Starting phenix.real_space_refine on Tue Sep 24 11:15:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9euy_19989/09_2024/9euy_19989_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9euy_19989/09_2024/9euy_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9euy_19989/09_2024/9euy_19989.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9euy_19989/09_2024/9euy_19989.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9euy_19989/09_2024/9euy_19989_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9euy_19989/09_2024/9euy_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-5461/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: 5.49, per 1000 atoms: 0.70 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: 1.87 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.81 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: 2.23 Time building geometry restraints manager: 2.18 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: 0.00 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: 3.090 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.900 Find NCS groups from input model: 0.200 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: 0.010 Load rotamer database and sin/cos tables:11.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.100 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 2 poor density : 178 time to evaluate : 0.790 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: 1.2331 time to fit residues: 234.1004 Evaluate side-chains 112 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 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 fitting. rotamer outliers: 28 poor density : 121 time to evaluate : 0.895 Fit side-chains REVERT: A 394 ASN cc_start: 0.7988 (t0) cc_final: 0.7625 (t160) REVERT: A 395 TRP cc_start: 0.7311 (t-100) cc_final: 0.7053 (t60) REVERT: A 465 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7209 (tt0) REVERT: A 470 HIS cc_start: 0.7597 (m90) cc_final: 0.7008 (m170) REVERT: B 228 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7317 (mm-30) REVERT: B 353 ASP cc_start: 0.7091 (m-30) cc_final: 0.6685 (m-30) REVERT: B 430 GLU cc_start: 0.4121 (tt0) cc_final: 0.3848 (tt0) outliers start: 28 outliers final: 13 residues processed: 141 average time/residue: 1.2148 time to fit residues: 181.7668 Evaluate side-chains 113 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 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 49 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 0.1980 chunk 89 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 88 optimal weight: 0.0870 chunk 30 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2527 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= 0.219 Angle : 0.527 5.348 10912 Z= 0.279 Chirality : 0.044 0.171 1188 Planarity : 0.004 0.042 1434 Dihedral : 6.821 89.602 1142 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.82 % Allowed : 11.46 % Favored : 84.73 % 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: 1.56 (0.27), residues: 980 helix: 2.09 (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 B 33 *********************** 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 139 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 107 time to evaluate : 0.898 Fit side-chains REVERT: A 9 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7735 (mp) REVERT: A 219 MET cc_start: 0.6452 (OUTLIER) cc_final: 0.5813 (mmt) REVERT: A 394 ASN cc_start: 0.7901 (t0) cc_final: 0.7681 (t160) REVERT: A 395 TRP cc_start: 0.7305 (t-100) cc_final: 0.6994 (t60) REVERT: A 465 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7217 (tt0) REVERT: A 470 HIS cc_start: 0.7705 (m90) cc_final: 0.7399 (m170) REVERT: B 135 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8406 (mp10) REVERT: B 353 ASP cc_start: 0.7073 (m-30) cc_final: 0.6665 (m-30) REVERT: B 430 GLU cc_start: 0.4175 (tt0) cc_final: 0.3907 (tt0) outliers start: 32 outliers final: 15 residues processed: 130 average time/residue: 1.0517 time to fit residues: 146.0781 Evaluate side-chains 115 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 59 optimal weight: 0.0020 chunk 89 optimal weight: 0.4980 chunk 94 optimal weight: 0.0980 chunk 84 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 overall best weight: 0.3588 ------------------------------------------------------------------------------- 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 B 391 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2775 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= 0.156 Angle : 0.506 10.591 10912 Z= 0.262 Chirality : 0.043 0.164 1188 Planarity : 0.004 0.035 1434 Dihedral : 6.703 89.205 1142 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.58 % Allowed : 14.08 % Favored : 82.34 % 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: 1.73 (0.27), residues: 980 helix: 2.33 (0.26), residues: 360 sheet: 0.61 (0.43), residues: 162 loop : 0.50 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 426 HIS 0.007 0.001 HIS B 391 PHE 0.009 0.001 PHE B 425 TYR 0.010 0.001 TYR A 163 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 136 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 106 time to evaluate : 0.766 Fit side-chains REVERT: A 9 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7707 (mp) REVERT: A 219 MET cc_start: 0.6444 (OUTLIER) cc_final: 0.5789 (mmt) REVERT: A 394 ASN cc_start: 0.7865 (t0) cc_final: 0.7610 (t0) REVERT: A 395 TRP cc_start: 0.7202 (t-100) cc_final: 0.6793 (t60) REVERT: A 465 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7154 (tt0) REVERT: B 88 THR cc_start: 0.8682 (t) cc_final: 0.8440 (p) REVERT: B 353 ASP cc_start: 0.7199 (m-30) cc_final: 0.6756 (m-30) outliers start: 30 outliers final: 13 residues processed: 126 average time/residue: 1.0798 time to fit residues: 144.9641 Evaluate side-chains 113 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 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 67 GLU Chi-restraints excluded: chain B residue 83 SER 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 53 optimal weight: 1.9990 chunk 1 optimal weight: 0.0030 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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 391 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8028 Z= 0.215 Angle : 0.542 14.895 10912 Z= 0.276 Chirality : 0.044 0.164 1188 Planarity : 0.004 0.035 1434 Dihedral : 6.655 85.970 1142 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.70 % Allowed : 15.87 % Favored : 80.43 % 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 (0.27), residues: 980 helix: 2.33 (0.27), residues: 360 sheet: 0.56 (0.43), residues: 162 loop : 0.45 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 426 HIS 0.009 0.001 HIS B 391 PHE 0.011 0.001 PHE B 295 TYR 0.010 0.001 TYR B 286 ARG 0.004 0.000 ARG A 113 *********************** 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 131 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 100 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 9 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7759 (mp) REVERT: A 394 ASN cc_start: 0.7852 (t0) cc_final: 0.7629 (t160) REVERT: A 395 TRP cc_start: 0.7243 (t-100) cc_final: 0.6854 (t60) REVERT: A 465 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7242 (tt0) REVERT: A 470 HIS cc_start: 0.7718 (m90) cc_final: 0.7396 (m170) REVERT: B 88 THR cc_start: 0.8770 (t) cc_final: 0.8517 (p) REVERT: B 353 ASP cc_start: 0.7285 (m-30) cc_final: 0.6829 (m-30) outliers start: 31 outliers final: 14 residues processed: 121 average time/residue: 1.0772 time to fit residues: 139.1512 Evaluate side-chains 112 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 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 83 SER Chi-restraints excluded: chain B residue 101 SER 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 85 optimal weight: 8.9990 chunk 18 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8028 Z= 0.226 Angle : 0.556 17.356 10912 Z= 0.277 Chirality : 0.044 0.164 1188 Planarity : 0.004 0.034 1434 Dihedral : 6.604 81.212 1142 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.70 % Allowed : 16.11 % Favored : 80.19 % 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: 1.65 (0.27), residues: 980 helix: 2.31 (0.27), residues: 360 sheet: 0.51 (0.43), residues: 162 loop : 0.42 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 426 HIS 0.009 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 33 *********************** 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 127 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 96 time to evaluate : 0.904 Fit side-chains REVERT: A 9 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7757 (mp) REVERT: A 46 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7642 (tp40) REVERT: A 219 MET cc_start: 0.6502 (OUTLIER) cc_final: 0.5786 (mmt) REVERT: A 394 ASN cc_start: 0.7848 (t0) cc_final: 0.7402 (t160) REVERT: A 395 TRP cc_start: 0.7273 (t-100) cc_final: 0.6905 (t60) REVERT: A 465 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7242 (tt0) REVERT: B 88 THR cc_start: 0.8753 (t) cc_final: 0.8512 (p) REVERT: B 353 ASP cc_start: 0.7299 (m-30) cc_final: 0.6885 (m-30) REVERT: B 443 LYS cc_start: 0.7406 (mmtm) cc_final: 0.7044 (mptt) outliers start: 31 outliers final: 18 residues processed: 119 average time/residue: 1.0434 time to fit residues: 132.8064 Evaluate side-chains 115 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 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 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 186 LEU Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain B residue 477 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 69 optimal weight: 0.4980 chunk 53 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 59 optimal weight: 0.0060 chunk 57 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8028 Z= 0.174 Angle : 0.522 14.778 10912 Z= 0.266 Chirality : 0.043 0.177 1188 Planarity : 0.004 0.032 1434 Dihedral : 6.517 76.615 1142 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.22 % Allowed : 17.30 % 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: 1.78 (0.28), residues: 980 helix: 2.44 (0.27), residues: 360 sheet: 0.61 (0.42), residues: 172 loop : 0.47 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 426 HIS 0.010 0.001 HIS B 391 PHE 0.009 0.001 PHE B 295 TYR 0.014 0.001 TYR A 58 ARG 0.004 0.000 ARG A 33 *********************** 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 124 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 97 time to evaluate : 0.866 Fit side-chains REVERT: A 43 GLU cc_start: 0.7486 (pt0) cc_final: 0.7272 (pt0) REVERT: A 46 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7624 (tp40) REVERT: A 219 MET cc_start: 0.6508 (OUTLIER) cc_final: 0.5799 (mmt) REVERT: A 394 ASN cc_start: 0.7786 (t0) cc_final: 0.7527 (t0) REVERT: A 395 TRP cc_start: 0.7235 (t-100) cc_final: 0.6814 (t60) REVERT: A 465 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7288 (tt0) REVERT: B 88 THR cc_start: 0.8700 (t) cc_final: 0.8467 (p) REVERT: B 353 ASP cc_start: 0.7323 (m-30) cc_final: 0.6890 (m-30) REVERT: B 443 LYS cc_start: 0.7361 (mmtm) cc_final: 0.6945 (mptt) REVERT: B 485 LEU cc_start: 0.8378 (tt) cc_final: 0.8174 (tt) outliers start: 27 outliers final: 14 residues processed: 117 average time/residue: 1.0854 time to fit residues: 135.8111 Evaluate side-chains 112 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 46 GLN 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 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 101 SER Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 477 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 90 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS B 188 GLN B 391 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8028 Z= 0.194 Angle : 0.527 13.235 10912 Z= 0.269 Chirality : 0.043 0.184 1188 Planarity : 0.004 0.032 1434 Dihedral : 6.461 71.675 1142 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.46 % Allowed : 17.42 % 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: 1.74 (0.27), residues: 980 helix: 2.41 (0.27), residues: 362 sheet: 0.64 (0.42), residues: 172 loop : 0.40 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 426 HIS 0.006 0.001 HIS B 391 PHE 0.009 0.001 PHE B 295 TYR 0.010 0.001 TYR B 286 ARG 0.009 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 121 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 92 time to evaluate : 0.878 Fit side-chains REVERT: A 9 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7631 (mp) REVERT: A 43 GLU cc_start: 0.7500 (pt0) cc_final: 0.7283 (pt0) REVERT: A 219 MET cc_start: 0.6513 (OUTLIER) cc_final: 0.5794 (mmt) REVERT: A 394 ASN cc_start: 0.7782 (t0) cc_final: 0.7537 (t0) REVERT: A 395 TRP cc_start: 0.7244 (t-100) cc_final: 0.6861 (t60) REVERT: A 465 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7260 (tt0) REVERT: B 88 THR cc_start: 0.8714 (t) cc_final: 0.8476 (p) REVERT: B 443 LYS cc_start: 0.7374 (mmtm) cc_final: 0.7060 (mptt) REVERT: B 485 LEU cc_start: 0.8388 (tt) cc_final: 0.8183 (tt) outliers start: 29 outliers final: 17 residues processed: 113 average time/residue: 1.0959 time to fit residues: 132.0952 Evaluate side-chains 108 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 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 183 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 90 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 38 optimal weight: 0.2980 chunk 69 optimal weight: 0.2980 chunk 27 optimal weight: 0.0970 chunk 79 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 308 GLN ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8028 Z= 0.172 Angle : 0.519 10.677 10912 Z= 0.265 Chirality : 0.043 0.191 1188 Planarity : 0.004 0.048 1434 Dihedral : 6.434 66.989 1142 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.63 % Allowed : 18.14 % 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: 1.77 (0.28), residues: 980 helix: 2.44 (0.27), residues: 362 sheet: 0.66 (0.42), residues: 172 loop : 0.42 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 423 HIS 0.011 0.001 HIS B 391 PHE 0.008 0.001 PHE B 295 TYR 0.012 0.001 TYR A 58 ARG 0.012 0.000 ARG A 33 *********************** 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 115 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 0.825 Fit side-chains REVERT: A 43 GLU cc_start: 0.7498 (pt0) cc_final: 0.7292 (pt0) REVERT: A 219 MET cc_start: 0.6512 (OUTLIER) cc_final: 0.5800 (mmt) REVERT: A 394 ASN cc_start: 0.7747 (t0) cc_final: 0.7498 (t0) REVERT: A 395 TRP cc_start: 0.7232 (t-100) cc_final: 0.6841 (t60) REVERT: A 465 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7334 (tt0) REVERT: B 88 THR cc_start: 0.8665 (t) cc_final: 0.8436 (p) REVERT: B 101 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8618 (m) REVERT: B 443 LYS cc_start: 0.7417 (mmtm) cc_final: 0.7159 (mptt) outliers start: 22 outliers final: 14 residues processed: 108 average time/residue: 1.0858 time to fit residues: 125.6403 Evaluate side-chains 105 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 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 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 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 93 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 97 optimal weight: 0.0870 chunk 89 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 47 optimal weight: 0.0770 chunk 61 optimal weight: 0.6980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 8028 Z= 0.211 Angle : 0.894 59.199 10912 Z= 0.516 Chirality : 0.044 0.350 1188 Planarity : 0.004 0.067 1434 Dihedral : 6.502 66.949 1142 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.39 % Allowed : 18.62 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.77 (0.28), residues: 980 helix: 2.43 (0.27), residues: 362 sheet: 0.66 (0.42), residues: 172 loop : 0.43 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 423 HIS 0.009 0.001 HIS B 391 PHE 0.008 0.001 PHE B 295 TYR 0.011 0.001 TYR A 190 ARG 0.010 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 109 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 89 time to evaluate : 0.778 Fit side-chains REVERT: A 9 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7612 (mp) REVERT: A 43 GLU cc_start: 0.7501 (pt0) cc_final: 0.7295 (pt0) REVERT: A 219 MET cc_start: 0.6512 (OUTLIER) cc_final: 0.5799 (mmt) REVERT: A 394 ASN cc_start: 0.7748 (t0) cc_final: 0.7498 (t0) REVERT: A 395 TRP cc_start: 0.7232 (t-100) cc_final: 0.6840 (t60) REVERT: A 465 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7334 (tt0) REVERT: B 88 THR cc_start: 0.8670 (t) cc_final: 0.8437 (p) REVERT: B 101 SER cc_start: 0.8828 (OUTLIER) cc_final: 0.8619 (m) REVERT: B 443 LYS cc_start: 0.7418 (mmtm) cc_final: 0.7158 (mptt) outliers start: 20 outliers final: 13 residues processed: 104 average time/residue: 1.0302 time to fit residues: 114.7567 Evaluate side-chains 106 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 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 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 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 82 optimal weight: 5.9990 chunk 23 optimal weight: 0.0980 chunk 71 optimal weight: 0.0370 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 0.0870 chunk 77 optimal weight: 0.1980 chunk 32 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 overall best weight: 0.2036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 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 = 0.4250 r_free = 0.4250 target = 0.192958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.142594 restraints weight = 9082.677| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.18 r_work: 0.3486 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 8028 Z= 0.211 Angle : 0.894 59.199 10912 Z= 0.516 Chirality : 0.044 0.350 1188 Planarity : 0.004 0.067 1434 Dihedral : 6.502 66.949 1142 Min Nonbonded Distance : 1.320 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.15 % Allowed : 18.85 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.77 (0.28), residues: 980 helix: 2.43 (0.27), residues: 362 sheet: 0.66 (0.42), residues: 172 loop : 0.43 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 423 HIS 0.009 0.001 HIS B 391 PHE 0.008 0.001 PHE B 295 TYR 0.011 0.001 TYR A 190 ARG 0.010 0.000 ARG A 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3363.63 seconds wall clock time: 59 minutes 17.68 seconds (3557.68 seconds total)