Starting phenix.real_space_refine on Sun Mar 10 21:31:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8m_15233/03_2024/8a8m_15233_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8m_15233/03_2024/8a8m_15233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8m_15233/03_2024/8a8m_15233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8m_15233/03_2024/8a8m_15233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8m_15233/03_2024/8a8m_15233_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8m_15233/03_2024/8a8m_15233_updated.pdb" } resolution = 4.0 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= -0.000 sd= 0.004 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 4 5.49 5 Mg 4 5.21 5 S 29 5.16 5 C 3348 2.51 5 N 886 2.21 5 O 973 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 9": "OE1" <-> "OE2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5244 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2816 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 17, 'TRANS': 331} Chain: "B" Number of atoms: 2370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2370 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 18, 'TRANS': 279} Chain breaks: 2 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'AP2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'AP2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASP A 177 " occ=0.78 ... (6 atoms not shown) pdb=" OD2 ASP A 177 " occ=0.78 Time building chain proxies: 3.58, per 1000 atoms: 0.68 Number of scatterers: 5244 At special positions: 0 Unit cell: (61.248, 81.026, 102.08, 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 29 16.00 P 4 15.00 Mg 4 11.99 O 973 8.00 N 886 7.00 C 3348 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: 2.24 Conformation dependent library (CDL) restraints added in 990.0 milliseconds 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1228 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 5 sheets defined 36.8% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 113 through 119 removed outlier: 4.298A pdb=" N LYS A 118 " --> pdb=" O ASN A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 144 Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 230 through 239 removed outlier: 4.118A pdb=" N LEU A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 260 removed outlier: 4.028A pdb=" N TYR A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLN A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 289 Processing helix chain 'A' and resid 299 through 304 removed outlier: 4.395A pdb=" N ALA A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 removed outlier: 4.635A pdb=" N GLN A 310 " --> pdb=" O TYR A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 327 through 329 No H-bonds generated for 'chain 'A' and resid 327 through 329' Processing helix chain 'A' and resid 334 through 345 removed outlier: 4.059A pdb=" N SER A 339 " --> pdb=" O ASP A 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 52 No H-bonds generated for 'chain 'B' and resid 50 through 52' Processing helix chain 'B' and resid 90 through 105 removed outlier: 4.447A pdb=" N ARG B 95 " --> pdb=" O GLN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 146 removed outlier: 3.659A pdb=" N ASP B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS B 146 " --> pdb=" O GLN B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 172 removed outlier: 3.745A pdb=" N LYS B 164 " --> pdb=" O VAL B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 222 through 225 No H-bonds generated for 'chain 'B' and resid 222 through 225' Processing helix chain 'B' and resid 236 through 252 Processing helix chain 'B' and resid 263 through 272 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 312 through 319 removed outlier: 3.914A pdb=" N SER B 319 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 332 Processing sheet with id= A, first strand: chain 'A' and resid 9 through 13 removed outlier: 3.544A pdb=" N LEU A 13 " --> pdb=" O THR A 16 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 51 through 53 Processing sheet with id= C, first strand: chain 'B' and resid 39 through 41 removed outlier: 3.684A pdb=" N ILE B 41 " --> pdb=" O GLN B 44 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN B 44 " --> pdb=" O ILE B 41 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 78 through 80 removed outlier: 5.899A pdb=" N ARG B 71 " --> pdb=" O PRO B 55 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 185 through 187 147 hydrogen bonds defined for protein. 423 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.19 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1709 1.35 - 1.48: 1265 1.48 - 1.61: 2331 1.61 - 1.74: 2 1.74 - 1.87: 53 Bond restraints: 5360 Sorted by residual: bond pdb=" CA VAL A 89 " pdb=" CB VAL A 89 " ideal model delta sigma weight residual 1.553 1.539 0.014 7.40e-03 1.83e+04 3.55e+00 bond pdb=" CA LEU A 74 " pdb=" C LEU A 74 " ideal model delta sigma weight residual 1.524 1.505 0.018 1.27e-02 6.20e+03 2.06e+00 bond pdb=" N HIS A 312 " pdb=" CA HIS A 312 " ideal model delta sigma weight residual 1.456 1.474 -0.018 1.44e-02 4.82e+03 1.49e+00 bond pdb=" CB LYS B 329 " pdb=" CG LYS B 329 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.34e+00 bond pdb=" N VAL A 83 " pdb=" CA VAL A 83 " ideal model delta sigma weight residual 1.459 1.445 0.014 1.25e-02 6.40e+03 1.32e+00 ... (remaining 5355 not shown) Histogram of bond angle deviations from ideal: 98.40 - 105.55: 154 105.55 - 112.70: 2797 112.70 - 119.85: 1835 119.85 - 126.99: 2408 126.99 - 134.14: 78 Bond angle restraints: 7272 Sorted by residual: angle pdb=" N LEU A 74 " pdb=" CA LEU A 74 " pdb=" C LEU A 74 " ideal model delta sigma weight residual 111.07 105.64 5.43 1.07e+00 8.73e-01 2.57e+01 angle pdb=" CA LYS B 329 " pdb=" CB LYS B 329 " pdb=" CG LYS B 329 " ideal model delta sigma weight residual 114.10 122.34 -8.24 2.00e+00 2.50e-01 1.70e+01 angle pdb=" N SER B 275 " pdb=" CA SER B 275 " pdb=" C SER B 275 " ideal model delta sigma weight residual 109.81 118.62 -8.81 2.21e+00 2.05e-01 1.59e+01 angle pdb=" CA GLU B 68 " pdb=" CB GLU B 68 " pdb=" CG GLU B 68 " ideal model delta sigma weight residual 114.10 121.53 -7.43 2.00e+00 2.50e-01 1.38e+01 angle pdb=" C ILE A 235 " pdb=" N LEU A 236 " pdb=" CA LEU A 236 " ideal model delta sigma weight residual 120.28 125.16 -4.88 1.34e+00 5.57e-01 1.33e+01 ... (remaining 7267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 2740 17.80 - 35.61: 394 35.61 - 53.41: 100 53.41 - 71.21: 29 71.21 - 89.02: 13 Dihedral angle restraints: 3276 sinusoidal: 1381 harmonic: 1895 Sorted by residual: dihedral pdb=" CA LEU A 108 " pdb=" C LEU A 108 " pdb=" N MET A 109 " pdb=" CA MET A 109 " ideal model delta harmonic sigma weight residual -180.00 -155.02 -24.98 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA LEU A 234 " pdb=" C LEU A 234 " pdb=" N ILE A 235 " pdb=" CA ILE A 235 " ideal model delta harmonic sigma weight residual 180.00 156.46 23.54 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA LEU B 131 " pdb=" C LEU B 131 " pdb=" N MET B 132 " pdb=" CA MET B 132 " ideal model delta harmonic sigma weight residual 180.00 157.05 22.95 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 3273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 565 0.043 - 0.087: 186 0.087 - 0.130: 49 0.130 - 0.173: 10 0.173 - 0.217: 4 Chirality restraints: 814 Sorted by residual: chirality pdb=" CA LEU B 267 " pdb=" N LEU B 267 " pdb=" C LEU B 267 " pdb=" CB LEU B 267 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB ILE B 84 " pdb=" CA ILE B 84 " pdb=" CG1 ILE B 84 " pdb=" CG2 ILE B 84 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.55e-01 chirality pdb=" CA TYR B 305 " pdb=" N TYR B 305 " pdb=" C TYR B 305 " pdb=" CB TYR B 305 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.93e-01 ... (remaining 811 not shown) Planarity restraints: 920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 68 " 0.012 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" CD GLU B 68 " -0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU B 68 " 0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU B 68 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 152 " -0.033 5.00e-02 4.00e+02 4.97e-02 3.94e+00 pdb=" N PRO A 153 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 153 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 153 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 150 " 0.028 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO B 151 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 151 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 151 " 0.024 5.00e-02 4.00e+02 ... (remaining 917 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 737 2.75 - 3.29: 5816 3.29 - 3.83: 9246 3.83 - 4.36: 10936 4.36 - 4.90: 16821 Nonbonded interactions: 43556 Sorted by model distance: nonbonded pdb=" O SER B 235 " pdb=" OG SER B 238 " model vdw 2.218 2.440 nonbonded pdb=" OH TYR B 140 " pdb=" OE1 GLU B 249 " model vdw 2.230 2.440 nonbonded pdb=" OE2 GLU A 215 " pdb=" OG1 THR A 221 " model vdw 2.233 2.440 nonbonded pdb=" O ASP A 205 " pdb=" OG SER A 208 " model vdw 2.240 2.440 nonbonded pdb=" NH2 ARG B 178 " pdb=" O TYR B 203 " model vdw 2.243 2.520 ... (remaining 43551 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=0.78 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: 2.870 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: 12.790 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 19.330 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5469 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 : 0.004 0.037 5360 Z= 0.233 Angle : 0.888 9.558 7272 Z= 0.471 Chirality : 0.048 0.217 814 Planarity : 0.005 0.050 920 Dihedral : 18.817 89.016 2048 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 29.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.45 % Favored : 91.39 % Rotamer: Outliers : 1.56 % Allowed : 26.39 % Favored : 72.05 % 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: -2.63 (0.31), residues: 639 helix: -0.84 (0.34), residues: 219 sheet: -2.27 (0.64), residues: 53 loop : -2.31 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 18 HIS 0.013 0.002 HIS A 312 PHE 0.013 0.002 PHE B 313 TYR 0.012 0.001 TYR B 140 ARG 0.005 0.001 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 MET cc_start: -0.1395 (ttm) cc_final: -0.3126 (tmm) REVERT: B 79 MET cc_start: 0.3563 (tmm) cc_final: 0.3054 (tpp) REVERT: B 141 LYS cc_start: 0.9204 (tptt) cc_final: 0.8769 (tptp) REVERT: B 184 ASN cc_start: 0.7238 (OUTLIER) cc_final: 0.7021 (p0) REVERT: B 220 MET cc_start: 0.5295 (mmm) cc_final: 0.4956 (tmm) outliers start: 9 outliers final: 3 residues processed: 91 average time/residue: 0.1647 time to fit residues: 19.6942 Evaluate side-chains 73 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 184 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 0.0270 chunk 47 optimal weight: 0.2980 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 0.0670 chunk 25 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 HIS ** A 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 45 ASN B 77 GLN B 170 HIS B 177 HIS B 184 ASN B 226 ASN B 265 GLN ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN B 293 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5469 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5360 Z= 0.202 Angle : 0.771 9.398 7272 Z= 0.382 Chirality : 0.049 0.215 814 Planarity : 0.005 0.050 920 Dihedral : 9.855 83.071 762 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 25.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 3.30 % Allowed : 25.69 % Favored : 71.01 % 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: -2.41 (0.31), residues: 639 helix: -0.58 (0.34), residues: 220 sheet: -2.30 (0.70), residues: 46 loop : -2.23 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 187 HIS 0.008 0.002 HIS B 317 PHE 0.012 0.001 PHE B 264 TYR 0.010 0.001 TYR A 24 ARG 0.004 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 72 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: A 179 MET cc_start: 0.1021 (tpt) cc_final: 0.0815 (tpt) REVERT: A 265 MET cc_start: -0.1277 (ttm) cc_final: -0.3263 (tmm) REVERT: B 70 MET cc_start: 0.1631 (ttt) cc_final: 0.0824 (ttt) REVERT: B 125 VAL cc_start: 0.1780 (OUTLIER) cc_final: 0.1551 (m) REVERT: B 129 MET cc_start: 0.7695 (mmm) cc_final: 0.7105 (mmm) REVERT: B 141 LYS cc_start: 0.9229 (tptt) cc_final: 0.8766 (tptp) REVERT: B 184 ASN cc_start: 0.7324 (OUTLIER) cc_final: 0.6903 (p0) outliers start: 19 outliers final: 7 residues processed: 86 average time/residue: 0.1485 time to fit residues: 17.3089 Evaluate side-chains 75 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 275 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 HIS ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN B 317 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5538 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5360 Z= 0.194 Angle : 0.736 9.132 7272 Z= 0.366 Chirality : 0.046 0.188 814 Planarity : 0.004 0.049 920 Dihedral : 7.908 74.742 757 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 27.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 3.65 % Allowed : 27.43 % Favored : 68.92 % 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: -2.36 (0.31), residues: 639 helix: -0.53 (0.34), residues: 225 sheet: -2.47 (0.66), residues: 46 loop : -2.20 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 197 HIS 0.005 0.001 HIS A 126 PHE 0.020 0.001 PHE B 255 TYR 0.012 0.001 TYR B 140 ARG 0.003 0.000 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 71 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.1235 (tpt) cc_final: 0.1012 (tpt) REVERT: A 265 MET cc_start: -0.1151 (ttm) cc_final: -0.3270 (tmm) REVERT: B 70 MET cc_start: 0.1671 (ttt) cc_final: 0.0841 (ttt) REVERT: B 129 MET cc_start: 0.7954 (mmm) cc_final: 0.7324 (mmm) REVERT: B 141 LYS cc_start: 0.9249 (tptt) cc_final: 0.8773 (tptp) REVERT: B 255 PHE cc_start: 0.6982 (OUTLIER) cc_final: 0.6760 (p90) outliers start: 21 outliers final: 11 residues processed: 85 average time/residue: 0.1494 time to fit residues: 17.2618 Evaluate side-chains 79 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 310 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 6.9990 chunk 43 optimal weight: 20.0000 chunk 29 optimal weight: 0.0050 chunk 6 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 60 optimal weight: 0.4980 chunk 30 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 overall best weight: 1.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5673 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5360 Z= 0.233 Angle : 0.747 8.879 7272 Z= 0.372 Chirality : 0.046 0.221 814 Planarity : 0.005 0.047 920 Dihedral : 7.178 69.340 755 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 31.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 4.86 % Allowed : 25.69 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.32), residues: 639 helix: -0.55 (0.34), residues: 227 sheet: -2.29 (0.61), residues: 62 loop : -2.13 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 18 HIS 0.015 0.002 HIS B 317 PHE 0.011 0.002 PHE B 264 TYR 0.011 0.001 TYR A 132 ARG 0.004 0.000 ARG A 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 70 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.1292 (tpt) cc_final: 0.0754 (tpt) REVERT: B 70 MET cc_start: 0.1975 (ttt) cc_final: 0.0934 (ttt) REVERT: B 129 MET cc_start: 0.8293 (mmm) cc_final: 0.7626 (mmm) REVERT: B 141 LYS cc_start: 0.9284 (tptt) cc_final: 0.8809 (tptp) REVERT: B 255 PHE cc_start: 0.7116 (p90) cc_final: 0.6850 (p90) REVERT: B 309 MET cc_start: 0.8538 (ptp) cc_final: 0.8129 (ptp) outliers start: 28 outliers final: 15 residues processed: 91 average time/residue: 0.1607 time to fit residues: 19.5286 Evaluate side-chains 83 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 275 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5714 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5360 Z= 0.227 Angle : 0.745 8.701 7272 Z= 0.371 Chirality : 0.045 0.224 814 Planarity : 0.005 0.050 920 Dihedral : 7.145 70.094 755 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 32.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 5.03 % Allowed : 26.39 % Favored : 68.58 % 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: -2.27 (0.32), residues: 639 helix: -0.57 (0.33), residues: 230 sheet: -2.45 (0.60), residues: 61 loop : -2.01 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 187 HIS 0.008 0.002 HIS B 311 PHE 0.012 0.001 PHE B 255 TYR 0.017 0.001 TYR B 140 ARG 0.004 0.000 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 68 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.1461 (tpt) cc_final: 0.0871 (tpt) REVERT: A 186 ARG cc_start: 0.8002 (ttp-110) cc_final: 0.7793 (ttp-110) REVERT: A 193 ILE cc_start: 0.6849 (OUTLIER) cc_final: 0.6514 (mt) REVERT: B 129 MET cc_start: 0.8357 (mmm) cc_final: 0.7702 (mmm) REVERT: B 141 LYS cc_start: 0.9316 (tptt) cc_final: 0.8815 (tptp) REVERT: B 157 LYS cc_start: 0.9163 (mmtt) cc_final: 0.8919 (mmtt) REVERT: B 240 ILE cc_start: 0.9313 (mt) cc_final: 0.9056 (pt) REVERT: B 255 PHE cc_start: 0.7184 (p90) cc_final: 0.6920 (p90) outliers start: 29 outliers final: 20 residues processed: 91 average time/residue: 0.1656 time to fit residues: 19.8779 Evaluate side-chains 86 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 65 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 324 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 20.0000 chunk 58 optimal weight: 0.5980 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 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5633 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5360 Z= 0.193 Angle : 0.762 8.619 7272 Z= 0.367 Chirality : 0.045 0.223 814 Planarity : 0.004 0.051 920 Dihedral : 7.025 68.751 755 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 28.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 3.99 % Allowed : 28.12 % Favored : 67.88 % 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: -2.17 (0.32), residues: 639 helix: -0.42 (0.34), residues: 229 sheet: -2.31 (0.60), residues: 61 loop : -2.02 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 18 HIS 0.011 0.001 HIS B 317 PHE 0.011 0.001 PHE B 255 TYR 0.010 0.001 TYR A 132 ARG 0.003 0.000 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 67 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: A 179 MET cc_start: 0.1337 (tpt) cc_final: 0.0973 (tpt) REVERT: A 193 ILE cc_start: 0.6724 (OUTLIER) cc_final: 0.6387 (mt) REVERT: A 265 MET cc_start: -0.0563 (ttm) cc_final: -0.3096 (tmm) REVERT: B 70 MET cc_start: 0.1810 (ttt) cc_final: 0.0937 (ttt) REVERT: B 129 MET cc_start: 0.8348 (mmm) cc_final: 0.7726 (mmm) REVERT: B 140 TYR cc_start: 0.7652 (t80) cc_final: 0.7387 (t80) REVERT: B 141 LYS cc_start: 0.9284 (tptt) cc_final: 0.8761 (tptp) REVERT: B 157 LYS cc_start: 0.9119 (mmtt) cc_final: 0.8872 (mmtt) REVERT: B 240 ILE cc_start: 0.9262 (mt) cc_final: 0.9026 (pt) REVERT: B 255 PHE cc_start: 0.7125 (OUTLIER) cc_final: 0.6858 (p90) outliers start: 23 outliers final: 16 residues processed: 85 average time/residue: 0.1683 time to fit residues: 19.0400 Evaluate side-chains 82 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 64 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 324 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6055 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 5360 Z= 0.455 Angle : 0.967 9.833 7272 Z= 0.490 Chirality : 0.053 0.334 814 Planarity : 0.006 0.064 920 Dihedral : 8.144 72.881 755 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 55.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.23 % Favored : 90.61 % Rotamer: Outliers : 7.47 % Allowed : 25.69 % Favored : 66.84 % 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: -2.84 (0.31), residues: 639 helix: -1.29 (0.33), residues: 216 sheet: -2.93 (0.63), residues: 49 loop : -2.16 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 207 HIS 0.012 0.003 HIS B 317 PHE 0.019 0.003 PHE B 314 TYR 0.018 0.002 TYR A 311 ARG 0.007 0.001 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 67 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.1902 (OUTLIER) cc_final: 0.1296 (mmm160) REVERT: A 179 MET cc_start: 0.2107 (tpt) cc_final: 0.1688 (tpt) REVERT: A 265 MET cc_start: 0.0134 (ttm) cc_final: -0.1984 (tmm) REVERT: B 58 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8781 (tm-30) REVERT: B 129 MET cc_start: 0.8722 (mmm) cc_final: 0.7732 (mmm) REVERT: B 141 LYS cc_start: 0.9398 (tptt) cc_final: 0.8897 (tptp) REVERT: B 155 LEU cc_start: 0.8268 (mt) cc_final: 0.7994 (mt) REVERT: B 157 LYS cc_start: 0.9175 (mmtt) cc_final: 0.8974 (mmtt) REVERT: B 257 TYR cc_start: 0.7394 (OUTLIER) cc_final: 0.5727 (m-80) outliers start: 43 outliers final: 25 residues processed: 99 average time/residue: 0.2111 time to fit residues: 26.9072 Evaluate side-chains 92 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 64 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 257 TYR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 324 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 0.0970 chunk 53 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 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 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5776 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5360 Z= 0.226 Angle : 0.875 17.499 7272 Z= 0.411 Chirality : 0.052 0.523 814 Planarity : 0.005 0.052 920 Dihedral : 7.620 71.441 755 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 31.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.14 % Favored : 91.71 % Rotamer: Outliers : 3.99 % Allowed : 28.30 % Favored : 67.71 % 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: -2.66 (0.31), residues: 639 helix: -1.03 (0.33), residues: 224 sheet: -2.93 (0.65), residues: 49 loop : -2.13 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 126 HIS 0.010 0.002 HIS B 317 PHE 0.012 0.002 PHE B 255 TYR 0.013 0.001 TYR B 234 ARG 0.003 0.001 ARG A 136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 67 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 MET cc_start: -0.0110 (ttm) cc_final: -0.2221 (tmm) REVERT: B 57 MET cc_start: 0.8086 (ppp) cc_final: 0.7220 (ppp) REVERT: B 129 MET cc_start: 0.8456 (mmm) cc_final: 0.7820 (mmm) REVERT: B 141 LYS cc_start: 0.9354 (tptt) cc_final: 0.8814 (tptp) REVERT: B 157 LYS cc_start: 0.9059 (mmtt) cc_final: 0.8804 (mmtt) REVERT: B 220 MET cc_start: 0.5513 (mmm) cc_final: 0.5042 (tmm) REVERT: B 240 ILE cc_start: 0.9343 (mt) cc_final: 0.9117 (pt) REVERT: B 257 TYR cc_start: 0.7156 (OUTLIER) cc_final: 0.5807 (m-80) REVERT: B 331 ILE cc_start: 0.7823 (tp) cc_final: 0.7617 (tp) outliers start: 23 outliers final: 20 residues processed: 84 average time/residue: 0.1599 time to fit residues: 17.7591 Evaluate side-chains 87 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 66 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 257 TYR Chi-restraints excluded: chain B residue 270 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 0.0060 chunk 44 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 53 optimal weight: 0.0870 chunk 56 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 36 optimal weight: 0.0070 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5703 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5360 Z= 0.203 Angle : 0.822 10.296 7272 Z= 0.395 Chirality : 0.047 0.235 814 Planarity : 0.004 0.050 920 Dihedral : 7.322 68.222 755 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 28.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 3.82 % Allowed : 28.82 % Favored : 67.36 % 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: -2.50 (0.32), residues: 639 helix: -0.84 (0.34), residues: 220 sheet: -2.76 (0.68), residues: 39 loop : -2.12 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 126 HIS 0.007 0.001 HIS B 317 PHE 0.013 0.001 PHE B 264 TYR 0.039 0.002 TYR B 305 ARG 0.003 0.000 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 67 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.1604 (ttt) cc_final: 0.1148 (tpt) REVERT: A 265 MET cc_start: -0.0099 (ttm) cc_final: -0.2246 (tmm) REVERT: B 70 MET cc_start: 0.1673 (ttt) cc_final: 0.0957 (ttt) REVERT: B 129 MET cc_start: 0.8558 (mmm) cc_final: 0.7900 (mmm) REVERT: B 141 LYS cc_start: 0.9339 (tptt) cc_final: 0.8793 (tptp) REVERT: B 157 LYS cc_start: 0.9074 (mmtt) cc_final: 0.8800 (mmtt) REVERT: B 220 MET cc_start: 0.5380 (mmm) cc_final: 0.4954 (tmm) REVERT: B 240 ILE cc_start: 0.9325 (mt) cc_final: 0.9082 (pt) REVERT: B 257 TYR cc_start: 0.6985 (OUTLIER) cc_final: 0.5553 (m-80) outliers start: 22 outliers final: 16 residues processed: 82 average time/residue: 0.1814 time to fit residues: 19.2427 Evaluate side-chains 81 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 64 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 257 TYR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 324 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 30 optimal weight: 0.0870 chunk 39 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 overall best weight: 1.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5809 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5360 Z= 0.242 Angle : 0.814 10.578 7272 Z= 0.393 Chirality : 0.047 0.243 814 Planarity : 0.005 0.060 920 Dihedral : 7.377 68.492 755 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 35.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.14 % Favored : 91.71 % Rotamer: Outliers : 3.30 % Allowed : 28.99 % Favored : 67.71 % 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: -2.55 (0.32), residues: 639 helix: -0.89 (0.33), residues: 228 sheet: -3.01 (0.61), residues: 51 loop : -2.07 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 126 HIS 0.007 0.002 HIS B 317 PHE 0.013 0.001 PHE B 255 TYR 0.043 0.002 TYR B 305 ARG 0.008 0.001 ARG B 85 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 65 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.2218 (OUTLIER) cc_final: 0.1633 (tp) REVERT: A 109 MET cc_start: 0.1949 (ttt) cc_final: 0.1447 (ttt) REVERT: A 265 MET cc_start: -0.0057 (ttm) cc_final: -0.2085 (tmm) REVERT: B 57 MET cc_start: 0.8074 (ppp) cc_final: 0.7160 (ppp) REVERT: B 129 MET cc_start: 0.8672 (mmm) cc_final: 0.7907 (mmm) REVERT: B 141 LYS cc_start: 0.9356 (tptt) cc_final: 0.8800 (tptp) REVERT: B 157 LYS cc_start: 0.9096 (mmtt) cc_final: 0.8847 (mmtt) REVERT: B 220 MET cc_start: 0.5556 (mmm) cc_final: 0.5071 (tmm) REVERT: B 240 ILE cc_start: 0.9361 (mt) cc_final: 0.9132 (pt) REVERT: B 257 TYR cc_start: 0.7024 (OUTLIER) cc_final: 0.5650 (m-80) outliers start: 19 outliers final: 17 residues processed: 80 average time/residue: 0.1741 time to fit residues: 18.3760 Evaluate side-chains 84 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 65 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 257 TYR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 324 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.144996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.120464 restraints weight = 34961.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.122811 restraints weight = 25534.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.124313 restraints weight = 20403.206| |-----------------------------------------------------------------------------| r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4046 r_free = 0.4046 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5360 Z= 0.233 Angle : 0.833 11.477 7272 Z= 0.397 Chirality : 0.047 0.248 814 Planarity : 0.005 0.045 920 Dihedral : 7.411 69.154 755 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 34.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.76 % Favored : 91.08 % Rotamer: Outliers : 3.82 % Allowed : 28.47 % Favored : 67.71 % 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: -2.53 (0.32), residues: 639 helix: -0.89 (0.34), residues: 227 sheet: -3.00 (0.61), residues: 51 loop : -2.04 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 126 HIS 0.009 0.002 HIS B 317 PHE 0.013 0.001 PHE B 255 TYR 0.047 0.002 TYR B 305 ARG 0.010 0.001 ARG B 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1554.62 seconds wall clock time: 28 minutes 50.14 seconds (1730.14 seconds total)