Starting phenix.real_space_refine on Wed Mar 4 02:56:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tyi_56420/03_2026/9tyi_56420.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tyi_56420/03_2026/9tyi_56420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9tyi_56420/03_2026/9tyi_56420.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tyi_56420/03_2026/9tyi_56420.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9tyi_56420/03_2026/9tyi_56420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tyi_56420/03_2026/9tyi_56420.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.014 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: 5 Type Number sf(0) Gaussians S 29 5.16 5 C 3193 2.51 5 N 851 2.21 5 O 898 1.98 5 H 5024 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9995 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 5729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 5729 Classifications: {'peptide': 350} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 330} Chain: "A" Number of atoms: 4266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 4266 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 17, 'TRANS': 249} Chain breaks: 3 Time building chain proxies: 1.93, per 1000 atoms: 0.19 Number of scatterers: 9995 At special positions: 0 Unit cell: (62.56, 77.28, 98.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 O 898 8.00 N 851 7.00 C 3193 6.00 H 5024 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 152.8 milliseconds 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1166 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 6 sheets defined 47.3% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'B' and resid 63 through 77 removed outlier: 3.522A pdb=" N LEU B 76 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG B 77 " --> pdb=" O LYS B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 98 Processing helix chain 'B' and resid 112 through 119 Processing helix chain 'B' and resid 122 through 143 Processing helix chain 'B' and resid 151 through 153 No H-bonds generated for 'chain 'B' and resid 151 through 153' Processing helix chain 'B' and resid 196 through 201 Processing helix chain 'B' and resid 207 through 224 removed outlier: 3.687A pdb=" N ILE B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 244 Processing helix chain 'B' and resid 248 through 254 removed outlier: 3.536A pdb=" N LEU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 267 Processing helix chain 'B' and resid 274 through 279 Processing helix chain 'B' and resid 283 through 294 removed outlier: 4.154A pdb=" N LYS B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 309 removed outlier: 3.772A pdb=" N ALA B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 314 Processing helix chain 'B' and resid 318 through 322 Processing helix chain 'B' and resid 339 through 351 Processing helix chain 'B' and resid 352 through 355 Processing helix chain 'A' and resid 4 through 8 Processing helix chain 'A' and resid 112 through 127 removed outlier: 4.083A pdb=" N GLN A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 165 removed outlier: 3.871A pdb=" N LYS A 163 " --> pdb=" O GLN A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 190 removed outlier: 3.674A pdb=" N LYS A 181 " --> pdb=" O ILE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 237 through 242 Processing helix chain 'A' and resid 248 through 265 removed outlier: 3.597A pdb=" N ILE A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 326 removed outlier: 3.962A pdb=" N LEU A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 364 through 373 Processing helix chain 'A' and resid 376 through 386 Processing sheet with id=AA1, first strand: chain 'B' and resid 12 through 14 removed outlier: 3.519A pdb=" N GLN B 17 " --> pdb=" O VAL B 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 25 through 34 removed outlier: 7.183A pdb=" N LEU B 28 " --> pdb=" O TYR B 43 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N TYR B 43 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N TYR B 30 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N SER B 41 " --> pdb=" O TYR B 30 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET B 38 " --> pdb=" O LYS B 55 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP B 88 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 110 through 111 Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 146 Processing sheet with id=AA5, first strand: chain 'A' and resid 87 through 92 removed outlier: 6.528A pdb=" N GLU A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TYR A 140 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N SER A 146 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ALA A 138 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N CYS A 148 " --> pdb=" O TYR A 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 204 210 hydrogen bonds defined for protein. 582 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: 1.65 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5012 1.03 - 1.23: 14 1.23 - 1.42: 2093 1.42 - 1.61: 2944 1.61 - 1.81: 46 Bond restraints: 10109 Sorted by residual: bond pdb=" N PRO A 168 " pdb=" CA PRO A 168 " ideal model delta sigma weight residual 1.469 1.487 -0.018 1.28e-02 6.10e+03 1.98e+00 bond pdb=" CG GLU B 197 " pdb=" CD GLU B 197 " ideal model delta sigma weight residual 1.516 1.548 -0.032 2.50e-02 1.60e+03 1.63e+00 bond pdb=" CB GLU B 197 " pdb=" CG GLU B 197 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.50e+00 bond pdb=" CA ASP A 196 " pdb=" CB ASP A 196 " ideal model delta sigma weight residual 1.528 1.545 -0.017 1.47e-02 4.63e+03 1.31e+00 bond pdb=" CB GLN B 97 " pdb=" CG GLN B 97 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.86e-01 ... (remaining 10104 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 17296 1.26 - 2.53: 943 2.53 - 3.79: 82 3.79 - 5.05: 12 5.05 - 6.31: 8 Bond angle restraints: 18341 Sorted by residual: angle pdb=" N VAL A 363 " pdb=" CA VAL A 363 " pdb=" C VAL A 363 " ideal model delta sigma weight residual 112.43 109.09 3.34 9.20e-01 1.18e+00 1.32e+01 angle pdb=" CA GLU B 197 " pdb=" CB GLU B 197 " pdb=" CG GLU B 197 " ideal model delta sigma weight residual 114.10 120.41 -6.31 2.00e+00 2.50e-01 9.96e+00 angle pdb=" C HIS A 93 " pdb=" N LYS A 94 " pdb=" CA LYS A 94 " ideal model delta sigma weight residual 120.09 124.03 -3.94 1.25e+00 6.40e-01 9.94e+00 angle pdb=" CA ARG A 195 " pdb=" CB ARG A 195 " pdb=" CG ARG A 195 " ideal model delta sigma weight residual 114.10 120.22 -6.12 2.00e+00 2.50e-01 9.35e+00 angle pdb=" C LEU A 361 " pdb=" N MET A 362 " pdb=" CA MET A 362 " ideal model delta sigma weight residual 122.31 116.47 5.84 2.00e+00 2.50e-01 8.52e+00 ... (remaining 18336 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 4188 17.62 - 35.24: 413 35.24 - 52.87: 102 52.87 - 70.49: 32 70.49 - 88.11: 11 Dihedral angle restraints: 4746 sinusoidal: 2620 harmonic: 2126 Sorted by residual: dihedral pdb=" CA ILE A 167 " pdb=" C ILE A 167 " pdb=" N PRO A 168 " pdb=" CA PRO A 168 " ideal model delta harmonic sigma weight residual 180.00 -158.63 -21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA HIS A 245 " pdb=" C HIS A 245 " pdb=" N TYR A 246 " pdb=" CA TYR A 246 " ideal model delta harmonic sigma weight residual -180.00 -159.48 -20.52 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA THR B 190 " pdb=" C THR B 190 " pdb=" N ARG B 191 " pdb=" CA ARG B 191 " ideal model delta harmonic sigma weight residual 180.00 -160.98 -19.02 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 4743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 439 0.028 - 0.056: 200 0.056 - 0.083: 64 0.083 - 0.111: 42 0.111 - 0.139: 15 Chirality restraints: 760 Sorted by residual: chirality pdb=" CA ASP A 196 " pdb=" N ASP A 196 " pdb=" C ASP A 196 " pdb=" CB ASP A 196 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA ILE A 210 " pdb=" N ILE A 210 " pdb=" C ILE A 210 " pdb=" CB ILE A 210 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CA VAL B 273 " pdb=" N VAL B 273 " pdb=" C VAL B 273 " pdb=" CB VAL B 273 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.09e-01 ... (remaining 757 not shown) Planarity restraints: 1457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 63 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.56e+00 pdb=" C THR B 63 " -0.033 2.00e-02 2.50e+03 pdb=" O THR B 63 " 0.012 2.00e-02 2.50e+03 pdb=" N TYR B 64 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 22 " 0.025 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO B 23 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 23 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 23 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 196 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.93e+00 pdb=" N GLU B 197 " -0.024 2.00e-02 2.50e+03 pdb=" CA GLU B 197 " 0.006 2.00e-02 2.50e+03 pdb=" H GLU B 197 " 0.011 2.00e-02 2.50e+03 ... (remaining 1454 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.34: 3447 2.34 - 2.91: 23222 2.91 - 3.47: 26900 3.47 - 4.04: 35535 4.04 - 4.60: 52644 Nonbonded interactions: 141748 Sorted by model distance: nonbonded pdb=" HD1 HIS A 364 " pdb=" H PHE A 366 " model vdw 1.777 2.100 nonbonded pdb=" HG SER A 237 " pdb=" HG SER A 250 " model vdw 1.872 2.100 nonbonded pdb=" HG1 THR A 232 " pdb=" HD1 TYR A 235 " model vdw 1.877 2.100 nonbonded pdb=" HD1 PHE A 336 " pdb=" H SER A 337 " model vdw 1.879 2.100 nonbonded pdb=" H ASN A 201 " pdb="HD21 ASN A 201 " model vdw 1.896 2.100 ... (remaining 141743 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 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: 0.030 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.960 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5085 Z= 0.133 Angle : 0.666 6.313 6877 Z= 0.367 Chirality : 0.042 0.139 760 Planarity : 0.004 0.037 880 Dihedral : 15.351 80.327 1935 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.08 % Allowed : 23.51 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.35), residues: 607 helix: 0.22 (0.36), residues: 237 sheet: -1.16 (0.68), residues: 50 loop : -0.70 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 195 TYR 0.014 0.001 TYR B 113 PHE 0.012 0.001 PHE A 215 TRP 0.014 0.001 TRP A 380 HIS 0.004 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 5085) covalent geometry : angle 0.66593 ( 6877) hydrogen bonds : bond 0.17486 ( 210) hydrogen bonds : angle 8.33970 ( 582) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8109 (tmm) REVERT: B 99 LYS cc_start: 0.9443 (mttt) cc_final: 0.9062 (tptt) REVERT: B 102 TYR cc_start: 0.9168 (m-80) cc_final: 0.8866 (m-80) REVERT: B 123 ASN cc_start: 0.9522 (p0) cc_final: 0.9130 (t0) REVERT: B 149 ASP cc_start: 0.8540 (t0) cc_final: 0.8105 (t0) REVERT: B 221 MET cc_start: 0.9627 (mtp) cc_final: 0.9347 (mtp) REVERT: B 330 LYS cc_start: 0.9449 (pttt) cc_final: 0.9015 (tptp) REVERT: A 151 HIS cc_start: 0.7749 (t70) cc_final: 0.7172 (p-80) REVERT: A 242 GLN cc_start: 0.9059 (mt0) cc_final: 0.8858 (mp10) REVERT: A 262 MET cc_start: 0.9203 (ttm) cc_final: 0.8715 (ptp) REVERT: A 314 MET cc_start: -0.0280 (tpt) cc_final: -0.2335 (ppp) REVERT: A 322 TYR cc_start: 0.9090 (t80) cc_final: 0.8769 (t80) outliers start: 6 outliers final: 5 residues processed: 128 average time/residue: 0.2158 time to fit residues: 33.3913 Evaluate side-chains 126 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 343 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 0.0170 chunk 25 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 overall best weight: 2.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.104837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.075788 restraints weight = 45054.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.080729 restraints weight = 23494.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.084153 restraints weight = 14659.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.086563 restraints weight = 10302.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.088200 restraints weight = 7896.941| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5085 Z= 0.238 Angle : 0.646 4.947 6877 Z= 0.355 Chirality : 0.043 0.133 760 Planarity : 0.005 0.062 880 Dihedral : 6.190 51.466 687 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.99 % Allowed : 23.33 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.33), residues: 607 helix: -0.02 (0.34), residues: 238 sheet: -1.26 (0.58), residues: 60 loop : -0.90 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 77 TYR 0.011 0.001 TYR B 233 PHE 0.013 0.001 PHE B 329 TRP 0.007 0.001 TRP A 380 HIS 0.005 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 5085) covalent geometry : angle 0.64632 ( 6877) hydrogen bonds : bond 0.04349 ( 210) hydrogen bonds : angle 7.14227 ( 582) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 TYR cc_start: 0.9219 (m-80) cc_final: 0.8901 (m-80) REVERT: B 149 ASP cc_start: 0.8473 (t0) cc_final: 0.8047 (t0) REVERT: B 330 LYS cc_start: 0.9420 (pttt) cc_final: 0.8988 (tptp) REVERT: A 151 HIS cc_start: 0.7776 (t70) cc_final: 0.7282 (p-80) REVERT: A 190 HIS cc_start: 0.7563 (m90) cc_final: 0.7188 (m90) REVERT: A 242 GLN cc_start: 0.9228 (mt0) cc_final: 0.8889 (mp10) REVERT: A 262 MET cc_start: 0.9194 (ttm) cc_final: 0.8722 (ptp) REVERT: A 314 MET cc_start: -0.0045 (tpt) cc_final: -0.2279 (ppp) REVERT: A 322 TYR cc_start: 0.9161 (t80) cc_final: 0.8881 (t80) outliers start: 11 outliers final: 8 residues processed: 126 average time/residue: 0.1837 time to fit residues: 28.3357 Evaluate side-chains 119 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 321 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 0.2980 chunk 19 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 42 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.107108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.076928 restraints weight = 44636.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.082163 restraints weight = 23310.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.085806 restraints weight = 14518.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.088313 restraints weight = 10183.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.089990 restraints weight = 7825.440| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5085 Z= 0.124 Angle : 0.593 5.860 6877 Z= 0.310 Chirality : 0.043 0.134 760 Planarity : 0.005 0.059 880 Dihedral : 5.344 31.792 678 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.17 % Allowed : 22.60 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.34), residues: 607 helix: 0.31 (0.35), residues: 235 sheet: -1.19 (0.60), residues: 60 loop : -0.87 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 91 TYR 0.011 0.001 TYR B 233 PHE 0.013 0.001 PHE A 317 TRP 0.010 0.001 TRP A 380 HIS 0.004 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 5085) covalent geometry : angle 0.59327 ( 6877) hydrogen bonds : bond 0.03789 ( 210) hydrogen bonds : angle 6.50655 ( 582) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 MET cc_start: 0.5502 (tpt) cc_final: 0.4942 (tpp) REVERT: B 102 TYR cc_start: 0.9213 (m-80) cc_final: 0.8836 (m-80) REVERT: B 123 ASN cc_start: 0.9433 (p0) cc_final: 0.9093 (t0) REVERT: B 149 ASP cc_start: 0.8383 (t0) cc_final: 0.7896 (t0) REVERT: B 221 MET cc_start: 0.9657 (mtp) cc_final: 0.9361 (mtp) REVERT: B 267 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7815 (mp) REVERT: B 330 LYS cc_start: 0.9419 (pttt) cc_final: 0.8971 (tptp) REVERT: A 242 GLN cc_start: 0.9143 (mt0) cc_final: 0.8878 (mp10) REVERT: A 262 MET cc_start: 0.9177 (ttm) cc_final: 0.8697 (ptp) REVERT: A 314 MET cc_start: -0.0150 (tpt) cc_final: -0.2309 (ppp) REVERT: A 322 TYR cc_start: 0.9128 (t80) cc_final: 0.8879 (t80) outliers start: 12 outliers final: 10 residues processed: 127 average time/residue: 0.1955 time to fit residues: 30.8070 Evaluate side-chains 125 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 340 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 56 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.106235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.076916 restraints weight = 44477.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.081990 restraints weight = 22829.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.085505 restraints weight = 14091.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.087957 restraints weight = 9842.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.089601 restraints weight = 7510.905| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5085 Z= 0.121 Angle : 0.582 6.201 6877 Z= 0.301 Chirality : 0.042 0.134 760 Planarity : 0.004 0.051 880 Dihedral : 4.989 25.312 676 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 3.25 % Allowed : 21.34 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.34), residues: 607 helix: 0.42 (0.35), residues: 235 sheet: -1.24 (0.58), residues: 62 loop : -0.84 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 91 TYR 0.011 0.001 TYR B 233 PHE 0.010 0.001 PHE B 329 TRP 0.011 0.001 TRP A 380 HIS 0.006 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 5085) covalent geometry : angle 0.58206 ( 6877) hydrogen bonds : bond 0.03528 ( 210) hydrogen bonds : angle 6.21824 ( 582) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 MET cc_start: 0.5687 (tpt) cc_final: 0.5092 (tpp) REVERT: B 102 TYR cc_start: 0.9231 (m-80) cc_final: 0.8816 (m-80) REVERT: B 123 ASN cc_start: 0.9441 (p0) cc_final: 0.9027 (t0) REVERT: B 149 ASP cc_start: 0.8361 (t0) cc_final: 0.7882 (t0) REVERT: B 194 ARG cc_start: 0.8525 (ptm160) cc_final: 0.7919 (ptp-170) REVERT: B 221 MET cc_start: 0.9658 (mtp) cc_final: 0.9457 (mtp) REVERT: B 330 LYS cc_start: 0.9419 (pttt) cc_final: 0.8961 (tptp) REVERT: A 151 HIS cc_start: 0.7827 (t-170) cc_final: 0.7302 (p-80) REVERT: A 242 GLN cc_start: 0.9110 (mt0) cc_final: 0.8850 (mp10) REVERT: A 262 MET cc_start: 0.9175 (ttm) cc_final: 0.8699 (ptp) REVERT: A 314 MET cc_start: -0.0210 (tpt) cc_final: -0.2237 (ppp) REVERT: A 322 TYR cc_start: 0.9106 (t80) cc_final: 0.8835 (t80) outliers start: 18 outliers final: 14 residues processed: 132 average time/residue: 0.1830 time to fit residues: 30.1700 Evaluate side-chains 128 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 358 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 55 optimal weight: 0.0010 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** 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 = 0.3858 r_free = 0.3858 target = 0.103334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.074223 restraints weight = 44919.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.079171 restraints weight = 23306.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.082578 restraints weight = 14484.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.084987 restraints weight = 10196.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.086597 restraints weight = 7821.089| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5085 Z= 0.172 Angle : 0.602 5.923 6877 Z= 0.320 Chirality : 0.042 0.134 760 Planarity : 0.005 0.047 880 Dihedral : 5.007 25.627 676 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.44 % Allowed : 21.70 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.33), residues: 607 helix: 0.22 (0.34), residues: 235 sheet: -1.20 (0.59), residues: 60 loop : -0.99 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 67 TYR 0.012 0.001 TYR B 233 PHE 0.016 0.001 PHE A 317 TRP 0.012 0.001 TRP A 380 HIS 0.004 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 5085) covalent geometry : angle 0.60210 ( 6877) hydrogen bonds : bond 0.03611 ( 210) hydrogen bonds : angle 6.26618 ( 582) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 ASP cc_start: 0.8906 (OUTLIER) cc_final: 0.8559 (m-30) REVERT: B 102 TYR cc_start: 0.9251 (m-80) cc_final: 0.8815 (m-80) REVERT: B 149 ASP cc_start: 0.8251 (t0) cc_final: 0.7780 (t0) REVERT: B 221 MET cc_start: 0.9666 (mtp) cc_final: 0.9464 (mtp) REVERT: B 330 LYS cc_start: 0.9419 (pttt) cc_final: 0.8961 (tptp) REVERT: A 190 HIS cc_start: 0.7745 (m90) cc_final: 0.7363 (m90) REVERT: A 242 GLN cc_start: 0.9164 (mt0) cc_final: 0.8808 (mp10) REVERT: A 262 MET cc_start: 0.9193 (ttm) cc_final: 0.8700 (ptp) REVERT: A 314 MET cc_start: -0.0094 (tpt) cc_final: -0.2326 (ppp) REVERT: A 322 TYR cc_start: 0.9109 (t80) cc_final: 0.8894 (t80) outliers start: 19 outliers final: 18 residues processed: 130 average time/residue: 0.1798 time to fit residues: 29.1788 Evaluate side-chains 134 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 358 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 43 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 36 optimal weight: 0.0020 chunk 51 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN A 151 HIS ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.106110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.076339 restraints weight = 43977.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.081409 restraints weight = 23007.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.084952 restraints weight = 14344.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.087436 restraints weight = 10100.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.089129 restraints weight = 7746.054| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5085 Z= 0.105 Angle : 0.584 6.536 6877 Z= 0.298 Chirality : 0.042 0.138 760 Planarity : 0.004 0.048 880 Dihedral : 4.846 25.160 676 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.25 % Allowed : 22.24 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.34), residues: 607 helix: 0.53 (0.35), residues: 235 sheet: -1.23 (0.57), residues: 62 loop : -0.81 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 91 TYR 0.012 0.001 TYR B 233 PHE 0.010 0.001 PHE B 329 TRP 0.013 0.001 TRP A 380 HIS 0.006 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 5085) covalent geometry : angle 0.58416 ( 6877) hydrogen bonds : bond 0.03369 ( 210) hydrogen bonds : angle 5.90047 ( 582) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 TYR cc_start: 0.9192 (m-80) cc_final: 0.8757 (m-80) REVERT: B 123 ASN cc_start: 0.9404 (p0) cc_final: 0.9001 (t0) REVERT: B 149 ASP cc_start: 0.8263 (t0) cc_final: 0.7799 (t0) REVERT: B 330 LYS cc_start: 0.9388 (pttt) cc_final: 0.8894 (tptp) REVERT: A 190 HIS cc_start: 0.7794 (m90) cc_final: 0.7413 (m90) REVERT: A 242 GLN cc_start: 0.9086 (mt0) cc_final: 0.8760 (mp10) REVERT: A 262 MET cc_start: 0.9153 (ttm) cc_final: 0.8672 (ptp) REVERT: A 314 MET cc_start: -0.0026 (tpt) cc_final: -0.2299 (ppp) REVERT: A 322 TYR cc_start: 0.9094 (t80) cc_final: 0.8855 (t80) outliers start: 18 outliers final: 16 residues processed: 136 average time/residue: 0.1784 time to fit residues: 30.5101 Evaluate side-chains 135 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 358 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 58 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 HIS ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.104662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.075019 restraints weight = 43986.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.080073 restraints weight = 22912.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.083542 restraints weight = 14270.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.086033 restraints weight = 10033.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.087713 restraints weight = 7683.586| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5085 Z= 0.129 Angle : 0.588 6.648 6877 Z= 0.306 Chirality : 0.043 0.165 760 Planarity : 0.004 0.047 880 Dihedral : 4.812 25.333 676 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 3.62 % Allowed : 22.97 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.34), residues: 607 helix: 0.58 (0.35), residues: 235 sheet: -1.25 (0.58), residues: 60 loop : -0.87 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 91 TYR 0.011 0.001 TYR B 233 PHE 0.021 0.001 PHE B 129 TRP 0.014 0.001 TRP A 380 HIS 0.005 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 5085) covalent geometry : angle 0.58753 ( 6877) hydrogen bonds : bond 0.03418 ( 210) hydrogen bonds : angle 5.89179 ( 582) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 MET cc_start: 0.5843 (tpt) cc_final: 0.5490 (tpp) REVERT: B 123 ASN cc_start: 0.9420 (p0) cc_final: 0.8999 (t0) REVERT: B 149 ASP cc_start: 0.8286 (t0) cc_final: 0.7819 (t0) REVERT: B 194 ARG cc_start: 0.8412 (ptm160) cc_final: 0.7777 (mtp-110) REVERT: B 330 LYS cc_start: 0.9402 (pttt) cc_final: 0.8906 (tptp) REVERT: A 190 HIS cc_start: 0.7778 (m90) cc_final: 0.7391 (m90) REVERT: A 242 GLN cc_start: 0.9130 (mt0) cc_final: 0.8785 (mp10) REVERT: A 262 MET cc_start: 0.9162 (ttm) cc_final: 0.8648 (ptp) REVERT: A 314 MET cc_start: 0.0004 (tpt) cc_final: -0.2292 (ppp) REVERT: A 322 TYR cc_start: 0.9090 (t80) cc_final: 0.8880 (t80) outliers start: 20 outliers final: 19 residues processed: 131 average time/residue: 0.1793 time to fit residues: 29.5094 Evaluate side-chains 134 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 358 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 19 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 53 optimal weight: 0.0050 chunk 32 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 overall best weight: 2.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 HIS ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.101594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.072545 restraints weight = 44632.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.077404 restraints weight = 23250.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.080795 restraints weight = 14509.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.083157 restraints weight = 10229.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.084757 restraints weight = 7872.983| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5085 Z= 0.194 Angle : 0.620 5.356 6877 Z= 0.334 Chirality : 0.043 0.143 760 Planarity : 0.005 0.046 880 Dihedral : 4.936 25.954 676 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.44 % Allowed : 23.87 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.33), residues: 607 helix: 0.24 (0.34), residues: 235 sheet: -1.34 (0.56), residues: 65 loop : -1.01 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 67 TYR 0.012 0.001 TYR B 233 PHE 0.020 0.002 PHE B 129 TRP 0.015 0.001 TRP A 380 HIS 0.005 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 5085) covalent geometry : angle 0.62025 ( 6877) hydrogen bonds : bond 0.03720 ( 210) hydrogen bonds : angle 6.15637 ( 582) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 MET cc_start: 0.6013 (tpt) cc_final: 0.5223 (tpp) REVERT: B 102 TYR cc_start: 0.9263 (m-80) cc_final: 0.8812 (m-80) REVERT: B 123 ASN cc_start: 0.9438 (p0) cc_final: 0.9001 (t0) REVERT: B 149 ASP cc_start: 0.8201 (t0) cc_final: 0.7720 (t0) REVERT: B 194 ARG cc_start: 0.8432 (ptm160) cc_final: 0.7819 (mtp-110) REVERT: B 330 LYS cc_start: 0.9428 (pttt) cc_final: 0.8932 (tptp) REVERT: A 190 HIS cc_start: 0.7843 (m90) cc_final: 0.7443 (m90) REVERT: A 242 GLN cc_start: 0.9194 (mt0) cc_final: 0.8825 (mp10) REVERT: A 262 MET cc_start: 0.9201 (ttm) cc_final: 0.8653 (ptp) REVERT: A 314 MET cc_start: 0.0055 (tpt) cc_final: -0.2273 (ppp) REVERT: A 344 VAL cc_start: 0.8241 (m) cc_final: 0.7726 (t) outliers start: 19 outliers final: 17 residues processed: 126 average time/residue: 0.1741 time to fit residues: 27.6958 Evaluate side-chains 127 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 358 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 HIS ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.104712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.075744 restraints weight = 43033.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.080756 restraints weight = 22270.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.084134 restraints weight = 13823.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.086707 restraints weight = 9704.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.088283 restraints weight = 7381.978| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5085 Z= 0.113 Angle : 0.602 6.373 6877 Z= 0.310 Chirality : 0.043 0.149 760 Planarity : 0.004 0.046 880 Dihedral : 4.795 25.509 676 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.71 % Allowed : 24.59 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.34), residues: 607 helix: 0.56 (0.35), residues: 230 sheet: -1.11 (0.62), residues: 55 loop : -0.77 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 91 TYR 0.013 0.001 TYR B 233 PHE 0.015 0.001 PHE B 129 TRP 0.013 0.001 TRP A 380 HIS 0.004 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 5085) covalent geometry : angle 0.60238 ( 6877) hydrogen bonds : bond 0.03415 ( 210) hydrogen bonds : angle 5.81483 ( 582) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 MET cc_start: 0.5689 (tpt) cc_final: 0.5397 (tpp) REVERT: B 123 ASN cc_start: 0.9415 (p0) cc_final: 0.8958 (t0) REVERT: B 149 ASP cc_start: 0.8217 (t0) cc_final: 0.7752 (t0) REVERT: B 194 ARG cc_start: 0.8372 (ptm160) cc_final: 0.7904 (mtp-110) REVERT: B 212 TRP cc_start: 0.8829 (t-100) cc_final: 0.8424 (t-100) REVERT: B 330 LYS cc_start: 0.9400 (pttt) cc_final: 0.8917 (tptp) REVERT: A 190 HIS cc_start: 0.7843 (m90) cc_final: 0.7607 (m90) REVERT: A 242 GLN cc_start: 0.9162 (mt0) cc_final: 0.8819 (mp10) REVERT: A 262 MET cc_start: 0.9145 (ttm) cc_final: 0.8631 (ptp) REVERT: A 314 MET cc_start: 0.0097 (tpt) cc_final: -0.2269 (ppp) outliers start: 15 outliers final: 15 residues processed: 130 average time/residue: 0.1688 time to fit residues: 27.7450 Evaluate side-chains 132 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 358 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 36 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 HIS ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.104551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.074937 restraints weight = 43701.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.080036 restraints weight = 22695.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.083487 restraints weight = 14156.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.085951 restraints weight = 10002.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.087567 restraints weight = 7696.886| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5085 Z= 0.122 Angle : 0.602 6.138 6877 Z= 0.312 Chirality : 0.043 0.145 760 Planarity : 0.004 0.045 880 Dihedral : 4.748 25.505 676 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.07 % Allowed : 24.23 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.34), residues: 607 helix: 0.65 (0.35), residues: 231 sheet: -1.09 (0.62), residues: 55 loop : -0.76 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 91 TYR 0.012 0.001 TYR B 233 PHE 0.015 0.001 PHE B 129 TRP 0.014 0.001 TRP A 380 HIS 0.003 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 5085) covalent geometry : angle 0.60215 ( 6877) hydrogen bonds : bond 0.03421 ( 210) hydrogen bonds : angle 5.79014 ( 582) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 MET cc_start: 0.5788 (tpt) cc_final: 0.5470 (tpp) REVERT: B 123 ASN cc_start: 0.9414 (p0) cc_final: 0.8961 (t0) REVERT: B 149 ASP cc_start: 0.8233 (t0) cc_final: 0.7768 (t0) REVERT: B 194 ARG cc_start: 0.8366 (ptm160) cc_final: 0.7868 (mtp-110) REVERT: B 212 TRP cc_start: 0.8832 (t-100) cc_final: 0.8455 (t-100) REVERT: B 330 LYS cc_start: 0.9401 (pttt) cc_final: 0.8909 (tptp) REVERT: A 190 HIS cc_start: 0.7847 (m90) cc_final: 0.7612 (m90) REVERT: A 242 GLN cc_start: 0.9182 (mt0) cc_final: 0.8828 (mp10) REVERT: A 262 MET cc_start: 0.9152 (ttm) cc_final: 0.8635 (ptp) REVERT: A 314 MET cc_start: -0.0004 (tpt) cc_final: -0.2340 (ppp) outliers start: 17 outliers final: 17 residues processed: 127 average time/residue: 0.1866 time to fit residues: 29.5028 Evaluate side-chains 132 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 358 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 57 optimal weight: 20.0000 chunk 0 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 HIS ** 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 = 0.3859 r_free = 0.3859 target = 0.103506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.074364 restraints weight = 43815.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.079294 restraints weight = 22699.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.082760 restraints weight = 14168.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.085216 restraints weight = 9930.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.086817 restraints weight = 7600.376| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5085 Z= 0.143 Angle : 0.606 5.877 6877 Z= 0.316 Chirality : 0.043 0.140 760 Planarity : 0.004 0.044 880 Dihedral : 4.763 25.635 676 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.07 % Allowed : 24.41 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.34), residues: 607 helix: 0.63 (0.35), residues: 231 sheet: -1.25 (0.55), residues: 65 loop : -0.85 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 91 TYR 0.012 0.001 TYR B 233 PHE 0.011 0.001 PHE B 329 TRP 0.014 0.001 TRP A 380 HIS 0.004 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 5085) covalent geometry : angle 0.60648 ( 6877) hydrogen bonds : bond 0.03461 ( 210) hydrogen bonds : angle 5.83996 ( 582) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2160.54 seconds wall clock time: 37 minutes 24.98 seconds (2244.98 seconds total)