Starting phenix.real_space_refine on Wed Jan 15 03:29:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9euy_19989/01_2025/9euy_19989_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9euy_19989/01_2025/9euy_19989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9euy_19989/01_2025/9euy_19989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9euy_19989/01_2025/9euy_19989.map" model { file = "/net/cci-nas-00/data/ceres_data/9euy_19989/01_2025/9euy_19989_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9euy_19989/01_2025/9euy_19989_neut.cif" } resolution = 2.95 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= 0.022 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 38 5.16 5 C 4942 2.51 5 N 1400 2.21 5 O 1466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 7846 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3880 Classifications: {'peptide': 492} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 463} Chain: "B" Number of atoms: 3880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3880 Classifications: {'peptide': 492} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 463} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.25, per 1000 atoms: 0.80 Number of scatterers: 7846 At special positions: 0 Unit cell: (85.284, 105.156, 119.232, 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 38 16.00 O 1466 8.00 N 1400 7.00 C 4942 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 876.7 milliseconds 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1824 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 6 sheets defined 42.4% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 Processing helix chain 'A' and resid 44 through 50 Processing helix chain 'A' and resid 60 through 78 Proline residue: A 66 - end of helix Processing helix chain 'A' and resid 116 through 134 removed outlier: 3.830A pdb=" N ILE A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N SER A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 139 through 156 Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 196 through 206 Processing helix chain 'A' and resid 244 through 254 Processing helix chain 'A' and resid 285 through 332 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 345 through 350 removed outlier: 3.627A pdb=" N LEU A 349 " --> pdb=" O GLY A 345 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 345 through 350' Processing helix chain 'A' and resid 370 through 382 Processing helix chain 'A' and resid 430 through 437 removed outlier: 3.934A pdb=" N TRP A 437 " --> pdb=" O HIS A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 468 Processing helix chain 'A' and resid 475 through 492 Processing helix chain 'B' and resid 11 through 15 Processing helix chain 'B' and resid 44 through 50 Processing helix chain 'B' and resid 64 through 77 removed outlier: 4.351A pdb=" N VAL B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 134 Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 139 through 156 removed outlier: 3.550A pdb=" N ASP B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 196 through 206 Processing helix chain 'B' and resid 244 through 254 Processing helix chain 'B' and resid 285 through 332 removed outlier: 4.018A pdb=" N ARG B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 340 Processing helix chain 'B' and resid 345 through 349 Processing helix chain 'B' and resid 370 through 382 Processing helix chain 'B' and resid 418 through 421 removed outlier: 4.045A pdb=" N SER B 421 " --> pdb=" O ARG B 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 418 through 421' Processing helix chain 'B' and resid 432 through 437 removed outlier: 4.578A pdb=" N TRP B 437 " --> pdb=" O HIS B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 467 Processing helix chain 'B' and resid 475 through 490 Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 23 removed outlier: 3.548A pdb=" N ALA A 40 " --> pdb=" O THR A 31 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU A 29 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 190 removed outlier: 5.916A pdb=" N VAL A 173 " --> pdb=" O ARG A 164 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ARG A 164 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA A 175 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU A 270 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL A 266 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 362 through 366 removed outlier: 6.196A pdb=" N GLY A 422 " --> pdb=" O PHE A 416 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 22 through 23 removed outlier: 3.561A pdb=" N ALA B 40 " --> pdb=" O THR B 31 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU B 29 " --> pdb=" O SER B 42 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 189 through 190 removed outlier: 5.719A pdb=" N VAL B 173 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG B 164 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA B 175 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N LEU B 270 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL B 266 " --> pdb=" O LEU B 270 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 362 through 366 removed outlier: 7.162A pdb=" N ILE B 424 " --> pdb=" O ARG B 415 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ARG B 415 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N TRP B 426 " --> pdb=" O ALA B 413 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ALA B 413 " --> pdb=" O TRP B 426 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ARG B 428 " --> pdb=" O VAL B 411 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL B 411 " --> pdb=" O ARG B 428 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.49 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1410 1.32 - 1.44: 2081 1.44 - 1.57: 4475 1.57 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 8028 Sorted by residual: bond pdb=" CB MET B 154 " pdb=" CG MET B 154 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.33e+00 bond pdb=" CB MET A 154 " pdb=" CG MET A 154 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" CB ILE B 447 " pdb=" CG2 ILE B 447 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 bond pdb=" CG1 ILE A 294 " pdb=" CD1 ILE A 294 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.11e+00 bond pdb=" CG1 ILE B 294 " pdb=" CD1 ILE B 294 " ideal model delta sigma weight residual 1.513 1.474 0.039 3.90e-02 6.57e+02 9.93e-01 ... (remaining 8023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 10415 1.62 - 3.24: 430 3.24 - 4.86: 54 4.86 - 6.49: 9 6.49 - 8.11: 4 Bond angle restraints: 10912 Sorted by residual: angle pdb=" CD ARG A 453 " pdb=" NE ARG A 453 " pdb=" CZ ARG A 453 " ideal model delta sigma weight residual 124.40 129.06 -4.66 1.40e+00 5.10e-01 1.11e+01 angle pdb=" CB ARG B 453 " pdb=" CG ARG B 453 " pdb=" CD ARG B 453 " ideal model delta sigma weight residual 111.30 118.61 -7.31 2.30e+00 1.89e-01 1.01e+01 angle pdb=" N PRO B 452 " pdb=" CA PRO B 452 " pdb=" C PRO B 452 " ideal model delta sigma weight residual 113.86 117.57 -3.71 1.25e+00 6.40e-01 8.83e+00 angle pdb=" CG ARG A 453 " pdb=" CD ARG A 453 " pdb=" NE ARG A 453 " ideal model delta sigma weight residual 112.00 118.12 -6.12 2.20e+00 2.07e-01 7.75e+00 angle pdb=" CB MET A 154 " pdb=" CG MET A 154 " pdb=" SD MET A 154 " ideal model delta sigma weight residual 112.70 104.59 8.11 3.00e+00 1.11e-01 7.30e+00 ... (remaining 10907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 4513 17.15 - 34.31: 239 34.31 - 51.46: 51 51.46 - 68.61: 14 68.61 - 85.76: 9 Dihedral angle restraints: 4826 sinusoidal: 1994 harmonic: 2832 Sorted by residual: dihedral pdb=" CG ARG A 453 " pdb=" CD ARG A 453 " pdb=" NE ARG A 453 " pdb=" CZ ARG A 453 " ideal model delta sinusoidal sigma weight residual 90.00 5.38 84.62 2 1.50e+01 4.44e-03 2.11e+01 dihedral pdb=" CA ASP B 96 " pdb=" CB ASP B 96 " pdb=" CG ASP B 96 " pdb=" OD1 ASP B 96 " ideal model delta sinusoidal sigma weight residual -30.00 -83.23 53.23 1 2.00e+01 2.50e-03 9.63e+00 dihedral pdb=" CG ARG A 201 " pdb=" CD ARG A 201 " pdb=" NE ARG A 201 " pdb=" CZ ARG A 201 " ideal model delta sinusoidal sigma weight residual -90.00 -132.08 42.08 2 1.50e+01 4.44e-03 9.58e+00 ... (remaining 4823 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 785 0.038 - 0.075: 257 0.075 - 0.113: 93 0.113 - 0.150: 48 0.150 - 0.188: 5 Chirality restraints: 1188 Sorted by residual: chirality pdb=" CA PRO B 452 " pdb=" N PRO B 452 " pdb=" C PRO B 452 " pdb=" CB PRO B 452 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CA PRO A 452 " pdb=" N PRO A 452 " pdb=" C PRO A 452 " pdb=" CB PRO A 452 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CA ILE A 264 " pdb=" N ILE A 264 " pdb=" C ILE A 264 " pdb=" CB ILE A 264 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 1185 not shown) Planarity restraints: 1434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 152 " 0.236 9.50e-02 1.11e+02 1.06e-01 8.43e+00 pdb=" NE ARG B 152 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG B 152 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG B 152 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B 152 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 434 " 0.212 9.50e-02 1.11e+02 9.57e-02 7.46e+00 pdb=" NE ARG B 434 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG B 434 " 0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG B 434 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 434 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 152 " -0.211 9.50e-02 1.11e+02 9.49e-02 6.69e+00 pdb=" NE ARG A 152 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 152 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG A 152 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 152 " -0.001 2.00e-02 2.50e+03 ... (remaining 1431 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2280 2.83 - 3.35: 7229 3.35 - 3.86: 12967 3.86 - 4.38: 15202 4.38 - 4.90: 26273 Nonbonded interactions: 63951 Sorted by model distance: nonbonded pdb=" NH1 ARG A 178 " pdb=" O LEU A 182 " model vdw 2.311 3.120 nonbonded pdb=" NH1 ARG B 178 " pdb=" O LEU B 182 " model vdw 2.339 3.120 nonbonded pdb=" NH1 ARG A 322 " pdb=" OD2 ASP A 488 " model vdw 2.369 3.120 nonbonded pdb=" OG SER A 399 " pdb=" OD1 ASP A 401 " model vdw 2.406 3.040 nonbonded pdb=" OD1 ASP B 234 " pdb=" OG SER B 236 " model vdw 2.411 3.040 ... (remaining 63946 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.720 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.810 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 : 0.003 0.041 8028 Z= 0.226 Angle : 0.735 8.108 10912 Z= 0.419 Chirality : 0.048 0.188 1188 Planarity : 0.010 0.106 1434 Dihedral : 11.993 85.765 3002 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.24 % Allowed : 2.03 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.26), residues: 980 helix: 0.76 (0.26), residues: 352 sheet: 0.42 (0.40), residues: 166 loop : -0.03 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 82 HIS 0.008 0.002 HIS A 167 PHE 0.020 0.003 PHE A 274 TYR 0.017 0.004 TYR B 163 ARG 0.024 0.003 ARG B 434 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 178 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: A 139 ASP cc_start: 0.7286 (t70) cc_final: 0.6880 (p0) REVERT: A 394 ASN cc_start: 0.8018 (t0) cc_final: 0.7629 (t160) REVERT: A 395 TRP cc_start: 0.7284 (t-100) cc_final: 0.7046 (t60) REVERT: A 470 HIS cc_start: 0.7316 (m90) cc_final: 0.6840 (m90) REVERT: B 228 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7259 (mm-30) REVERT: B 314 LEU cc_start: 0.7674 (mt) cc_final: 0.7435 (mp) REVERT: B 353 ASP cc_start: 0.7189 (m-30) cc_final: 0.6969 (m-30) REVERT: B 430 GLU cc_start: 0.3794 (tt0) cc_final: 0.3572 (tt0) outliers start: 2 outliers final: 1 residues processed: 180 average time/residue: 1.3305 time to fit residues: 252.2297 Evaluate side-chains 112 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 9.9990 chunk 74 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 88 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 79 ASN A 137 HIS ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 HIS B 137 HIS B 278 HIS B 391 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.189882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.135394 restraints weight = 9255.296| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.27 r_work: 0.3442 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8028 Z= 0.222 Angle : 0.574 7.940 10912 Z= 0.305 Chirality : 0.045 0.172 1188 Planarity : 0.004 0.039 1434 Dihedral : 6.964 86.649 1142 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.34 % Allowed : 9.55 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.27), residues: 980 helix: 1.79 (0.27), residues: 360 sheet: 0.59 (0.41), residues: 162 loop : 0.55 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 423 HIS 0.005 0.001 HIS B 391 PHE 0.013 0.002 PHE B 295 TYR 0.010 0.001 TYR B 163 ARG 0.004 0.001 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.930 Fit side-chains REVERT: A 394 ASN cc_start: 0.8038 (t0) cc_final: 0.7650 (t160) REVERT: A 395 TRP cc_start: 0.7236 (t-100) cc_final: 0.6803 (t60) REVERT: A 440 LYS cc_start: 0.7680 (mttt) cc_final: 0.7414 (mtpt) REVERT: A 465 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7150 (tt0) REVERT: A 470 HIS cc_start: 0.7450 (m90) cc_final: 0.6962 (m170) REVERT: B 43 GLU cc_start: 0.8109 (tt0) cc_final: 0.7719 (tp30) REVERT: B 48 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7217 (tt) REVERT: B 220 ARG cc_start: 0.7715 (mtm180) cc_final: 0.7157 (mmt180) REVERT: B 228 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7367 (mm-30) REVERT: B 353 ASP cc_start: 0.7036 (m-30) cc_final: 0.6614 (m-30) REVERT: B 430 GLU cc_start: 0.3891 (tt0) cc_final: 0.3620 (tt0) outliers start: 28 outliers final: 13 residues processed: 141 average time/residue: 1.2510 time to fit residues: 187.0021 Evaluate side-chains 115 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 392 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 36 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 78 optimal weight: 0.0980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 206 ASN ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.190013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.135062 restraints weight = 9335.354| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.31 r_work: 0.3448 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8028 Z= 0.216 Angle : 0.523 5.336 10912 Z= 0.278 Chirality : 0.044 0.172 1188 Planarity : 0.004 0.042 1434 Dihedral : 6.815 89.699 1142 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.82 % Allowed : 11.58 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.27), residues: 980 helix: 2.13 (0.26), residues: 360 sheet: 0.60 (0.42), residues: 162 loop : 0.46 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 423 HIS 0.008 0.001 HIS B 391 PHE 0.012 0.002 PHE B 295 TYR 0.009 0.001 TYR B 163 ARG 0.003 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.842 Fit side-chains REVERT: A 9 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7729 (mp) REVERT: A 37 MET cc_start: 0.7439 (ttp) cc_final: 0.7234 (ttp) REVERT: A 219 MET cc_start: 0.6582 (OUTLIER) cc_final: 0.5942 (mmt) REVERT: A 395 TRP cc_start: 0.7259 (t-100) cc_final: 0.6767 (t60) REVERT: A 440 LYS cc_start: 0.7652 (mttt) cc_final: 0.7378 (mtpt) REVERT: A 465 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7169 (tt0) REVERT: A 470 HIS cc_start: 0.7542 (m90) cc_final: 0.7332 (m170) REVERT: B 43 GLU cc_start: 0.8133 (tt0) cc_final: 0.7758 (tp30) REVERT: B 48 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7232 (tt) REVERT: B 135 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8183 (mp10) REVERT: B 220 ARG cc_start: 0.7700 (mtm180) cc_final: 0.7141 (mmt180) REVERT: B 228 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7426 (mm-30) REVERT: B 353 ASP cc_start: 0.7034 (m-30) cc_final: 0.6609 (m-30) REVERT: B 430 GLU cc_start: 0.3996 (tt0) cc_final: 0.3720 (tt0) REVERT: B 485 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8143 (tt) outliers start: 32 outliers final: 15 residues processed: 131 average time/residue: 1.0565 time to fit residues: 147.5987 Evaluate side-chains 121 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 485 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 54 optimal weight: 0.0470 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 206 ASN A 394 ASN B 391 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.190635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.140110 restraints weight = 9158.535| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.20 r_work: 0.3459 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8028 Z= 0.217 Angle : 0.524 10.532 10912 Z= 0.273 Chirality : 0.044 0.167 1188 Planarity : 0.004 0.039 1434 Dihedral : 6.712 86.223 1142 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 4.06 % Allowed : 13.48 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.27), residues: 980 helix: 2.26 (0.26), residues: 360 sheet: 0.54 (0.42), residues: 162 loop : 0.41 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 426 HIS 0.009 0.001 HIS B 391 PHE 0.012 0.002 PHE B 295 TYR 0.009 0.001 TYR B 286 ARG 0.002 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 9 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7688 (mp) REVERT: A 37 MET cc_start: 0.7505 (ttp) cc_final: 0.7032 (ttp) REVERT: A 395 TRP cc_start: 0.7162 (t-100) cc_final: 0.6608 (t60) REVERT: A 440 LYS cc_start: 0.7622 (mttt) cc_final: 0.7382 (mtpt) REVERT: A 465 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7347 (tt0) REVERT: B 43 GLU cc_start: 0.8180 (tt0) cc_final: 0.7818 (tp30) REVERT: B 88 THR cc_start: 0.8763 (t) cc_final: 0.8468 (p) REVERT: B 135 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8276 (mp10) REVERT: B 220 ARG cc_start: 0.7808 (mtm180) cc_final: 0.7258 (mmt180) REVERT: B 228 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7477 (mm-30) REVERT: B 353 ASP cc_start: 0.7158 (m-30) cc_final: 0.6728 (m-30) REVERT: B 430 GLU cc_start: 0.4127 (tt0) cc_final: 0.3816 (tt0) outliers start: 34 outliers final: 14 residues processed: 124 average time/residue: 1.1637 time to fit residues: 153.3563 Evaluate side-chains 117 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 391 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 52 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 1 optimal weight: 0.0060 chunk 54 optimal weight: 0.0870 chunk 9 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.4174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN B 188 GLN B 391 HIS ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.191343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.142713 restraints weight = 9235.122| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.17 r_work: 0.3464 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8028 Z= 0.162 Angle : 0.529 17.883 10912 Z= 0.265 Chirality : 0.043 0.163 1188 Planarity : 0.004 0.034 1434 Dihedral : 6.611 83.213 1142 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 3.82 % Allowed : 14.56 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.27), residues: 980 helix: 2.37 (0.26), residues: 360 sheet: 0.56 (0.43), residues: 162 loop : 0.46 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 426 HIS 0.008 0.001 HIS B 391 PHE 0.009 0.001 PHE B 295 TYR 0.009 0.001 TYR B 286 ARG 0.002 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 0.857 Fit side-chains REVERT: A 9 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7612 (mp) REVERT: A 73 GLU cc_start: 0.7287 (mm-30) cc_final: 0.7057 (tm-30) REVERT: A 219 MET cc_start: 0.6690 (OUTLIER) cc_final: 0.5979 (mmt) REVERT: A 395 TRP cc_start: 0.7120 (t-100) cc_final: 0.6527 (t60) REVERT: A 440 LYS cc_start: 0.7795 (mttt) cc_final: 0.7467 (mtpt) REVERT: A 465 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7138 (tt0) REVERT: B 43 GLU cc_start: 0.8055 (tt0) cc_final: 0.7626 (tp30) REVERT: B 88 THR cc_start: 0.8712 (t) cc_final: 0.8427 (p) REVERT: B 135 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8171 (mp10) REVERT: B 220 ARG cc_start: 0.7633 (mtm180) cc_final: 0.7105 (mmt180) REVERT: B 228 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7405 (mm-30) REVERT: B 353 ASP cc_start: 0.7214 (m-30) cc_final: 0.6749 (m-30) outliers start: 32 outliers final: 13 residues processed: 118 average time/residue: 1.1655 time to fit residues: 146.4783 Evaluate side-chains 108 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 391 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 69 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 226 ASN B 188 GLN B 391 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.190762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.141153 restraints weight = 9169.007| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.09 r_work: 0.3472 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8028 Z= 0.223 Angle : 0.541 14.092 10912 Z= 0.276 Chirality : 0.044 0.166 1188 Planarity : 0.004 0.043 1434 Dihedral : 6.573 79.015 1142 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.94 % Allowed : 15.16 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.27), residues: 980 helix: 2.34 (0.27), residues: 360 sheet: 0.59 (0.41), residues: 172 loop : 0.42 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 426 HIS 0.008 0.001 HIS B 391 PHE 0.011 0.001 PHE B 295 TYR 0.010 0.001 TYR B 286 ARG 0.003 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 92 time to evaluate : 0.792 Fit side-chains REVERT: A 9 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7686 (mp) REVERT: A 46 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7574 (tp40) REVERT: A 73 GLU cc_start: 0.7300 (mm-30) cc_final: 0.7061 (tm-30) REVERT: A 219 MET cc_start: 0.6632 (OUTLIER) cc_final: 0.5904 (mmt) REVERT: A 395 TRP cc_start: 0.7197 (t-100) cc_final: 0.6666 (t60) REVERT: A 465 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7323 (tt0) REVERT: B 43 GLU cc_start: 0.8062 (tt0) cc_final: 0.7673 (tp30) REVERT: B 88 THR cc_start: 0.8657 (t) cc_final: 0.8396 (p) REVERT: B 135 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8234 (mp10) REVERT: B 220 ARG cc_start: 0.7713 (mtm180) cc_final: 0.7214 (mmt180) REVERT: B 228 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7478 (mm-30) REVERT: B 353 ASP cc_start: 0.7245 (m-30) cc_final: 0.6793 (m-30) REVERT: B 485 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8156 (tt) outliers start: 33 outliers final: 17 residues processed: 115 average time/residue: 1.1388 time to fit residues: 139.5559 Evaluate side-chains 114 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain B residue 485 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 44 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN B 391 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.190548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.132681 restraints weight = 9146.901| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.30 r_work: 0.3458 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8028 Z= 0.253 Angle : 0.545 11.976 10912 Z= 0.279 Chirality : 0.044 0.177 1188 Planarity : 0.004 0.036 1434 Dihedral : 6.590 74.046 1142 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.82 % Allowed : 15.63 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.27), residues: 980 helix: 2.29 (0.27), residues: 360 sheet: 0.53 (0.41), residues: 172 loop : 0.35 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 426 HIS 0.009 0.001 HIS B 391 PHE 0.012 0.001 PHE B 295 TYR 0.010 0.002 TYR A 58 ARG 0.006 0.000 ARG B 321 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 0.937 Fit side-chains REVERT: A 9 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7678 (mp) REVERT: A 73 GLU cc_start: 0.7252 (mm-30) cc_final: 0.7034 (tm-30) REVERT: A 219 MET cc_start: 0.6628 (OUTLIER) cc_final: 0.5866 (mmt) REVERT: A 395 TRP cc_start: 0.7234 (t-100) cc_final: 0.6707 (t60) REVERT: A 465 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7352 (tt0) REVERT: B 43 GLU cc_start: 0.8132 (tt0) cc_final: 0.7727 (tp30) REVERT: B 88 THR cc_start: 0.8691 (t) cc_final: 0.8427 (p) REVERT: B 135 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8213 (mp10) REVERT: B 220 ARG cc_start: 0.7784 (mtm180) cc_final: 0.7291 (mmt180) REVERT: B 353 ASP cc_start: 0.7368 (m-30) cc_final: 0.6962 (m-30) REVERT: B 485 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8146 (tt) outliers start: 32 outliers final: 18 residues processed: 112 average time/residue: 1.1852 time to fit residues: 142.1062 Evaluate side-chains 110 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 485 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 27 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 93 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.191575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.133411 restraints weight = 9153.433| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.32 r_work: 0.3468 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8028 Z= 0.208 Angle : 0.521 10.630 10912 Z= 0.268 Chirality : 0.043 0.196 1188 Planarity : 0.004 0.034 1434 Dihedral : 6.552 69.486 1142 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.70 % Allowed : 16.59 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.27), residues: 980 helix: 2.35 (0.27), residues: 360 sheet: 0.48 (0.42), residues: 172 loop : 0.35 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 426 HIS 0.007 0.001 HIS B 391 PHE 0.010 0.001 PHE B 295 TYR 0.010 0.001 TYR B 286 ARG 0.006 0.000 ARG B 321 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 0.946 Fit side-chains REVERT: A 9 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7634 (mp) REVERT: A 46 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7614 (tp40) REVERT: A 73 GLU cc_start: 0.7287 (mm-30) cc_final: 0.7043 (tm-30) REVERT: A 219 MET cc_start: 0.6645 (OUTLIER) cc_final: 0.5887 (mmt) REVERT: A 395 TRP cc_start: 0.7160 (t-100) cc_final: 0.6647 (t60) REVERT: A 465 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7357 (tt0) REVERT: B 43 GLU cc_start: 0.8112 (tt0) cc_final: 0.7702 (tp30) REVERT: B 88 THR cc_start: 0.8706 (t) cc_final: 0.8436 (p) REVERT: B 135 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8207 (mp10) REVERT: B 220 ARG cc_start: 0.7774 (mtm180) cc_final: 0.7344 (mmt180) REVERT: B 353 ASP cc_start: 0.7364 (m-30) cc_final: 0.6964 (m-30) outliers start: 31 outliers final: 15 residues processed: 113 average time/residue: 1.1365 time to fit residues: 137.0011 Evaluate side-chains 109 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 391 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 74 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 16 optimal weight: 0.4980 chunk 71 optimal weight: 0.4980 chunk 11 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 28 optimal weight: 0.0570 chunk 86 optimal weight: 2.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN B 391 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.192157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.132877 restraints weight = 9266.090| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.40 r_work: 0.3503 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8028 Z= 0.173 Angle : 0.535 9.701 10912 Z= 0.272 Chirality : 0.043 0.213 1188 Planarity : 0.004 0.051 1434 Dihedral : 6.490 64.730 1142 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.86 % Allowed : 17.66 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.28), residues: 980 helix: 2.41 (0.27), residues: 362 sheet: 0.57 (0.42), residues: 172 loop : 0.33 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 423 HIS 0.009 0.001 HIS B 391 PHE 0.008 0.001 PHE B 295 TYR 0.014 0.001 TYR A 58 ARG 0.006 0.000 ARG B 321 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.834 Fit side-chains REVERT: A 9 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7630 (mp) REVERT: A 46 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7608 (tp40) REVERT: A 73 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7089 (tm-30) REVERT: A 219 MET cc_start: 0.6638 (OUTLIER) cc_final: 0.5917 (mmt) REVERT: A 395 TRP cc_start: 0.6973 (t-100) cc_final: 0.6554 (t60) REVERT: A 465 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7374 (tt0) REVERT: B 43 GLU cc_start: 0.8029 (tt0) cc_final: 0.7691 (tp30) REVERT: B 88 THR cc_start: 0.8672 (t) cc_final: 0.8427 (p) REVERT: B 135 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8264 (mp10) REVERT: B 220 ARG cc_start: 0.7685 (mtm180) cc_final: 0.7301 (mmt180) outliers start: 24 outliers final: 16 residues processed: 112 average time/residue: 1.1888 time to fit residues: 141.6865 Evaluate side-chains 106 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 477 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 33 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 22 optimal weight: 0.0570 chunk 30 optimal weight: 0.8980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN B 308 GLN B 391 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.191804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.133371 restraints weight = 9160.333| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.32 r_work: 0.3498 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8028 Z= 0.214 Angle : 0.534 9.169 10912 Z= 0.274 Chirality : 0.044 0.208 1188 Planarity : 0.004 0.046 1434 Dihedral : 6.512 62.209 1142 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.74 % Allowed : 18.02 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.27), residues: 980 helix: 2.34 (0.27), residues: 362 sheet: 0.53 (0.42), residues: 172 loop : 0.30 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 395 HIS 0.008 0.001 HIS B 391 PHE 0.010 0.001 PHE B 295 TYR 0.010 0.001 TYR B 286 ARG 0.016 0.000 ARG A 33 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.855 Fit side-chains REVERT: A 46 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7613 (tp40) REVERT: A 73 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7112 (tm-30) REVERT: A 219 MET cc_start: 0.6626 (OUTLIER) cc_final: 0.5900 (mmt) REVERT: A 395 TRP cc_start: 0.7017 (t-100) cc_final: 0.6621 (t60) REVERT: A 465 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7375 (tt0) REVERT: B 88 THR cc_start: 0.8687 (t) cc_final: 0.8446 (p) REVERT: B 135 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8232 (mp10) REVERT: B 220 ARG cc_start: 0.7663 (mtm180) cc_final: 0.7307 (mmt180) REVERT: B 485 LEU cc_start: 0.8394 (tt) cc_final: 0.8181 (tt) outliers start: 23 outliers final: 15 residues processed: 108 average time/residue: 1.1943 time to fit residues: 137.2344 Evaluate side-chains 106 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain B residue 477 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 69 optimal weight: 0.2980 chunk 96 optimal weight: 0.0570 chunk 19 optimal weight: 0.0870 chunk 60 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 62 optimal weight: 0.0020 overall best weight: 0.2284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 GLN B 391 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.194474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.143950 restraints weight = 9163.694| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.15 r_work: 0.3507 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8028 Z= 0.140 Angle : 0.503 7.535 10912 Z= 0.260 Chirality : 0.042 0.201 1188 Planarity : 0.004 0.029 1434 Dihedral : 6.442 58.333 1142 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.15 % Allowed : 18.74 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.28), residues: 980 helix: 2.53 (0.26), residues: 362 sheet: 0.71 (0.43), residues: 168 loop : 0.36 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 423 HIS 0.011 0.001 HIS B 391 PHE 0.009 0.001 PHE B 274 TYR 0.026 0.001 TYR A 190 ARG 0.007 0.000 ARG B 321 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6505.22 seconds wall clock time: 115 minutes 20.15 seconds (6920.15 seconds total)