C 52 SER cc_start: 0.8230 (t) cc_final: 0.7544 (p) REVERT: C 77 ASN cc_start: 0.8497 (t0) cc_final: 0.7807 (t0) REVERT: C 83 MET cc_start: 0.6674 (OUTLIER) cc_final: 0.6032 (mtm) REVERT: C 93 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.6953 (tt) REVERT: A 41 THR cc_start: 0.7775 (p) cc_final: 0.7523 (t) REVERT: A 44 VAL cc_start: 0.8481 (OUTLIER) cc_final: 0.8262 (t) REVERT: A 60 GLN cc_start: 0.7403 (tm-30) cc_final: 0.6523 (tm-30) REVERT: A 72 TRP cc_start: 0.8096 (t60) cc_final: 0.7678 (t60) REVERT: A 119 LYS cc_start: 0.7823 (tppt) cc_final: 0.7159 (tppt) REVERT: A 159 MET cc_start: 0.2594 (OUTLIER) cc_final: 0.2328 (ppp) REVERT: A 175 GLU cc_start: 0.8219 (tm-30) cc_final: 0.8012 (tm-30) REVERT: A 182 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7264 (mp) REVERT: A 201 LYS cc_start: 0.5754 (OUTLIER) cc_final: 0.5481 (ptpt) REVERT: A 250 LEU cc_start: 0.8177 (tp) cc_final: 0.7678 (tp) REVERT: A 255 LEU cc_start: 0.5019 (OUTLIER) cc_final: 0.4698 (tp) REVERT: A 302 LEU cc_start: 0.7960 (tp) cc_final: 0.7208 (tt) REVERT: A 305 THR cc_start: 0.8371 (m) cc_final: 0.8154 (p) REVERT: A 320 GLN cc_start: 0.7506 (mm-40) cc_final: 0.7265 (mm-40) REVERT: A 346 GLU cc_start: 0.8505 (mm-30) cc_final: 0.7913 (mm-30) REVERT: A 356 VAL cc_start: 0.8550 (OUTLIER) cc_final: 0.8330 (p) REVERT: A 360 ASN cc_start: 0.8452 (m-40) cc_final: 0.8120 (p0) REVERT: A 362 LYS cc_start: 0.7724 (tmtt) cc_final: 0.7143 (tmtt) REVERT: A 430 LYS cc_start: 0.8206 (mmmt) cc_final: 0.7442 (mmmt) REVERT: A 434 ASP cc_start: 0.7123 (t0) cc_final: 0.6805 (t0) REVERT: A 472 ARG cc_start: 0.7914 (ttm170) cc_final: 0.7624 (ttm-80) REVERT: A 473 ASP cc_start: 0.8446 (t0) cc_final: 0.7269 (m-30) REVERT: A 495 TYR cc_start: 0.8344 (OUTLIER) cc_final: 0.6769 (p90) REVERT: A 520 SER cc_start: 0.8070 (m) cc_final: 0.7594 (p) REVERT: A 534 LYS cc_start: 0.8632 (mmmm) cc_final: 0.8271 (mmmm) REVERT: A 538 ASN cc_start: 0.7227 (t0) cc_final: 0.6927 (t0) REVERT: A 568 PHE cc_start: 0.7323 (t80) cc_final: 0.6913 (t80) REVERT: A 580 ASP cc_start: 0.7313 (t70) cc_final: 0.6458 (t0) REVERT: A 639 TRP cc_start: 0.6548 (OUTLIER) cc_final: 0.6231 (t60) outliers start: 42 outliers final: 27 residues processed: 226 average time/residue: 0.1942 time to fit residues: 56.0033 Evaluate side-chains 238 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain A residue 44 VAL 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 159 MET 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 356 VAL 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 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 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 672 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 64 optimal weight: 0.1980 chunk 16 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.150980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.129110 restraints weight = 10650.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.134020 restraints weight = 5802.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.137379 restraints weight = 3667.163| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6228 Z= 0.155 Angle : 0.697 12.156 8486 Z= 0.351 Chirality : 0.046 0.182 921 Planarity : 0.005 0.042 1100 Dihedral : 8.454 87.858 881 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 6.77 % Allowed : 24.51 % 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: -3.56 (0.28), residues: 764 helix: -2.25 (1.01), residues: 28 sheet: -1.56 (0.34), residues: 207 loop : -2.91 (0.24), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 359 HIS 0.003 0.001 HIS A 525 PHE 0.042 0.002 PHE A 496 TYR 0.015 0.001 TYR A 642 ARG 0.006 0.001 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03028 ( 103) hydrogen bonds : angle 5.61375 ( 270) SS BOND : bond 0.00229 ( 9) SS BOND : angle 2.18487 ( 18) covalent geometry : bond 0.00350 ( 6219) covalent geometry : angle 0.69035 ( 8468) *********************** 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 246 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 201 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 18 LEU cc_start: 0.8259 (tp) cc_final: 0.7648 (tp) REVERT: C 27 PHE cc_start: 0.8135 (t80) cc_final: 0.7739 (t80) REVERT: C 29 PHE cc_start: 0.7421 (m-10) cc_final: 0.7092 (m-10) REVERT: C 31 TYR cc_start: 0.7688 (p90) cc_final: 0.7172 (p90) REVERT: C 52 SER cc_start: 0.8221 (t) cc_final: 0.7451 (p) REVERT: C 77 ASN cc_start: 0.8473 (t0) cc_final: 0.7732 (t0) REVERT: C 83 MET cc_start: 0.6703 (OUTLIER) cc_final: 0.6000 (mtm) REVERT: C 93 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.6831 (tt) REVERT: C 105 TYR cc_start: 0.8274 (m-80) cc_final: 0.8009 (m-80) REVERT: A 41 THR cc_start: 0.7749 (p) cc_final: 0.7423 (t) REVERT: A 44 VAL cc_start: 0.8464 (OUTLIER) cc_final: 0.8242 (t) REVERT: A 60 GLN cc_start: 0.7431 (tm-30) cc_final: 0.6564 (tm-30) REVERT: A 72 TRP cc_start: 0.8072 (t60) cc_final: 0.7616 (t60) REVERT: A 119 LYS cc_start: 0.7838 (tppt) cc_final: 0.7112 (tppt) REVERT: A 159 MET cc_start: 0.2403 (OUTLIER) cc_final: 0.2082 (ppp) REVERT: A 181 PHE cc_start: 0.6906 (OUTLIER) cc_final: 0.6544 (p90) REVERT: A 201 LYS cc_start: 0.5643 (OUTLIER) cc_final: 0.5400 (ptpt) REVERT: A 213 HIS cc_start: 0.6609 (t-90) cc_final: 0.6385 (m-70) REVERT: A 250 LEU cc_start: 0.8111 (tp) cc_final: 0.7601 (tp) REVERT: A 255 LEU cc_start: 0.4988 (OUTLIER) cc_final: 0.4636 (tp) REVERT: A 305 THR cc_start: 0.8364 (m) cc_final: 0.8112 (p) REVERT: A 320 GLN cc_start: 0.7529 (mm-40) cc_final: 0.7250 (mm-40) REVERT: A 346 GLU cc_start: 0.8516 (mm-30) cc_final: 0.7915 (mm-30) REVERT: A 356 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8268 (p) REVERT: A 360 ASN cc_start: 0.8475 (m-40) cc_final: 0.8045 (p0) REVERT: A 362 LYS cc_start: 0.7693 (tmtt) cc_final: 0.7109 (tmtt) REVERT: A 364 ILE cc_start: 0.8064 (mt) cc_final: 0.7828 (mt) REVERT: A 430 LYS cc_start: 0.8287 (mmmt) cc_final: 0.7707 (mmmt) REVERT: A 434 ASP cc_start: 0.7105 (t0) cc_final: 0.6794 (t0) REVERT: A 472 ARG cc_start: 0.7952 (ttm170) cc_final: 0.7608 (ttm-80) REVERT: A 473 ASP cc_start: 0.8408 (t0) cc_final: 0.6926 (m-30) REVERT: A 520 SER cc_start: 0.8047 (m) cc_final: 0.7547 (p) REVERT: A 534 LYS cc_start: 0.8608 (mmmm) cc_final: 0.8247 (mmmm) REVERT: A 538 ASN cc_start: 0.7319 (t0) cc_final: 0.6920 (t0) REVERT: A 568 PHE cc_start: 0.7430 (t80) cc_final: 0.7106 (t80) REVERT: A 580 ASP cc_start: 0.7157 (t70) cc_final: 0.6529 (t0) outliers start: 45 outliers final: 30 residues processed: 221 average time/residue: 0.1993 time to fit residues: 55.9954 Evaluate side-chains 237 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 83 MET Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 44 VAL 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 159 MET Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 181 PHE 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 318 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 464 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 535 LYS Chi-restraints excluded: chain A residue 559 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 40 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 54 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 0.0970 chunk 19 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.152135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.130963 restraints weight = 10410.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.135837 restraints weight = 5595.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.139139 restraints weight = 3491.806| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6228 Z= 0.144 Angle : 0.705 13.803 8486 Z= 0.353 Chirality : 0.046 0.196 921 Planarity : 0.004 0.041 1100 Dihedral : 8.139 88.044 879 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 6.92 % Allowed : 24.51 % Favored : 68.57 % 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: -3.42 (0.28), residues: 764 helix: -2.24 (1.01), residues: 28 sheet: -1.29 (0.35), residues: 208 loop : -2.89 (0.24), residues: 528 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 0.034 0.002 PHE A 496 TYR 0.013 0.001 TYR A 642 ARG 0.004 0.000 ARG A 279 Details of bonding type rmsd hydrogen bonds : bond 0.02934 ( 103) hydrogen bonds : angle 5.51680 ( 270) SS BOND : bond 0.00336 ( 9) SS BOND : angle 2.00605 ( 18) covalent geometry : bond 0.00326 ( 6219) covalent geometry : angle 0.69975 ( 8468) *********************** 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: 46 poor density : 195 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 27 PHE cc_start: 0.8166 (t80) cc_final: 0.7827 (t80) REVERT: C 31 TYR cc_start: 0.7678 (p90) cc_final: 0.7148 (p90) REVERT: C 52 SER cc_start: 0.8174 (t) cc_final: 0.7424 (p) REVERT: C 77 ASN cc_start: 0.8438 (t0) cc_final: 0.7801 (t0) REVERT: C 93 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6849 (tt) REVERT: C 105 TYR cc_start: 0.8284 (m-80) cc_final: 0.8070 (m-80) REVERT: A 41 THR cc_start: 0.7756 (p) cc_final: 0.7464 (t) REVERT: A 44 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8324 (t) REVERT: A 60 GLN cc_start: 0.7370 (tm-30) cc_final: 0.6497 (tm-30) REVERT: A 72 TRP cc_start: 0.8030 (t60) cc_final: 0.7597 (t60) REVERT: A 119 LYS cc_start: 0.7779 (tppt) cc_final: 0.7083 (tppt) REVERT: A 159 MET cc_start: 0.2374 (OUTLIER) cc_final: 0.2143 (ppp) REVERT: A 181 PHE cc_start: 0.6940 (OUTLIER) cc_final: 0.6606 (p90) REVERT: A 183 MET cc_start: 0.5687 (tmt) cc_final: 0.5344 (tmt) REVERT: A 201 LYS cc_start: 0.5709 (OUTLIER) cc_final: 0.5462 (ptpt) REVERT: A 250 LEU cc_start: 0.8125 (tp) cc_final: 0.7596 (tp) REVERT: A 255 LEU cc_start: 0.4872 (OUTLIER) cc_final: 0.4515 (tp) REVERT: A 302 LEU cc_start: 0.7863 (tp) cc_final: 0.7092 (tt) REVERT: A 305 THR cc_start: 0.8356 (m) cc_final: 0.8153 (p) REVERT: A 320 GLN cc_start: 0.7499 (mm-40) cc_final: 0.7231 (mm-40) REVERT: A 325 ARG cc_start: 0.7502 (ptp-170) cc_final: 0.7275 (ptt180) REVERT: A 346 GLU cc_start: 0.8489 (mm-30) cc_final: 0.7884 (mm-30) REVERT: A 356 VAL cc_start: 0.8500 (OUTLIER) cc_final: 0.8258 (p) REVERT: A 360 ASN cc_start: 0.8477 (m-40) cc_final: 0.8046 (p0) REVERT: A 361 ARG cc_start: 0.7821 (ttm170) cc_final: 0.7157 (ttm170) REVERT: A 362 LYS cc_start: 0.7693 (tmtt) cc_final: 0.7144 (tmtt) REVERT: A 364 ILE cc_start: 0.8005 (mt) cc_final: 0.7643 (mt) REVERT: A 430 LYS cc_start: 0.8269 (mmmt) cc_final: 0.7736 (mmmt) REVERT: A 472 ARG cc_start: 0.7941 (ttm170) cc_final: 0.7632 (ttm-80) REVERT: A 473 ASP cc_start: 0.8398 (t0) cc_final: 0.7242 (m-30) REVERT: A 520 SER cc_start: 0.8100 (m) cc_final: 0.7575 (p) REVERT: A 534 LYS cc_start: 0.8601 (mmmm) cc_final: 0.8355 (mmtp) REVERT: A 538 ASN cc_start: 0.7375 (t0) cc_final: 0.7016 (t0) REVERT: A 568 PHE cc_start: 0.7412 (t80) cc_final: 0.7101 (t80) REVERT: A 580 ASP cc_start: 0.7139 (t70) cc_final: 0.6502 (t0) outliers start: 46 outliers final: 29 residues processed: 217 average time/residue: 0.2025 time to fit residues: 56.3839 Evaluate side-chains 230 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 194 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 44 VAL 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 159 MET Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 181 PHE 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 333 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 439 VAL 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 464 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 535 LYS Chi-restraints excluded: chain A residue 559 THR 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 33 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.150444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.128902 restraints weight = 10614.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.133830 restraints weight = 5762.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.137190 restraints weight = 3623.216| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.5138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6228 Z= 0.163 Angle : 0.732 12.871 8486 Z= 0.365 Chirality : 0.047 0.208 921 Planarity : 0.004 0.041 1100 Dihedral : 8.204 88.131 879 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.91 % Favored : 88.09 % Rotamer: Outliers : 5.71 % Allowed : 25.56 % 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: -3.37 (0.28), residues: 764 helix: -1.97 (1.08), residues: 26 sheet: -1.15 (0.34), residues: 206 loop : -2.93 (0.24), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 359 HIS 0.010 0.001 HIS A 213 PHE 0.032 0.002 PHE A 496 TYR 0.021 0.002 TYR A 319 ARG 0.004 0.001 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03107 ( 103) hydrogen bonds : angle 5.52348 ( 270) SS BOND : bond 0.00288 ( 9) SS BOND : angle 2.13679 ( 18) covalent geometry : bond 0.00367 ( 6219) covalent geometry : angle 0.72633 ( 8468) *********************** 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 229 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 191 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 27 PHE cc_start: 0.8174 (t80) cc_final: 0.7817 (t80) REVERT: C 29 PHE cc_start: 0.7414 (m-10) cc_final: 0.6827 (m-10) REVERT: C 31 TYR cc_start: 0.7697 (p90) cc_final: 0.7156 (p90) REVERT: C 52 SER cc_start: 0.8129 (t) cc_final: 0.7387 (p) REVERT: C 77 ASN cc_start: 0.8450 (t0) cc_final: 0.7858 (t0) REVERT: C 93 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6810 (tt) REVERT: C 105 TYR cc_start: 0.8294 (m-80) cc_final: 0.8069 (m-80) REVERT: A 41 THR cc_start: 0.7780 (p) cc_final: 0.7487 (t) REVERT: A 44 VAL cc_start: 0.8533 (OUTLIER) cc_final: 0.8287 (t) REVERT: A 60 GLN cc_start: 0.7392 (tm-30) cc_final: 0.6538 (tm-30) REVERT: A 72 TRP cc_start: 0.8059 (t60) cc_final: 0.7586 (t60) REVERT: A 119 LYS cc_start: 0.7890 (tppt) cc_final: 0.7177 (tppt) REVERT: A 181 PHE cc_start: 0.7013 (OUTLIER) cc_final: 0.6639 (p90) REVERT: A 201 LYS cc_start: 0.5598 (OUTLIER) cc_final: 0.5358 (ptpt) REVERT: A 250 LEU cc_start: 0.8130 (tp) cc_final: 0.7592 (tp) REVERT: A 255 LEU cc_start: 0.5054 (OUTLIER) cc_final: 0.4674 (tp) REVERT: A 305 THR cc_start: 0.8353 (m) cc_final: 0.8127 (p) REVERT: A 316 LYS cc_start: 0.6594 (mtmt) cc_final: 0.6253 (mtpt) REVERT: A 320 GLN cc_start: 0.7432 (mm-40) cc_final: 0.7169 (mm-40) REVERT: A 325 ARG cc_start: 0.7565 (ptp-170) cc_final: 0.7341 (ptt180) REVERT: A 346 GLU cc_start: 0.8541 (mm-30) cc_final: 0.7940 (mm-30) REVERT: A 356 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8269 (p) REVERT: A 360 ASN cc_start: 0.8511 (m-40) cc_final: 0.8043 (p0) REVERT: A 361 ARG cc_start: 0.7822 (ttm170) cc_final: 0.7159 (ttm170) REVERT: A 362 LYS cc_start: 0.7673 (tmtt) cc_final: 0.7085 (tmtt) REVERT: A 430 LYS cc_start: 0.8238 (mmmt) cc_final: 0.7745 (mmmt) REVERT: A 434 ASP cc_start: 0.7110 (t0) cc_final: 0.6798 (t0) REVERT: A 472 ARG cc_start: 0.7962 (ttm170) cc_final: 0.7642 (ttm-80) REVERT: A 473 ASP cc_start: 0.8417 (t0) cc_final: 0.7274 (m-30) REVERT: A 520 SER cc_start: 0.8134 (m) cc_final: 0.7605 (p) REVERT: A 534 LYS cc_start: 0.8606 (mmmm) cc_final: 0.8369 (mmtp) REVERT: A 538 ASN cc_start: 0.7463 (t0) cc_final: 0.7088 (t0) REVERT: A 546 ASN cc_start: 0.7826 (t0) cc_final: 0.6797 (p0) REVERT: A 568 PHE cc_start: 0.7471 (t80) cc_final: 0.7131 (t80) REVERT: A 580 ASP cc_start: 0.7108 (t70) cc_final: 0.6456 (t0) REVERT: A 598 PHE cc_start: 0.8201 (t80) cc_final: 0.7943 (t80) outliers start: 38 outliers final: 27 residues processed: 209 average time/residue: 0.1946 time to fit residues: 51.6572 Evaluate side-chains 218 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 185 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 44 VAL 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 201 LYS Chi-restraints excluded: chain A residue 248 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 393 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 464 LYS 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 535 LYS Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 652 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 44 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 72 optimal weight: 0.2980 chunk 53 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 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 213 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.150646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.129096 restraints weight = 10700.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.134056 restraints weight = 5800.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.137438 restraints weight = 3644.209| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6228 Z= 0.150 Angle : 0.719 12.812 8486 Z= 0.358 Chirality : 0.046 0.207 921 Planarity : 0.004 0.041 1100 Dihedral : 8.122 88.175 879 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer: Outliers : 5.41 % Allowed : 25.86 % 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: -3.22 (0.28), residues: 764 helix: -1.31 (1.34), residues: 20 sheet: -1.07 (0.35), residues: 202 loop : -2.82 (0.24), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 359 HIS 0.003 0.001 HIS A 213 PHE 0.034 0.002 PHE A 649 TYR 0.019 0.002 TYR A 176 ARG 0.004 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.03069 ( 103) hydrogen bonds : angle 5.48866 ( 270) SS BOND : bond 0.00322 ( 9) SS BOND : angle 1.81752 ( 18) covalent geometry : bond 0.00340 ( 6219) covalent geometry : angle 0.71506 ( 8468) ********************** 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 228 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: C 27 PHE cc_start: 0.8152 (t80) cc_final: 0.7848 (t80) REVERT: C 29 PHE cc_start: 0.7412 (m-10) cc_final: 0.6878 (m-10) REVERT: C 31 TYR cc_start: 0.7724 (p90) cc_final: 0.7166 (p90) REVERT: C 52 SER cc_start: 0.8072 (t) cc_final: 0.7337 (p) REVERT: C 77 ASN cc_start: 0.8487 (t0) cc_final: 0.7865 (t0) REVERT: C 93 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6777 (tt) REVERT: C 105 TYR cc_start: 0.8282 (m-80) cc_final: 0.8064 (m-80) REVERT: A 41 THR cc_start: 0.7761 (p) cc_final: 0.7467 (t) REVERT: A 44 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.8303 (t) REVERT: A 60 GLN cc_start: 0.7364 (tm-30) cc_final: 0.6481 (tm-30) REVERT: A 72 TRP cc_start: 0.8055 (t60) cc_final: 0.7571 (t60) REVERT: A 119 LYS cc_start: 0.7906 (tppt) cc_final: 0.7178 (tppt) REVERT: A 134 ILE cc_start: 0.7660 (mt) cc_final: 0.7372 (tt) REVERT: A 181 PHE cc_start: 0.6897 (OUTLIER) cc_final: 0.6516 (p90) REVERT: A 201 LYS cc_start: 0.5532 (OUTLIER) cc_final: 0.5292 (ptpt) REVERT: A 250 LEU cc_start: 0.8050 (tp) cc_final: 0.7504 (tp) REVERT: A 255 LEU cc_start: 0.5083 (OUTLIER) cc_final: 0.4726 (tp) REVERT: A 302 LEU cc_start: 0.7784 (tp) cc_final: 0.7011 (tt) REVERT: A 305 THR cc_start: 0.8325 (m) cc_final: 0.8106 (p) REVERT: A 320 GLN cc_start: 0.7414 (mm-40) cc_final: 0.7185 (mm-40) REVERT: A 325 ARG cc_start: 0.7570 (ptp-170) cc_final: 0.7365 (ptt180) REVERT: A 346 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8061 (mm-30) REVERT: A 356 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8250 (p) REVERT: A 360 ASN cc_start: 0.8514 (m-40) cc_final: 0.8039 (p0) REVERT: A 361 ARG cc_start: 0.7806 (ttm170) cc_final: 0.7187 (ttm170) REVERT: A 362 LYS cc_start: 0.7655 (tmtt) cc_final: 0.7124 (tmtt) REVERT: A 364 ILE cc_start: 0.7967 (mt) cc_final: 0.7674 (mt) REVERT: A 430 LYS cc_start: 0.8205 (mmmt) cc_final: 0.7801 (mmmt) REVERT: A 434 ASP cc_start: 0.7124 (t0) cc_final: 0.6807 (t0) REVERT: A 472 ARG cc_start: 0.7974 (ttm170) cc_final: 0.7642 (ttm-80) REVERT: A 473 ASP cc_start: 0.8468 (t0) cc_final: 0.7309 (m-30) REVERT: A 520 SER cc_start: 0.8129 (m) cc_final: 0.7570 (p) REVERT: A 534 LYS cc_start: 0.8592 (mmmm) cc_final: 0.8341 (mmtp) REVERT: A 538 ASN cc_start: 0.7450 (t0) cc_final: 0.7088 (t0) REVERT: A 568 PHE cc_start: 0.7489 (t80) cc_final: 0.7128 (t80) REVERT: A 580 ASP cc_start: 0.7043 (t70) cc_final: 0.6369 (t0) REVERT: A 598 PHE cc_start: 0.8182 (t80) cc_final: 0.7939 (t80) REVERT: A 661 TYR cc_start: 0.6797 (t80) cc_final: 0.6362 (t80) outliers start: 36 outliers final: 28 residues processed: 210 average time/residue: 0.2007 time to fit residues: 53.5774 Evaluate side-chains 217 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 39 SER Chi-restraints excluded: chain A residue 44 VAL 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 181 PHE Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 248 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 393 LEU Chi-restraints excluded: chain A residue 439 VAL 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 464 LYS 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 535 LYS Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 681 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 15 optimal weight: 0.0270 chunk 5 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.150912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.129282 restraints weight = 10826.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.134301 restraints weight = 5808.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.137678 restraints weight = 3620.722| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6228 Z= 0.146 Angle : 0.716 12.597 8486 Z= 0.358 Chirality : 0.046 0.212 921 Planarity : 0.004 0.041 1100 Dihedral : 7.834 88.045 875 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer: Outliers : 5.41 % Allowed : 25.71 % Favored : 68.87 % 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: -3.15 (0.28), residues: 764 helix: -1.30 (1.33), residues: 20 sheet: -0.96 (0.35), residues: 202 loop : -2.79 (0.24), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 359 HIS 0.003 0.001 HIS A 57 PHE 0.031 0.002 PHE A 649 TYR 0.018 0.002 TYR A 176 ARG 0.004 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.02983 ( 103) hydrogen bonds : angle 5.42231 ( 270) SS BOND : bond 0.00304 ( 9) SS BOND : angle 2.01245 ( 18) covalent geometry : bond 0.00332 ( 6219) covalent geometry : angle 0.71108 ( 8468) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2488.60 seconds wall clock time: 44 minutes 10.26 seconds (2650.26 seconds total)