Starting phenix.real_space_refine on Thu Nov 14 11:41:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4g_35172/11_2024/8i4g_35172.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4g_35172/11_2024/8i4g_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4g_35172/11_2024/8i4g_35172.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4g_35172/11_2024/8i4g_35172.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4g_35172/11_2024/8i4g_35172.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4g_35172/11_2024/8i4g_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-5513/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: 4.10, per 1000 atoms: 0.68 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: 1.40 Conformation dependent library (CDL) restraints added in 923.0 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: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 300 through 310 removed outlier: 3.965A pdb=" N GLU A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 348 Processing helix chain 'A' and resid 370 through 375 removed outlier: 3.994A pdb=" N VAL A 373 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 375 " --> pdb=" O SER A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'A' and resid 625 through 630 Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.619A pdb=" N VAL C 5 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP C 73 " --> pdb=" O THR C 78 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER C 71 " --> pdb=" O TYR C 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.773A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N MET C 34 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 37 through 39 removed outlier: 3.640A pdb=" N VAL A 70 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER A 68 " --> pdb=" O SER A 39 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 273 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N PHE A 73 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 56 through 63 removed outlier: 3.741A pdb=" N HIS A 57 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP A 61 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 63 " --> pdb=" O GLN A 277 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU A 282 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ALA A 294 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LYS A 284 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.782A pdb=" N GLY A 109 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS A 137 " --> pdb=" O SER A 122 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 132 through 133 removed outlier: 3.782A pdb=" N GLY A 109 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU A 147 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 96 through 100 removed outlier: 3.641A pdb=" N VAL A 96 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER A 100 " --> pdb=" O ARG A 196 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR A 214 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU A 197 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS A 212 " --> pdb=" O GLU A 197 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 199 " --> pdb=" O TYR A 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 319 through 320 removed outlier: 3.555A pdb=" N TYR A 618 " --> pdb=" O CYS A 655 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 362 through 364 removed outlier: 3.567A pdb=" N ALA A 403 " --> pdb=" O LYS A 362 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 362 through 364 removed outlier: 3.567A pdb=" N ALA A 403 " --> pdb=" O LYS A 362 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 367 through 368 removed outlier: 6.868A pdb=" N CYS A 367 " --> pdb=" O CYS A 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 458 through 460 removed outlier: 3.662A pdb=" N TYR A 459 " --> pdb=" O GLN A 499 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 544 through 547 removed outlier: 4.008A pdb=" N VAL A 545 " --> pdb=" O GLY A 556 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY A 556 " --> pdb=" O VAL A 545 " (cutoff:3.500A) 117 hydrogen bonds defined for protein. 270 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.77 Time building geometry restraints manager: 1.67 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: 1.290 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.500 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6219 Z= 0.152 Angle : 0.631 5.665 8468 Z= 0.405 Chirality : 0.040 0.124 921 Planarity : 0.003 0.030 1100 Dihedral : 10.191 83.589 2197 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 5.71 % Allowed : 9.62 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.78 (0.24), residues: 764 helix: -4.28 (0.42), residues: 40 sheet: -2.50 (0.33), residues: 174 loop : -3.60 (0.22), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 359 HIS 0.001 0.000 HIS A 525 PHE 0.007 0.001 PHE A 406 TYR 0.006 0.001 TYR A 271 ARG 0.002 0.000 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 237 time to evaluate : 0.670 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: 0.1912 time to fit residues: 63.7347 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 : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 484 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 667 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 0.0980 chunk 56 optimal weight: 0.0060 chunk 31 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 GLN A 420 GLN A 445 ASN A 548 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6219 Z= 0.171 Angle : 0.597 11.531 8468 Z= 0.302 Chirality : 0.044 0.163 921 Planarity : 0.005 0.051 1100 Dihedral : 8.881 88.430 899 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 6.62 % Allowed : 15.64 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.26), residues: 764 helix: -3.06 (0.85), residues: 28 sheet: -2.23 (0.33), residues: 196 loop : -3.17 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 639 HIS 0.002 0.000 HIS A 213 PHE 0.030 0.002 PHE A 568 TYR 0.019 0.001 TYR C 94 ARG 0.005 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 204 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 31 TYR cc_start: 0.7560 (p90) cc_final: 0.6999 (p90) REVERT: C 77 ASN cc_start: 0.8239 (t0) cc_final: 0.7644 (t0) REVERT: C 99 ARG cc_start: 0.7578 (ptt90) cc_final: 0.7342 (ppt170) REVERT: A 40 PHE cc_start: 0.8314 (m-80) cc_final: 0.8088 (m-10) REVERT: A 42 ARG cc_start: 0.8010 (ttm110) cc_final: 0.7740 (ttm110) REVERT: A 60 GLN cc_start: 0.7408 (tm-30) cc_final: 0.6580 (tm-30) REVERT: A 119 LYS cc_start: 0.7741 (tppt) cc_final: 0.6976 (tppt) REVERT: A 134 ILE cc_start: 0.7699 (mt) cc_final: 0.7281 (tt) REVERT: A 250 LEU cc_start: 0.7921 (tp) cc_final: 0.7474 (tp) REVERT: A 255 LEU cc_start: 0.4971 (OUTLIER) cc_final: 0.4662 (tp) REVERT: A 299 LEU cc_start: 0.8137 (tp) cc_final: 0.7840 (tp) REVERT: A 302 LEU cc_start: 0.7709 (tp) cc_final: 0.7371 (tt) REVERT: A 310 LYS cc_start: 0.8651 (mmtp) cc_final: 0.8443 (mmtt) REVERT: A 320 GLN cc_start: 0.7471 (mm-40) cc_final: 0.7262 (mm-40) REVERT: A 346 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7942 (mm-30) REVERT: A 362 LYS cc_start: 0.7572 (tmtt) cc_final: 0.6950 (tmtt) REVERT: A 420 GLN cc_start: 0.7546 (mm-40) cc_final: 0.7336 (mm-40) REVERT: A 430 LYS cc_start: 0.8034 (mmmt) cc_final: 0.7358 (mmmt) REVERT: A 434 ASP cc_start: 0.6943 (t0) cc_final: 0.6455 (t0) REVERT: A 466 LYS cc_start: 0.7960 (mmmm) cc_final: 0.7727 (mmmm) REVERT: A 472 ARG cc_start: 0.7844 (ttm170) cc_final: 0.7403 (ttm-80) REVERT: A 473 ASP cc_start: 0.8437 (t0) cc_final: 0.6600 (m-30) REVERT: A 495 TYR cc_start: 0.7963 (OUTLIER) cc_final: 0.6605 (p90) REVERT: A 518 VAL cc_start: 0.8520 (t) cc_final: 0.8240 (p) REVERT: A 520 SER cc_start: 0.7513 (m) cc_final: 0.7238 (t) REVERT: A 534 LYS cc_start: 0.8521 (mmmm) cc_final: 0.8290 (mmtp) REVERT: A 535 LYS cc_start: 0.8159 (pptt) cc_final: 0.7699 (pptt) REVERT: A 542 ASN cc_start: 0.8220 (m-40) cc_final: 0.7944 (m110) REVERT: A 543 LYS cc_start: 0.7584 (ttmt) cc_final: 0.7115 (ttmm) REVERT: A 580 ASP cc_start: 0.6903 (t70) cc_final: 0.6416 (t0) REVERT: A 593 ILE cc_start: 0.8577 (mt) cc_final: 0.8352 (mt) outliers start: 44 outliers final: 29 residues processed: 228 average time/residue: 0.2212 time to fit residues: 64.9205 Evaluate side-chains 218 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 484 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 667 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 56 optimal weight: 0.0980 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 60 optimal weight: 0.0000 chunk 67 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN C 77 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6219 Z= 0.174 Angle : 0.593 11.217 8468 Z= 0.295 Chirality : 0.043 0.188 921 Planarity : 0.004 0.042 1100 Dihedral : 8.828 86.542 895 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 7.22 % Allowed : 17.89 % Favored : 74.89 % 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: -3.69 (0.27), residues: 764 helix: -2.03 (1.21), residues: 22 sheet: -1.68 (0.34), residues: 192 loop : -2.99 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 359 HIS 0.002 0.001 HIS A 525 PHE 0.023 0.002 PHE A 496 TYR 0.015 0.001 TYR A 97 ARG 0.004 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 195 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 31 TYR cc_start: 0.7586 (p90) cc_final: 0.7072 (p90) REVERT: C 77 ASN cc_start: 0.8309 (t0) cc_final: 0.7643 (t0) REVERT: C 83 MET cc_start: 0.6328 (OUTLIER) cc_final: 0.6030 (mpp) REVERT: A 40 PHE cc_start: 0.8367 (m-80) cc_final: 0.8075 (m-10) REVERT: A 42 ARG cc_start: 0.7993 (ttm110) cc_final: 0.7642 (ttm110) REVERT: A 60 GLN cc_start: 0.7398 (tm-30) cc_final: 0.6546 (tm-30) REVERT: A 72 TRP cc_start: 0.7978 (t60) cc_final: 0.7683 (t60) REVERT: A 119 LYS cc_start: 0.7757 (tppt) cc_final: 0.7023 (tppt) REVERT: A 183 MET cc_start: 0.5979 (tmt) cc_final: 0.5654 (tmt) REVERT: A 250 LEU cc_start: 0.8012 (tp) cc_final: 0.7524 (tp) REVERT: A 255 LEU cc_start: 0.4729 (OUTLIER) cc_final: 0.4388 (tp) REVERT: A 299 LEU cc_start: 0.8161 (tp) cc_final: 0.7909 (tp) REVERT: A 302 LEU cc_start: 0.7750 (tp) cc_final: 0.7442 (tt) REVERT: A 319 TYR cc_start: 0.7315 (m-10) cc_final: 0.7032 (m-10) REVERT: A 320 GLN cc_start: 0.7548 (mm-40) cc_final: 0.7204 (mm-40) REVERT: A 346 GLU cc_start: 0.8462 (mm-30) cc_final: 0.7803 (mm-30) REVERT: A 362 LYS cc_start: 0.7608 (tmtt) cc_final: 0.6995 (tmtt) REVERT: A 420 GLN cc_start: 0.7614 (mm-40) cc_final: 0.7391 (mm-40) REVERT: A 430 LYS cc_start: 0.8086 (mmmt) cc_final: 0.7361 (mmmt) REVERT: A 466 LYS cc_start: 0.7927 (mmmm) cc_final: 0.7706 (mmmm) REVERT: A 472 ARG cc_start: 0.7867 (ttm170) cc_final: 0.7585 (ttm-80) REVERT: A 473 ASP cc_start: 0.8458 (t0) cc_final: 0.7067 (m-30) REVERT: A 495 TYR cc_start: 0.8144 (OUTLIER) cc_final: 0.6677 (p90) REVERT: A 520 SER cc_start: 0.7706 (m) cc_final: 0.7011 (p) REVERT: A 534 LYS cc_start: 0.8580 (mmmm) cc_final: 0.8296 (mmtp) REVERT: A 542 ASN cc_start: 0.8245 (m-40) cc_final: 0.8017 (m110) REVERT: A 543 LYS cc_start: 0.7615 (ttmt) cc_final: 0.7146 (ttmm) REVERT: A 568 PHE cc_start: 0.7285 (t80) cc_final: 0.6956 (t80) REVERT: A 580 ASP cc_start: 0.7102 (t70) cc_final: 0.6311 (t0) REVERT: A 592 ASP cc_start: 0.7538 (t70) cc_final: 0.7268 (t0) REVERT: A 598 PHE cc_start: 0.7414 (t80) cc_final: 0.7214 (t80) outliers start: 48 outliers final: 27 residues processed: 219 average time/residue: 0.1950 time to fit residues: 54.2367 Evaluate side-chains 213 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 45 optimal weight: 0.0370 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6219 Z= 0.194 Angle : 0.623 11.143 8468 Z= 0.314 Chirality : 0.044 0.168 921 Planarity : 0.004 0.046 1100 Dihedral : 8.313 86.558 883 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 6.62 % Allowed : 18.35 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.63 (0.28), residues: 764 helix: -1.62 (1.31), residues: 22 sheet: -1.72 (0.34), residues: 203 loop : -2.94 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 359 HIS 0.002 0.001 HIS A 525 PHE 0.020 0.002 PHE A 649 TYR 0.013 0.001 TYR A 642 ARG 0.003 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 201 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 18 LEU cc_start: 0.7955 (tp) cc_final: 0.7432 (tp) REVERT: C 27 PHE cc_start: 0.7996 (t80) cc_final: 0.7593 (t80) REVERT: C 29 PHE cc_start: 0.7233 (m-10) cc_final: 0.6926 (m-10) REVERT: C 31 TYR cc_start: 0.7621 (p90) cc_final: 0.7189 (p90) REVERT: C 34 MET cc_start: 0.6196 (mtp) cc_final: 0.5989 (mtp) REVERT: C 52 SER cc_start: 0.8317 (t) cc_final: 0.7640 (p) REVERT: C 77 ASN cc_start: 0.8330 (t0) cc_final: 0.7705 (t0) REVERT: C 83 MET cc_start: 0.6376 (OUTLIER) cc_final: 0.6175 (mpp) REVERT: C 93 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.6806 (tt) REVERT: A 40 PHE cc_start: 0.8363 (m-80) cc_final: 0.8089 (m-10) REVERT: A 42 ARG cc_start: 0.8035 (ttm110) cc_final: 0.7535 (ttm110) REVERT: A 60 GLN cc_start: 0.7421 (tm-30) cc_final: 0.6525 (tm-30) REVERT: A 72 TRP cc_start: 0.8012 (t60) cc_final: 0.7665 (t60) REVERT: A 119 LYS cc_start: 0.7711 (tppt) cc_final: 0.6927 (tppt) REVERT: A 212 LYS cc_start: 0.8020 (tppt) cc_final: 0.7645 (tptm) REVERT: A 250 LEU cc_start: 0.8019 (tp) cc_final: 0.7514 (tp) REVERT: A 255 LEU cc_start: 0.4799 (OUTLIER) cc_final: 0.4460 (tp) REVERT: A 279 ARG cc_start: 0.7579 (mmm-85) cc_final: 0.7377 (mmt90) REVERT: A 299 LEU cc_start: 0.8145 (tp) cc_final: 0.7929 (tp) REVERT: A 302 LEU cc_start: 0.7849 (tp) cc_final: 0.7494 (tt) REVERT: A 319 TYR cc_start: 0.7309 (m-10) cc_final: 0.7106 (m-10) REVERT: A 320 GLN cc_start: 0.7542 (mm-40) cc_final: 0.7258 (mm-40) REVERT: A 346 GLU cc_start: 0.8496 (mm-30) cc_final: 0.7862 (mm-30) REVERT: A 356 VAL cc_start: 0.8520 (OUTLIER) cc_final: 0.8241 (p) REVERT: A 362 LYS cc_start: 0.7656 (tmtt) cc_final: 0.7308 (tptp) REVERT: A 420 GLN cc_start: 0.7714 (mm-40) cc_final: 0.7490 (mm-40) REVERT: A 430 LYS cc_start: 0.8188 (mmmt) cc_final: 0.7420 (mmmt) REVERT: A 459 TYR cc_start: 0.7377 (p90) cc_final: 0.7162 (p90) REVERT: A 472 ARG cc_start: 0.7901 (ttm170) cc_final: 0.7576 (ttm-80) REVERT: A 473 ASP cc_start: 0.8420 (t0) cc_final: 0.7080 (m-30) REVERT: A 495 TYR cc_start: 0.8239 (OUTLIER) cc_final: 0.6794 (p90) REVERT: A 520 SER cc_start: 0.7868 (m) cc_final: 0.7267 (p) REVERT: A 534 LYS cc_start: 0.8584 (mmmm) cc_final: 0.8314 (mmtp) REVERT: A 538 ASN cc_start: 0.7262 (t0) cc_final: 0.7032 (t0) REVERT: A 568 PHE cc_start: 0.7436 (t80) cc_final: 0.7097 (t80) REVERT: A 639 TRP cc_start: 0.6309 (OUTLIER) cc_final: 0.5910 (t60) outliers start: 44 outliers final: 30 residues processed: 222 average time/residue: 0.1959 time to fit residues: 55.6892 Evaluate side-chains 229 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 VAL 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 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 393 LEU Chi-restraints excluded: chain A residue 401 VAL 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 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 626 VAL Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 639 TRP Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 667 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 4.9990 chunk 1 optimal weight: 0.0980 chunk 53 optimal weight: 0.7980 chunk 29 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN A 105 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6219 Z= 0.188 Angle : 0.630 10.630 8468 Z= 0.321 Chirality : 0.044 0.167 921 Planarity : 0.004 0.045 1100 Dihedral : 8.290 86.657 883 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 6.77 % Allowed : 20.75 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.28), residues: 764 helix: -1.46 (1.34), residues: 22 sheet: -1.67 (0.34), residues: 205 loop : -2.92 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 359 HIS 0.003 0.001 HIS A 525 PHE 0.020 0.001 PHE A 649 TYR 0.013 0.001 TYR A 642 ARG 0.003 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 202 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 18 LEU cc_start: 0.8133 (tp) cc_final: 0.7384 (tp) REVERT: C 27 PHE cc_start: 0.8014 (t80) cc_final: 0.7508 (t80) REVERT: C 31 TYR cc_start: 0.7620 (p90) cc_final: 0.7194 (p90) REVERT: C 34 MET cc_start: 0.6202 (mtp) cc_final: 0.5933 (mtp) REVERT: C 52 SER cc_start: 0.8268 (t) cc_final: 0.7481 (p) REVERT: C 77 ASN cc_start: 0.8332 (t0) cc_final: 0.7585 (t0) REVERT: C 83 MET cc_start: 0.6385 (OUTLIER) cc_final: 0.6068 (mpp) REVERT: C 93 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6775 (tt) REVERT: A 44 VAL cc_start: 0.8508 (OUTLIER) cc_final: 0.8271 (t) REVERT: A 60 GLN cc_start: 0.7433 (tm-30) cc_final: 0.6537 (tm-30) REVERT: A 72 TRP cc_start: 0.8015 (t60) cc_final: 0.7650 (t60) REVERT: A 105 ASN cc_start: 0.7390 (m-40) cc_final: 0.6682 (p0) REVERT: A 119 LYS cc_start: 0.7666 (tppt) cc_final: 0.6912 (tppt) REVERT: A 173 THR cc_start: 0.7738 (p) cc_final: 0.7477 (p) REVERT: A 183 MET cc_start: 0.5839 (tmt) cc_final: 0.5520 (tmt) REVERT: A 201 LYS cc_start: 0.5456 (OUTLIER) cc_final: 0.5222 (ptpt) REVERT: A 212 LYS cc_start: 0.7990 (tppt) cc_final: 0.7565 (tptm) REVERT: A 250 LEU cc_start: 0.8025 (tp) cc_final: 0.7544 (tp) REVERT: A 255 LEU cc_start: 0.4778 (OUTLIER) cc_final: 0.4443 (tp) REVERT: A 279 ARG cc_start: 0.7610 (mmm-85) cc_final: 0.7323 (mmt90) REVERT: A 302 LEU cc_start: 0.7876 (tp) cc_final: 0.7491 (tt) REVERT: A 320 GLN cc_start: 0.7546 (mm-40) cc_final: 0.7249 (mm-40) REVERT: A 346 GLU cc_start: 0.8478 (mm-30) cc_final: 0.7857 (mm-30) REVERT: A 356 VAL cc_start: 0.8507 (OUTLIER) cc_final: 0.8216 (p) REVERT: A 361 ARG cc_start: 0.7741 (ttm170) cc_final: 0.6946 (ttm170) REVERT: A 362 LYS cc_start: 0.7661 (tmtt) cc_final: 0.7272 (tptp) REVERT: A 430 LYS cc_start: 0.8233 (mmmt) cc_final: 0.7516 (mmmt) REVERT: A 459 TYR cc_start: 0.7211 (p90) cc_final: 0.6418 (p90) REVERT: A 467 LEU cc_start: 0.7568 (mm) cc_final: 0.7066 (mt) REVERT: A 472 ARG cc_start: 0.7904 (ttm170) cc_final: 0.7569 (ttm-80) REVERT: A 495 TYR cc_start: 0.8255 (OUTLIER) cc_final: 0.6748 (p90) REVERT: A 499 GLN cc_start: 0.6899 (tm-30) cc_final: 0.6677 (tm-30) REVERT: A 517 VAL cc_start: 0.7465 (t) cc_final: 0.7231 (m) REVERT: A 520 SER cc_start: 0.7923 (m) cc_final: 0.7325 (p) REVERT: A 534 LYS cc_start: 0.8590 (mmmm) cc_final: 0.8321 (mmtp) REVERT: A 538 ASN cc_start: 0.7270 (t0) cc_final: 0.6959 (t0) REVERT: A 543 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7402 (ttpt) REVERT: A 568 PHE cc_start: 0.7449 (t80) cc_final: 0.7096 (t80) REVERT: A 616 VAL cc_start: 0.6922 (OUTLIER) cc_final: 0.6713 (t) REVERT: A 639 TRP cc_start: 0.6286 (OUTLIER) cc_final: 0.5927 (t60) outliers start: 45 outliers final: 28 residues processed: 222 average time/residue: 0.2113 time to fit residues: 58.9140 Evaluate side-chains 236 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 198 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 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 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 318 ILE Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 401 VAL 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 543 LYS Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 616 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 0.0470 chunk 72 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 6 optimal weight: 0.2980 chunk 24 optimal weight: 0.0000 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6219 Z= 0.199 Angle : 0.663 13.006 8468 Z= 0.331 Chirality : 0.045 0.183 921 Planarity : 0.004 0.042 1100 Dihedral : 8.129 86.300 881 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 6.77 % Allowed : 22.26 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.28), residues: 764 helix: -1.50 (1.24), residues: 22 sheet: -1.60 (0.35), residues: 205 loop : -2.84 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 639 HIS 0.003 0.001 HIS A 525 PHE 0.021 0.001 PHE A 649 TYR 0.014 0.001 TYR A 459 ARG 0.007 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 201 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 18 LEU cc_start: 0.8263 (tp) cc_final: 0.7552 (tp) REVERT: C 27 PHE cc_start: 0.8128 (t80) cc_final: 0.7720 (t80) REVERT: C 29 PHE cc_start: 0.7279 (m-10) cc_final: 0.6967 (m-10) REVERT: C 31 TYR cc_start: 0.7645 (p90) cc_final: 0.7206 (p90) REVERT: C 52 SER cc_start: 0.8235 (t) cc_final: 0.7466 (p) REVERT: C 77 ASN cc_start: 0.8372 (t0) cc_final: 0.7660 (t0) REVERT: C 83 MET cc_start: 0.6460 (OUTLIER) cc_final: 0.6229 (mpp) REVERT: C 93 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6753 (tt) REVERT: C 99 ARG cc_start: 0.7958 (ptt90) cc_final: 0.7567 (ppt170) REVERT: A 44 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8274 (t) REVERT: A 60 GLN cc_start: 0.7384 (tm-30) cc_final: 0.6493 (tm-30) REVERT: A 72 TRP cc_start: 0.8031 (t60) cc_final: 0.7659 (t60) REVERT: A 119 LYS cc_start: 0.7717 (tppt) cc_final: 0.6952 (tppt) REVERT: A 201 LYS cc_start: 0.5479 (OUTLIER) cc_final: 0.5070 (ptpt) REVERT: A 212 LYS cc_start: 0.7962 (tppt) cc_final: 0.7524 (tptm) REVERT: A 250 LEU cc_start: 0.8067 (tp) cc_final: 0.7550 (tp) REVERT: A 279 ARG cc_start: 0.7644 (mmm-85) cc_final: 0.7338 (mmt90) REVERT: A 302 LEU cc_start: 0.7881 (tp) cc_final: 0.7110 (tt) REVERT: A 319 TYR cc_start: 0.7359 (m-10) cc_final: 0.7119 (m-10) REVERT: A 320 GLN cc_start: 0.7532 (mm-40) cc_final: 0.7256 (mm-40) REVERT: A 346 GLU cc_start: 0.8501 (mm-30) cc_final: 0.7890 (mm-30) REVERT: A 356 VAL cc_start: 0.8488 (OUTLIER) cc_final: 0.8254 (p) REVERT: A 362 LYS cc_start: 0.7672 (tmtt) cc_final: 0.7325 (tptp) REVERT: A 430 LYS cc_start: 0.8225 (mmmt) cc_final: 0.7593 (mmmt) REVERT: A 431 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8699 (mm) REVERT: A 459 TYR cc_start: 0.7215 (p90) cc_final: 0.6333 (p90) REVERT: A 467 LEU cc_start: 0.7608 (mm) cc_final: 0.7361 (mt) REVERT: A 472 ARG cc_start: 0.7905 (ttm170) cc_final: 0.7605 (ttm-80) REVERT: A 473 ASP cc_start: 0.8432 (t0) cc_final: 0.7159 (m-30) REVERT: A 495 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.6805 (p90) REVERT: A 520 SER cc_start: 0.7986 (m) cc_final: 0.7476 (p) REVERT: A 534 LYS cc_start: 0.8596 (mmmm) cc_final: 0.8333 (mmtp) REVERT: A 538 ASN cc_start: 0.7307 (t0) cc_final: 0.6915 (t0) REVERT: A 568 PHE cc_start: 0.7456 (t80) cc_final: 0.7085 (t80) outliers start: 45 outliers final: 29 residues processed: 220 average time/residue: 0.2116 time to fit residues: 59.0214 Evaluate side-chains 231 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 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 182 LEU Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 431 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 487 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 672 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 72 optimal weight: 0.0040 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6219 Z= 0.236 Angle : 0.693 11.439 8468 Z= 0.346 Chirality : 0.046 0.186 921 Planarity : 0.005 0.040 1100 Dihedral : 8.106 87.392 879 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % Rotamer: Outliers : 6.47 % Allowed : 24.06 % Favored : 69.47 % 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: -1.34 (1.32), residues: 22 sheet: -1.46 (0.35), residues: 205 loop : -2.85 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 359 HIS 0.003 0.001 HIS A 525 PHE 0.019 0.001 PHE A 496 TYR 0.023 0.002 TYR A 459 ARG 0.008 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 200 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 18 LEU cc_start: 0.8334 (tp) cc_final: 0.7666 (tp) REVERT: C 27 PHE cc_start: 0.8151 (t80) cc_final: 0.7696 (t80) REVERT: C 31 TYR cc_start: 0.7677 (p90) cc_final: 0.7208 (p90) REVERT: C 52 SER cc_start: 0.8180 (t) cc_final: 0.7465 (p) REVERT: C 77 ASN cc_start: 0.8408 (t0) cc_final: 0.7647 (t0) REVERT: C 83 MET cc_start: 0.6458 (OUTLIER) cc_final: 0.6081 (mpp) REVERT: C 93 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6733 (tt) REVERT: A 41 THR cc_start: 0.7560 (p) cc_final: 0.7303 (t) REVERT: A 42 ARG cc_start: 0.8185 (ttm110) cc_final: 0.7782 (ttm170) REVERT: A 60 GLN cc_start: 0.7387 (tm-30) cc_final: 0.6510 (tm-30) REVERT: A 72 TRP cc_start: 0.8070 (t60) cc_final: 0.7654 (t60) REVERT: A 119 LYS cc_start: 0.7797 (tppt) cc_final: 0.7033 (tppt) REVERT: A 201 LYS cc_start: 0.5548 (OUTLIER) cc_final: 0.5140 (ptpt) REVERT: A 212 LYS cc_start: 0.7948 (tppt) cc_final: 0.7396 (tptm) REVERT: A 250 LEU cc_start: 0.8090 (tp) cc_final: 0.7588 (tp) REVERT: A 279 ARG cc_start: 0.7725 (mmm-85) cc_final: 0.7510 (mmt90) REVERT: A 302 LEU cc_start: 0.7598 (tp) cc_final: 0.7230 (tt) REVERT: A 320 GLN cc_start: 0.7472 (mm-40) cc_final: 0.7246 (mm-40) REVERT: A 346 GLU cc_start: 0.8485 (mm-30) cc_final: 0.7881 (mm-30) REVERT: A 356 VAL cc_start: 0.8517 (OUTLIER) cc_final: 0.8275 (p) REVERT: A 360 ASN cc_start: 0.8477 (m-40) cc_final: 0.8039 (p0) REVERT: A 362 LYS cc_start: 0.7638 (tmtt) cc_final: 0.7274 (tptp) REVERT: A 429 TYR cc_start: 0.7567 (t80) cc_final: 0.7282 (t80) REVERT: A 430 LYS cc_start: 0.8260 (mmmt) cc_final: 0.7697 (mmmt) REVERT: A 472 ARG cc_start: 0.7929 (ttm170) cc_final: 0.7651 (ttm-80) REVERT: A 495 TYR cc_start: 0.8267 (OUTLIER) cc_final: 0.6599 (p90) REVERT: A 520 SER cc_start: 0.8012 (m) cc_final: 0.7554 (p) REVERT: A 534 LYS cc_start: 0.8602 (mmmm) cc_final: 0.8331 (mmtp) REVERT: A 538 ASN cc_start: 0.7261 (t0) cc_final: 0.6854 (t0) REVERT: A 568 PHE cc_start: 0.7509 (t80) cc_final: 0.7110 (t80) outliers start: 43 outliers final: 29 residues processed: 220 average time/residue: 0.2079 time to fit residues: 58.3581 Evaluate side-chains 233 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 39 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 201 LYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 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 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 544 CYS 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 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 21 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 49 optimal weight: 0.0670 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6219 Z= 0.208 Angle : 0.688 13.892 8468 Z= 0.345 Chirality : 0.046 0.203 921 Planarity : 0.005 0.040 1100 Dihedral : 8.020 87.341 879 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer: Outliers : 6.02 % Allowed : 25.11 % 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: -3.36 (0.28), residues: 764 helix: -1.36 (1.30), residues: 22 sheet: -1.41 (0.34), residues: 217 loop : -2.83 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 639 HIS 0.003 0.001 HIS A 525 PHE 0.038 0.002 PHE A 649 TYR 0.028 0.002 TYR A 459 ARG 0.008 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 198 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 18 LEU cc_start: 0.8364 (tp) cc_final: 0.7758 (tp) REVERT: C 27 PHE cc_start: 0.8176 (t80) cc_final: 0.7820 (t80) REVERT: C 31 TYR cc_start: 0.7666 (p90) cc_final: 0.7231 (p90) REVERT: C 52 SER cc_start: 0.8139 (t) cc_final: 0.7432 (p) REVERT: C 77 ASN cc_start: 0.8388 (t0) cc_final: 0.7702 (t0) REVERT: C 83 MET cc_start: 0.6521 (OUTLIER) cc_final: 0.6220 (mpp) REVERT: C 93 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6754 (tt) REVERT: C 99 ARG cc_start: 0.7955 (ptt90) cc_final: 0.7503 (ppt170) REVERT: A 60 GLN cc_start: 0.7357 (tm-30) cc_final: 0.6473 (tm-30) REVERT: A 72 TRP cc_start: 0.8037 (t60) cc_final: 0.7649 (t60) REVERT: A 119 LYS cc_start: 0.7759 (tppt) cc_final: 0.6996 (tppt) REVERT: A 181 PHE cc_start: 0.6828 (OUTLIER) cc_final: 0.6568 (p90) REVERT: A 183 MET cc_start: 0.5521 (tmt) cc_final: 0.5291 (tmt) REVERT: A 212 LYS cc_start: 0.7944 (tppt) cc_final: 0.7644 (tptt) REVERT: A 250 LEU cc_start: 0.8019 (tp) cc_final: 0.7463 (tp) REVERT: A 279 ARG cc_start: 0.7589 (mmm-85) cc_final: 0.7026 (mmm-85) REVERT: A 302 LEU cc_start: 0.7563 (tp) cc_final: 0.7177 (tt) REVERT: A 320 GLN cc_start: 0.7480 (mm-40) cc_final: 0.7216 (mm-40) REVERT: A 325 ARG cc_start: 0.7587 (ptp-170) cc_final: 0.7165 (ptt180) REVERT: A 346 GLU cc_start: 0.8481 (mm-30) cc_final: 0.7886 (mm-30) REVERT: A 356 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8268 (p) REVERT: A 360 ASN cc_start: 0.8466 (m-40) cc_final: 0.8036 (p0) REVERT: A 362 LYS cc_start: 0.7669 (tmtt) cc_final: 0.7437 (tmtt) REVERT: A 430 LYS cc_start: 0.8184 (mmmt) cc_final: 0.7757 (mmmt) REVERT: A 459 TYR cc_start: 0.7377 (p90) cc_final: 0.6932 (p90) REVERT: A 472 ARG cc_start: 0.7891 (ttm170) cc_final: 0.7605 (ttm-80) REVERT: A 473 ASP cc_start: 0.8372 (t0) cc_final: 0.7107 (m-30) REVERT: A 520 SER cc_start: 0.8073 (m) cc_final: 0.7582 (p) REVERT: A 538 ASN cc_start: 0.7258 (t0) cc_final: 0.6892 (t0) REVERT: A 568 PHE cc_start: 0.7467 (t80) cc_final: 0.7086 (t80) REVERT: A 661 TYR cc_start: 0.6866 (t80) cc_final: 0.6392 (t80) outliers start: 40 outliers final: 28 residues processed: 214 average time/residue: 0.2046 time to fit residues: 55.2726 Evaluate side-chains 226 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 39 SER Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 182 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 352 THR Chi-restraints excluded: chain A residue 356 VAL 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 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 544 CYS 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 672 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 0.0970 chunk 67 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 0.0980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6219 Z= 0.211 Angle : 0.715 13.371 8468 Z= 0.357 Chirality : 0.046 0.210 921 Planarity : 0.005 0.040 1100 Dihedral : 7.906 87.650 877 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 5.11 % Allowed : 25.56 % Favored : 69.32 % 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: -3.28 (0.28), residues: 764 helix: -1.35 (1.30), residues: 22 sheet: -1.34 (0.34), residues: 215 loop : -2.78 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 359 HIS 0.003 0.001 HIS A 525 PHE 0.031 0.002 PHE A 649 TYR 0.043 0.002 TYR A 459 ARG 0.008 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 18 LEU cc_start: 0.8362 (tp) cc_final: 0.7738 (tp) REVERT: C 27 PHE cc_start: 0.8163 (t80) cc_final: 0.7771 (t80) REVERT: C 31 TYR cc_start: 0.7656 (p90) cc_final: 0.7189 (p90) REVERT: C 52 SER cc_start: 0.8084 (t) cc_final: 0.7356 (p) REVERT: C 77 ASN cc_start: 0.8400 (t0) cc_final: 0.7780 (t0) REVERT: C 83 MET cc_start: 0.6658 (OUTLIER) cc_final: 0.6326 (mpp) REVERT: C 93 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6705 (tt) REVERT: C 99 ARG cc_start: 0.7944 (ptt90) cc_final: 0.7564 (ppt170) REVERT: A 41 THR cc_start: 0.7555 (p) cc_final: 0.7308 (t) REVERT: A 60 GLN cc_start: 0.7328 (tm-30) cc_final: 0.6431 (tm-30) REVERT: A 72 TRP cc_start: 0.8007 (t60) cc_final: 0.7627 (t60) REVERT: A 119 LYS cc_start: 0.7758 (tppt) cc_final: 0.6993 (tppt) REVERT: A 172 CYS cc_start: 0.4691 (p) cc_final: 0.4110 (p) REVERT: A 199 VAL cc_start: 0.7036 (t) cc_final: 0.6670 (p) REVERT: A 212 LYS cc_start: 0.8003 (tppt) cc_final: 0.7699 (tptt) REVERT: A 250 LEU cc_start: 0.7991 (tp) cc_final: 0.7436 (tp) REVERT: A 279 ARG cc_start: 0.7554 (mmm-85) cc_final: 0.7206 (mmt90) REVERT: A 302 LEU cc_start: 0.7488 (tp) cc_final: 0.7109 (tt) REVERT: A 320 GLN cc_start: 0.7413 (mm-40) cc_final: 0.7174 (mm-40) REVERT: A 346 GLU cc_start: 0.8510 (mm-30) cc_final: 0.7932 (mm-30) REVERT: A 356 VAL cc_start: 0.8520 (OUTLIER) cc_final: 0.8287 (p) REVERT: A 360 ASN cc_start: 0.8430 (m-40) cc_final: 0.8045 (p0) REVERT: A 361 ARG cc_start: 0.7820 (ttm170) cc_final: 0.7157 (ttm170) REVERT: A 362 LYS cc_start: 0.7699 (tmtt) cc_final: 0.7443 (tptp) REVERT: A 430 LYS cc_start: 0.8117 (mmmt) cc_final: 0.7539 (mmmt) REVERT: A 434 ASP cc_start: 0.7026 (t0) cc_final: 0.6699 (t0) REVERT: A 472 ARG cc_start: 0.7898 (ttm170) cc_final: 0.7568 (ttm-80) REVERT: A 473 ASP cc_start: 0.8441 (t0) cc_final: 0.7184 (m-30) REVERT: A 517 VAL cc_start: 0.7251 (t) cc_final: 0.7026 (m) REVERT: A 520 SER cc_start: 0.7971 (m) cc_final: 0.7409 (p) REVERT: A 535 LYS cc_start: 0.8340 (mmmm) cc_final: 0.8033 (mmmm) REVERT: A 538 ASN cc_start: 0.7386 (t0) cc_final: 0.7045 (t0) REVERT: A 568 PHE cc_start: 0.7517 (t80) cc_final: 0.7108 (t80) REVERT: A 661 TYR cc_start: 0.6884 (t80) cc_final: 0.6419 (t80) outliers start: 34 outliers final: 24 residues processed: 214 average time/residue: 0.2023 time to fit residues: 55.2082 Evaluate side-chains 224 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 39 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 181 PHE Chi-restraints excluded: chain A residue 182 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 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 544 CYS 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 672 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 6 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN A 609 ASN A 681 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6219 Z= 0.318 Angle : 0.799 13.141 8468 Z= 0.405 Chirality : 0.048 0.211 921 Planarity : 0.005 0.044 1100 Dihedral : 7.830 89.380 873 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.04 % Favored : 87.96 % Rotamer: Outliers : 4.21 % Allowed : 26.92 % 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: -3.40 (0.28), residues: 764 helix: -2.07 (1.09), residues: 28 sheet: -1.29 (0.35), residues: 209 loop : -2.89 (0.24), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP C 36 HIS 0.003 0.001 HIS A 525 PHE 0.034 0.002 PHE A 496 TYR 0.052 0.002 TYR A 459 ARG 0.008 0.001 ARG A 42 ********************** 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: 28 poor density : 200 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 18 LEU cc_start: 0.8404 (tp) cc_final: 0.7713 (tp) REVERT: C 27 PHE cc_start: 0.8210 (t80) cc_final: 0.7930 (t80) REVERT: C 31 TYR cc_start: 0.7691 (p90) cc_final: 0.7213 (p90) REVERT: C 52 SER cc_start: 0.8051 (t) cc_final: 0.7376 (p) REVERT: C 77 ASN cc_start: 0.8471 (t0) cc_final: 0.7846 (t0) REVERT: C 83 MET cc_start: 0.6743 (OUTLIER) cc_final: 0.6521 (mpp) REVERT: C 93 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6635 (tt) REVERT: C 99 ARG cc_start: 0.7984 (ptt90) cc_final: 0.7494 (ppt170) REVERT: A 41 THR cc_start: 0.7678 (p) cc_final: 0.7438 (t) REVERT: A 60 GLN cc_start: 0.7362 (tm-30) cc_final: 0.6476 (tm-30) REVERT: A 72 TRP cc_start: 0.8097 (t60) cc_final: 0.7627 (t60) REVERT: A 119 LYS cc_start: 0.7913 (tppt) cc_final: 0.7199 (tppt) REVERT: A 199 VAL cc_start: 0.7063 (t) cc_final: 0.6685 (p) REVERT: A 212 LYS cc_start: 0.8052 (tppt) cc_final: 0.7820 (tptt) REVERT: A 250 LEU cc_start: 0.8081 (tp) cc_final: 0.7581 (tp) REVERT: A 255 LEU cc_start: 0.5008 (tp) cc_final: 0.4703 (tp) REVERT: A 279 ARG cc_start: 0.7761 (mmm-85) cc_final: 0.7164 (mmm-85) REVERT: A 302 LEU cc_start: 0.7632 (tp) cc_final: 0.7259 (tt) REVERT: A 346 GLU cc_start: 0.8508 (mm-30) cc_final: 0.7958 (mm-30) REVERT: A 356 VAL cc_start: 0.8571 (OUTLIER) cc_final: 0.8342 (p) REVERT: A 360 ASN cc_start: 0.8457 (m-40) cc_final: 0.8145 (p0) REVERT: A 361 ARG cc_start: 0.7845 (ttm170) cc_final: 0.7218 (ttm170) REVERT: A 362 LYS cc_start: 0.7696 (tmtt) cc_final: 0.7470 (tptm) REVERT: A 430 LYS cc_start: 0.8142 (mmmt) cc_final: 0.7910 (mmmt) REVERT: A 434 ASP cc_start: 0.7137 (t0) cc_final: 0.6849 (t0) REVERT: A 472 ARG cc_start: 0.7936 (ttm170) cc_final: 0.7607 (ttm-80) REVERT: A 520 SER cc_start: 0.8047 (m) cc_final: 0.7546 (p) REVERT: A 538 ASN cc_start: 0.7347 (t0) cc_final: 0.7068 (t0) REVERT: A 568 PHE cc_start: 0.7574 (t80) cc_final: 0.7139 (t80) REVERT: A 598 PHE cc_start: 0.8167 (t80) cc_final: 0.7944 (t80) REVERT: A 661 TYR cc_start: 0.6925 (t80) cc_final: 0.6424 (t80) outliers start: 28 outliers final: 24 residues processed: 210 average time/residue: 0.1998 time to fit residues: 53.9622 Evaluate side-chains 221 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 39 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 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 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 544 CYS 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 54 optimal weight: 0.9980 chunk 8 optimal weight: 0.0570 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 0.0870 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 52 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 overall best weight: 0.3876 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.150311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.128866 restraints weight = 10582.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.133769 restraints weight = 5718.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.137084 restraints weight = 3594.071| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.5353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.122 6219 Z= 0.348 Angle : 1.137 59.198 8468 Z= 0.650 Chirality : 0.047 0.204 921 Planarity : 0.005 0.044 1100 Dihedral : 7.676 89.404 871 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.91 % Favored : 88.09 % Rotamer: Outliers : 4.36 % Allowed : 27.37 % Favored : 68.27 % Cbeta Deviations : 0.14 % 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: -2.10 (1.08), residues: 28 sheet: -1.29 (0.34), residues: 209 loop : -2.91 (0.24), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP C 36 HIS 0.003 0.001 HIS A 525 PHE 0.033 0.002 PHE A 496 TYR 0.044 0.002 TYR A 459 ARG 0.003 0.000 ARG C 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2030.25 seconds wall clock time: 46 minutes 8.22 seconds (2768.22 seconds total)