Starting phenix.real_space_refine on Mon Mar 18 15:50:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fli_29279/03_2024/8fli_29279.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fli_29279/03_2024/8fli_29279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fli_29279/03_2024/8fli_29279.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fli_29279/03_2024/8fli_29279.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fli_29279/03_2024/8fli_29279.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fli_29279/03_2024/8fli_29279.pdb" } resolution = 3.8 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= 0.046 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: 6 Type Number sf(0) Gaussians P 828 5.49 5 Mg 3 5.21 5 S 8 5.16 5 C 10319 2.51 5 N 3961 2.21 5 O 6392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 95": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21511 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 17751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 828, 17751 Classifications: {'RNA': 828} Modifications used: {'rna2p_pur': 65, 'rna2p_pyr': 43, 'rna3p_pur': 400, 'rna3p_pyr': 320} Link IDs: {'rna2p': 108, 'rna3p': 719} Chain breaks: 2 Chain: "B" Number of atoms: 3757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3757 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 17, 'TRANS': 440} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 11.27, per 1000 atoms: 0.52 Number of scatterers: 21511 At special positions: 0 Unit cell: (117.3, 158.7, 238.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 8 16.00 P 828 15.00 Mg 3 11.99 O 6392 8.00 N 3961 7.00 C 10319 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 - 3.50 Amino acid : False - 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: 12.81 Conformation dependent library (CDL) restraints added in 814.1 milliseconds 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 858 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 4 sheets defined 38.9% alpha, 7.2% beta 211 base pairs and 351 stacking pairs defined. Time for finding SS restraints: 9.23 Creating SS restraints... Processing helix chain 'B' and resid 22 through 26 removed outlier: 3.706A pdb=" N ILE B 26 " --> pdb=" O TRP B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 48 removed outlier: 3.612A pdb=" N ALA B 31 " --> pdb=" O ASP B 27 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN B 32 " --> pdb=" O TRP B 28 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ARG B 33 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 48 " --> pdb=" O LYS B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 62 removed outlier: 5.088A pdb=" N TRP B 59 " --> pdb=" O LYS B 55 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 77 removed outlier: 3.608A pdb=" N ALA B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP B 77 " --> pdb=" O LYS B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 103 removed outlier: 3.966A pdb=" N LYS B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 143 removed outlier: 3.652A pdb=" N MET B 139 " --> pdb=" O LYS B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 154 Processing helix chain 'B' and resid 168 through 174 removed outlier: 4.171A pdb=" N ALA B 172 " --> pdb=" O THR B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 200 removed outlier: 3.568A pdb=" N ILE B 200 " --> pdb=" O PHE B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 207 Processing helix chain 'B' and resid 214 through 220 Processing helix chain 'B' and resid 243 through 252 removed outlier: 3.634A pdb=" N ALA B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 263 removed outlier: 3.597A pdb=" N HIS B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 297 removed outlier: 3.751A pdb=" N GLN B 295 " --> pdb=" O THR B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 349 removed outlier: 5.282A pdb=" N ALA B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE B 349 " --> pdb=" O PHE B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 378 Proline residue: B 370 - end of helix removed outlier: 3.571A pdb=" N LYS B 373 " --> pdb=" O ASN B 369 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY B 374 " --> pdb=" O PRO B 370 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TRP B 375 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ALA B 376 " --> pdb=" O ILE B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.586A pdb=" N ASN B 389 " --> pdb=" O LYS B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 404 removed outlier: 4.565A pdb=" N LYS B 398 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG B 401 " --> pdb=" O HIS B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 419 Processing sheet with id=AA1, first strand: chain 'B' and resid 115 through 119 removed outlier: 3.847A pdb=" N ARG B 115 " --> pdb=" O ILE B 131 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE B 131 " --> pdb=" O ARG B 115 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL B 117 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 129 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE B 119 " --> pdb=" O ARG B 127 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG B 127 " --> pdb=" O ILE B 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 269 through 272 removed outlier: 3.804A pdb=" N TYR B 187 " --> pdb=" O GLY B 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 319 through 321 removed outlier: 3.562A pdb=" N PHE B 319 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 326 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG B 327 " --> pdb=" O LEU B 334 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 334 " --> pdb=" O ARG B 327 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 420 through 421 removed outlier: 3.503A pdb=" N THR B 432 " --> pdb=" O ARG B 444 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG B 444 " --> pdb=" O THR B 432 " (cutoff:3.500A) 92 hydrogen bonds defined for protein. 255 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 544 hydrogen bonds 932 hydrogen bond angles 0 basepair planarities 211 basepair parallelities 351 stacking parallelities Total time for adding SS restraints: 12.05 Time building geometry restraints manager: 13.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2711 1.33 - 1.45: 10877 1.45 - 1.57: 8463 1.57 - 1.69: 1653 1.69 - 1.81: 12 Bond restraints: 23716 Sorted by residual: bond pdb=" N TYR B 419 " pdb=" CA TYR B 419 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.16e-02 7.43e+03 1.12e+01 bond pdb=" CA HIS B 397 " pdb=" C HIS B 397 " ideal model delta sigma weight residual 1.522 1.470 0.052 1.72e-02 3.38e+03 9.16e+00 bond pdb=" C THR B 415 " pdb=" O THR B 415 " ideal model delta sigma weight residual 1.235 1.271 -0.035 1.26e-02 6.30e+03 7.90e+00 bond pdb=" C LYS B 410 " pdb=" N PRO B 411 " ideal model delta sigma weight residual 1.328 1.357 -0.029 1.25e-02 6.40e+03 5.40e+00 bond pdb=" N TRP B 414 " pdb=" CA TRP B 414 " ideal model delta sigma weight residual 1.457 1.487 -0.029 1.29e-02 6.01e+03 5.13e+00 ... (remaining 23711 not shown) Histogram of bond angle deviations from ideal: 90.60 - 99.29: 2 99.29 - 107.99: 7453 107.99 - 116.68: 14552 116.68 - 125.37: 11129 125.37 - 134.06: 3034 Bond angle restraints: 36170 Sorted by residual: angle pdb=" O3' U A 859 " pdb=" C3' U A 859 " pdb=" C2' U A 859 " ideal model delta sigma weight residual 113.70 90.60 23.10 1.50e+00 4.44e-01 2.37e+02 angle pdb=" C4' U A 859 " pdb=" C3' U A 859 " pdb=" O3' U A 859 " ideal model delta sigma weight residual 113.00 126.61 -13.61 1.50e+00 4.44e-01 8.23e+01 angle pdb=" C LYS B 418 " pdb=" N TYR B 419 " pdb=" CA TYR B 419 " ideal model delta sigma weight residual 122.67 114.94 7.73 1.59e+00 3.96e-01 2.36e+01 angle pdb=" C3' G A 840 " pdb=" O3' G A 840 " pdb=" P G A 841 " ideal model delta sigma weight residual 120.20 126.84 -6.64 1.50e+00 4.44e-01 1.96e+01 angle pdb=" C4' U A 825 " pdb=" C3' U A 825 " pdb=" O3' U A 825 " ideal model delta sigma weight residual 113.00 106.42 6.58 1.50e+00 4.44e-01 1.92e+01 ... (remaining 36165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 12765 35.51 - 71.03: 2187 71.03 - 106.54: 298 106.54 - 142.06: 8 142.06 - 177.57: 8 Dihedral angle restraints: 15266 sinusoidal: 13939 harmonic: 1327 Sorted by residual: dihedral pdb=" O4' U A 595 " pdb=" C1' U A 595 " pdb=" N1 U A 595 " pdb=" C2 U A 595 " ideal model delta sinusoidal sigma weight residual 200.00 41.16 158.84 1 1.50e+01 4.44e-03 8.25e+01 dihedral pdb=" O4' C A -6 " pdb=" C1' C A -6 " pdb=" N1 C A -6 " pdb=" C2 C A -6 " ideal model delta sinusoidal sigma weight residual 200.00 50.66 149.34 1 1.50e+01 4.44e-03 7.94e+01 dihedral pdb=" O4' U A 498 " pdb=" C1' U A 498 " pdb=" N1 U A 498 " pdb=" C2 U A 498 " ideal model delta sinusoidal sigma weight residual 232.00 56.66 175.34 1 1.70e+01 3.46e-03 6.63e+01 ... (remaining 15263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4201 0.054 - 0.107: 409 0.107 - 0.161: 53 0.161 - 0.215: 16 0.215 - 0.268: 8 Chirality restraints: 4687 Sorted by residual: chirality pdb=" P G A 828 " pdb=" OP1 G A 828 " pdb=" OP2 G A 828 " pdb=" O5' G A 828 " both_signs ideal model delta sigma weight residual True 2.41 -2.68 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C1' G A 531 " pdb=" O4' G A 531 " pdb=" C2' G A 531 " pdb=" N9 G A 531 " both_signs ideal model delta sigma weight residual False 2.46 2.22 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C1' A A 630 " pdb=" O4' A A 630 " pdb=" C2' A A 630 " pdb=" N9 A A 630 " both_signs ideal model delta sigma weight residual False 2.46 2.23 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 4684 not shown) Planarity restraints: 1481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A 305 " 0.025 2.00e-02 2.50e+03 2.79e-02 1.75e+01 pdb=" N1 C A 305 " -0.033 2.00e-02 2.50e+03 pdb=" C2 C A 305 " 0.054 2.00e-02 2.50e+03 pdb=" O2 C A 305 " -0.032 2.00e-02 2.50e+03 pdb=" N3 C A 305 " -0.016 2.00e-02 2.50e+03 pdb=" C4 C A 305 " 0.026 2.00e-02 2.50e+03 pdb=" N4 C A 305 " -0.003 2.00e-02 2.50e+03 pdb=" C5 C A 305 " -0.006 2.00e-02 2.50e+03 pdb=" C6 C A 305 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 112 " -0.058 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO B 113 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO B 113 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 113 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 410 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C LYS B 410 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS B 410 " 0.021 2.00e-02 2.50e+03 pdb=" N PRO B 411 " 0.019 2.00e-02 2.50e+03 ... (remaining 1478 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 16 2.19 - 2.86: 7122 2.86 - 3.54: 33277 3.54 - 4.22: 64014 4.22 - 4.90: 81169 Nonbonded interactions: 185598 Sorted by model distance: nonbonded pdb=" OE1 GLU B 470 " pdb=" CD1 TRP B 471 " model vdw 1.508 3.260 nonbonded pdb=" O3' G A 0 " pdb="MG MG A 903 " model vdw 1.862 2.170 nonbonded pdb=" OP2 U A 1 " pdb="MG MG A 903 " model vdw 1.895 2.170 nonbonded pdb=" OP1 A A 6 " pdb="MG MG A 901 " model vdw 1.901 2.170 nonbonded pdb=" O LYS B 348 " pdb=" OD1 ASP B 351 " model vdw 1.923 3.040 ... (remaining 185593 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.590 Check model and map are aligned: 0.270 Set scattering table: 0.210 Process input model: 67.350 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 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 : 0.005 0.055 23716 Z= 0.288 Angle : 0.680 23.097 36170 Z= 0.356 Chirality : 0.036 0.268 4687 Planarity : 0.005 0.088 1481 Dihedral : 26.204 177.569 14408 Min Nonbonded Distance : 1.508 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.66 % Allowed : 16.45 % Favored : 82.89 % Rotamer: Outliers : 0.26 % Allowed : 41.33 % Favored : 58.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.36), residues: 456 helix: -2.28 (0.36), residues: 188 sheet: -1.99 (0.88), residues: 38 loop : -2.69 (0.36), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 471 HIS 0.004 0.001 HIS B 379 PHE 0.013 0.002 PHE B 430 TYR 0.016 0.002 TYR B 66 ARG 0.006 0.001 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 1.015 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 35 average time/residue: 0.3784 time to fit residues: 20.6097 Evaluate side-chains 35 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 64 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 115 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23716 Z= 0.236 Angle : 0.642 13.224 36170 Z= 0.319 Chirality : 0.032 0.245 4687 Planarity : 0.005 0.086 1481 Dihedral : 26.071 177.058 13453 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.66 % Allowed : 16.45 % Favored : 82.89 % Rotamer: Outliers : 5.61 % Allowed : 36.99 % Favored : 57.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.36), residues: 456 helix: -2.03 (0.36), residues: 187 sheet: -2.13 (0.86), residues: 38 loop : -2.53 (0.36), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 226 HIS 0.001 0.001 HIS B 202 PHE 0.011 0.002 PHE B 430 TYR 0.013 0.002 TYR B 66 ARG 0.005 0.001 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 38 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 417 ASN cc_start: 0.9085 (t0) cc_final: 0.8864 (t0) outliers start: 22 outliers final: 14 residues processed: 56 average time/residue: 0.3633 time to fit residues: 31.4090 Evaluate side-chains 50 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 36 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 427 HIS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 458 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 102 optimal weight: 0.0000 chunk 114 optimal weight: 0.8980 chunk 39 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 GLN ** B 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23716 Z= 0.248 Angle : 0.651 13.129 36170 Z= 0.324 Chirality : 0.033 0.263 4687 Planarity : 0.005 0.085 1481 Dihedral : 25.966 179.272 13451 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.66 % Allowed : 16.45 % Favored : 82.89 % Rotamer: Outliers : 7.65 % Allowed : 35.97 % Favored : 56.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.36), residues: 456 helix: -1.88 (0.37), residues: 188 sheet: -1.96 (1.10), residues: 22 loop : -2.44 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 226 HIS 0.002 0.001 HIS B 407 PHE 0.011 0.002 PHE B 297 TYR 0.014 0.001 TYR B 66 ARG 0.004 0.001 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 36 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 390 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.7411 (tmm-80) REVERT: B 416 LYS cc_start: 0.8921 (tptt) cc_final: 0.8602 (tppt) REVERT: B 438 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7939 (pp20) outliers start: 30 outliers final: 19 residues processed: 60 average time/residue: 0.3737 time to fit residues: 33.2129 Evaluate side-chains 55 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 34 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 427 HIS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 458 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 115 optimal weight: 0.0970 chunk 122 optimal weight: 0.4980 chunk 60 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 HIS ** B 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23716 Z= 0.228 Angle : 0.633 13.200 36170 Z= 0.315 Chirality : 0.032 0.282 4687 Planarity : 0.005 0.086 1481 Dihedral : 25.886 179.736 13451 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.88 % Allowed : 16.23 % Favored : 82.89 % Rotamer: Outliers : 9.69 % Allowed : 34.18 % Favored : 56.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.37), residues: 456 helix: -1.69 (0.37), residues: 193 sheet: -1.87 (1.07), residues: 22 loop : -2.37 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 226 HIS 0.002 0.000 HIS B 379 PHE 0.009 0.001 PHE B 297 TYR 0.017 0.001 TYR B 66 ARG 0.017 0.001 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 35 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8209 (mtm-85) REVERT: B 226 TRP cc_start: 0.7407 (t60) cc_final: 0.7041 (t60) REVERT: B 260 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8130 (ptmt) REVERT: B 350 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8581 (tmm-80) REVERT: B 432 THR cc_start: 0.9611 (OUTLIER) cc_final: 0.9332 (p) REVERT: B 438 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7926 (pp20) REVERT: B 470 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7766 (pp20) outliers start: 38 outliers final: 22 residues processed: 68 average time/residue: 0.3771 time to fit residues: 38.5878 Evaluate side-chains 63 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 35 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 427 HIS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 470 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23716 Z= 0.211 Angle : 0.616 13.437 36170 Z= 0.307 Chirality : 0.032 0.290 4687 Planarity : 0.005 0.087 1481 Dihedral : 25.844 179.995 13451 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.88 % Allowed : 16.45 % Favored : 82.68 % Rotamer: Outliers : 8.16 % Allowed : 36.22 % Favored : 55.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.37), residues: 456 helix: -1.57 (0.37), residues: 193 sheet: -1.84 (1.07), residues: 22 loop : -2.27 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 400 HIS 0.004 0.001 HIS B 24 PHE 0.010 0.001 PHE B 297 TYR 0.016 0.002 TYR B 66 ARG 0.014 0.001 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 37 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8223 (mtm-85) REVERT: B 226 TRP cc_start: 0.7392 (t60) cc_final: 0.7038 (t60) REVERT: B 350 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8530 (tmm-80) REVERT: B 432 THR cc_start: 0.9615 (OUTLIER) cc_final: 0.9330 (p) REVERT: B 438 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7939 (pp20) REVERT: B 448 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8483 (tmtt) REVERT: B 470 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7720 (pp20) outliers start: 32 outliers final: 24 residues processed: 65 average time/residue: 0.3813 time to fit residues: 36.9428 Evaluate side-chains 64 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 34 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 427 HIS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 448 LYS Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 470 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 64 optimal weight: 20.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 HIS ** B 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 23716 Z= 0.421 Angle : 0.795 13.131 36170 Z= 0.385 Chirality : 0.038 0.308 4687 Planarity : 0.006 0.089 1481 Dihedral : 25.983 179.198 13451 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.66 % Allowed : 18.20 % Favored : 81.14 % Rotamer: Outliers : 10.97 % Allowed : 34.18 % Favored : 54.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.35), residues: 456 helix: -2.02 (0.35), residues: 187 sheet: -2.15 (1.08), residues: 24 loop : -2.43 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 402 HIS 0.006 0.001 HIS B 407 PHE 0.018 0.003 PHE B 420 TYR 0.015 0.002 TYR B 109 ARG 0.011 0.001 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 33 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 ARG cc_start: 0.9230 (OUTLIER) cc_final: 0.8178 (mtm-85) REVERT: B 328 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8233 (mmmm) REVERT: B 390 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.7651 (tmm-80) REVERT: B 432 THR cc_start: 0.9658 (OUTLIER) cc_final: 0.9363 (p) REVERT: B 438 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8181 (pp20) REVERT: B 448 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8502 (tmtt) REVERT: B 470 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7840 (pp20) outliers start: 43 outliers final: 25 residues processed: 73 average time/residue: 0.3876 time to fit residues: 41.6221 Evaluate side-chains 64 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 32 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 427 HIS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 448 LYS Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 470 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 89 optimal weight: 0.0670 chunk 69 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 68 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 overall best weight: 2.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 HIS ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23716 Z= 0.209 Angle : 0.627 13.592 36170 Z= 0.312 Chirality : 0.032 0.324 4687 Planarity : 0.005 0.089 1481 Dihedral : 25.870 178.953 13451 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.88 % Allowed : 16.23 % Favored : 82.89 % Rotamer: Outliers : 10.97 % Allowed : 33.67 % Favored : 55.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.36), residues: 456 helix: -1.62 (0.37), residues: 193 sheet: -1.83 (1.07), residues: 22 loop : -2.38 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 226 HIS 0.002 0.001 HIS B 407 PHE 0.011 0.001 PHE B 321 TYR 0.016 0.002 TYR B 66 ARG 0.009 0.001 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 37 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8111 (mtm-85) REVERT: B 328 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8175 (mmmm) REVERT: B 350 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8609 (tmm-80) REVERT: B 390 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.7395 (tmm-80) REVERT: B 432 THR cc_start: 0.9621 (OUTLIER) cc_final: 0.9306 (p) REVERT: B 438 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7995 (pp20) REVERT: B 448 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8459 (tmtt) REVERT: B 470 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7859 (pp20) outliers start: 43 outliers final: 25 residues processed: 75 average time/residue: 0.4020 time to fit residues: 44.4550 Evaluate side-chains 70 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 37 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 283 SER Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 427 HIS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 437 LYS Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 448 LYS Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 470 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 HIS ** B 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 GLN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 23716 Z= 0.470 Angle : 0.864 12.985 36170 Z= 0.419 Chirality : 0.042 0.361 4687 Planarity : 0.006 0.093 1481 Dihedral : 26.277 179.981 13451 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 21.65 Ramachandran Plot: Outliers : 0.88 % Allowed : 18.86 % Favored : 80.26 % Rotamer: Outliers : 8.93 % Allowed : 34.95 % Favored : 56.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.34), residues: 456 helix: -2.16 (0.34), residues: 182 sheet: -2.23 (1.08), residues: 24 loop : -2.70 (0.34), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 400 HIS 0.006 0.001 HIS B 407 PHE 0.016 0.003 PHE B 430 TYR 0.017 0.002 TYR B 66 ARG 0.010 0.001 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 31 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 328 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8159 (mtmm) REVERT: B 350 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8697 (tmm-80) REVERT: B 390 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.7697 (tmm-80) REVERT: B 448 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8464 (tmtt) outliers start: 35 outliers final: 25 residues processed: 64 average time/residue: 0.4160 time to fit residues: 38.9552 Evaluate side-chains 59 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 30 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 283 SER Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 427 HIS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 437 LYS Chi-restraints excluded: chain B residue 448 LYS Chi-restraints excluded: chain B residue 458 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 0.4980 chunk 117 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 68 optimal weight: 20.0000 chunk 49 optimal weight: 4.9990 chunk 89 optimal weight: 0.3980 chunk 35 optimal weight: 3.9990 chunk 103 optimal weight: 0.0570 chunk 107 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 23716 Z= 0.128 Angle : 0.587 13.775 36170 Z= 0.294 Chirality : 0.030 0.434 4687 Planarity : 0.005 0.092 1481 Dihedral : 25.787 178.647 13451 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.88 % Allowed : 14.04 % Favored : 85.09 % Rotamer: Outliers : 4.08 % Allowed : 39.03 % Favored : 56.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.37), residues: 456 helix: -1.61 (0.37), residues: 195 sheet: -1.89 (0.82), residues: 37 loop : -2.31 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 226 HIS 0.006 0.001 HIS B 346 PHE 0.021 0.002 PHE B 321 TYR 0.016 0.001 TYR B 66 ARG 0.009 0.001 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 43 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8151 (mtm-85) REVERT: B 328 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8103 (mmmm) outliers start: 16 outliers final: 12 residues processed: 57 average time/residue: 0.3681 time to fit residues: 31.6962 Evaluate side-chains 50 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 36 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 470 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 10.0000 chunk 120 optimal weight: 0.2980 chunk 73 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 126 optimal weight: 0.0670 chunk 116 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 61 optimal weight: 20.0000 overall best weight: 1.3920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 23716 Z= 0.154 Angle : 0.573 13.175 36170 Z= 0.287 Chirality : 0.030 0.412 4687 Planarity : 0.005 0.092 1481 Dihedral : 25.735 178.071 13451 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.66 % Allowed : 15.13 % Favored : 84.21 % Rotamer: Outliers : 4.08 % Allowed : 39.80 % Favored : 56.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.38), residues: 456 helix: -1.39 (0.37), residues: 193 sheet: -2.26 (0.71), residues: 49 loop : -2.16 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 226 HIS 0.002 0.000 HIS B 379 PHE 0.023 0.001 PHE B 321 TYR 0.015 0.001 TYR B 66 ARG 0.006 0.001 ARG B 401 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 36 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.8227 (mtm-85) REVERT: B 328 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8127 (mmmm) outliers start: 16 outliers final: 13 residues processed: 48 average time/residue: 0.3771 time to fit residues: 28.2748 Evaluate side-chains 51 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 36 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 470 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 9.9990 chunk 107 optimal weight: 0.6980 chunk 30 optimal weight: 10.9990 chunk 92 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 100 optimal weight: 0.0770 chunk 42 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 overall best weight: 2.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.097325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.070455 restraints weight = 84213.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.072391 restraints weight = 34102.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.073616 restraints weight = 22119.717| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23716 Z= 0.205 Angle : 0.598 12.618 36170 Z= 0.298 Chirality : 0.031 0.416 4687 Planarity : 0.005 0.093 1481 Dihedral : 25.720 179.118 13451 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.88 % Allowed : 16.01 % Favored : 83.11 % Rotamer: Outliers : 4.34 % Allowed : 39.80 % Favored : 55.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.38), residues: 456 helix: -1.34 (0.37), residues: 192 sheet: -1.88 (0.83), residues: 37 loop : -2.22 (0.39), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 226 HIS 0.002 0.001 HIS B 379 PHE 0.023 0.002 PHE B 321 TYR 0.016 0.002 TYR B 66 ARG 0.007 0.001 ARG B 401 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2434.56 seconds wall clock time: 46 minutes 29.64 seconds (2789.64 seconds total)