Starting phenix.real_space_refine on Tue Aug 4 17:20:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b2z_44118/08_2026/9b2z_44118.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b2z_44118/08_2026/9b2z_44118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b2z_44118/08_2026/9b2z_44118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b2z_44118/08_2026/9b2z_44118.map" model { file = "/net/cci-nas-00/data/ceres_data/9b2z_44118/08_2026/9b2z_44118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b2z_44118/08_2026/9b2z_44118.cif" } resolution = 2.83 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= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 4 5.49 5 S 26 5.16 5 C 3509 2.51 5 N 926 2.21 5 O 1040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5506 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2638 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 15, 'TRANS': 335} Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 260 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 17, 'ASP:plan': 12, 'ARG:plan': 2, 'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 141 Chain: "B" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2787 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 19, 'TRANS': 340} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'AMP%rna3p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna3p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' CA': 1, 'ATP': 1, 'LAB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.46, per 1000 atoms: 0.27 Number of scatterers: 5506 At special positions: 0 Unit cell: (71.514, 81.378, 112.614, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 26 16.00 P 4 15.00 O 1040 8.00 N 926 7.00 C 3509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 212.0 milliseconds 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1352 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 6 sheets defined 59.9% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 23 through 32 Processing helix chain 'A' and resid 38 through 54 Processing helix chain 'A' and resid 63 through 73 Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.532A pdb=" N ALA A 79 " --> pdb=" O ASN A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 107 through 109 No H-bonds generated for 'chain 'A' and resid 107 through 109' Processing helix chain 'A' and resid 112 through 115 Processing helix chain 'A' and resid 116 through 135 removed outlier: 3.688A pdb=" N LEU A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 154 removed outlier: 3.507A pdb=" N ASN A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 177 Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 186 through 193 removed outlier: 3.500A pdb=" N GLN A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 263 through 279 removed outlier: 3.549A pdb=" N LEU A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 301 Processing helix chain 'A' and resid 306 through 315 removed outlier: 4.290A pdb=" N VAL A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 326 removed outlier: 4.509A pdb=" N ILE A 322 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 326 " --> pdb=" O ILE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 373 removed outlier: 3.591A pdb=" N LYS A 369 " --> pdb=" O ARG A 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 61 through 65 removed outlier: 3.630A pdb=" N LEU B 65 " --> pdb=" O ARG B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.560A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.745A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 195 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.579A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 289 Processing helix chain 'B' and resid 290 through 295 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 350 through 355 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 4.099A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 211 Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.502A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N VAL B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ALA B 135 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA4, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA5, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.188A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N MET B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 238 through 241 287 hydrogen bonds defined for protein. 780 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: 0.75 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 897 1.30 - 1.43: 1414 1.43 - 1.56: 3261 1.56 - 1.69: 8 1.69 - 1.82: 45 Bond restraints: 5625 Sorted by residual: bond pdb=" C5 AMP A 601 " pdb=" N7 AMP A 601 " ideal model delta sigma weight residual 1.350 1.552 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" CE1 HIS A 305 " pdb=" NE2 HIS A 305 " ideal model delta sigma weight residual 1.321 1.408 -0.087 1.00e-02 1.00e+04 7.62e+01 bond pdb=" C4 ATP B 402 " pdb=" C5 ATP B 402 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.44e+01 bond pdb=" O1P AMP A 601 " pdb=" P AMP A 601 " ideal model delta sigma weight residual 1.510 1.654 -0.144 2.00e-02 2.50e+03 5.20e+01 bond pdb=" C5 ATP B 402 " pdb=" C6 ATP B 402 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.07e+01 ... (remaining 5620 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 7568 3.25 - 6.50: 67 6.50 - 9.75: 11 9.75 - 13.01: 1 13.01 - 16.26: 3 Bond angle restraints: 7650 Sorted by residual: angle pdb=" PB ATP B 402 " pdb=" O3B ATP B 402 " pdb=" PG ATP B 402 " ideal model delta sigma weight residual 139.87 123.61 16.26 1.00e+00 1.00e+00 2.64e+02 angle pdb=" PA ATP B 402 " pdb=" O3A ATP B 402 " pdb=" PB ATP B 402 " ideal model delta sigma weight residual 136.83 122.51 14.32 1.00e+00 1.00e+00 2.05e+02 angle pdb=" C5 ATP B 402 " pdb=" C4 ATP B 402 " pdb=" N3 ATP B 402 " ideal model delta sigma weight residual 126.80 118.89 7.91 1.00e+00 1.00e+00 6.26e+01 angle pdb=" CA HIS A 305 " pdb=" CB HIS A 305 " pdb=" CG HIS A 305 " ideal model delta sigma weight residual 113.80 106.90 6.90 1.00e+00 1.00e+00 4.76e+01 angle pdb=" N3 ATP B 402 " pdb=" C4 ATP B 402 " pdb=" N9 ATP B 402 " ideal model delta sigma weight residual 127.04 134.80 -7.76 1.15e+00 7.59e-01 4.56e+01 ... (remaining 7645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.47: 3342 31.47 - 62.95: 80 62.95 - 94.42: 9 94.42 - 125.89: 5 125.89 - 157.36: 2 Dihedral angle restraints: 3438 sinusoidal: 1348 harmonic: 2090 Sorted by residual: dihedral pdb=" C2 LAB B 401 " pdb=" C3 LAB B 401 " pdb=" C4 LAB B 401 " pdb=" C5 LAB B 401 " ideal model delta sinusoidal sigma weight residual 275.91 118.55 157.36 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" C11 LAB B 401 " pdb=" C10 LAB B 401 " pdb=" C9 LAB B 401 " pdb=" C8 LAB B 401 " ideal model delta sinusoidal sigma weight residual 129.60 -77.75 -152.65 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" C3 LAB B 401 " pdb=" C1 LAB B 401 " pdb=" C2 LAB B 401 " pdb=" O2 LAB B 401 " ideal model delta sinusoidal sigma weight residual -142.77 -20.23 -122.54 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 3435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 864 0.118 - 0.236: 13 0.236 - 0.353: 3 0.353 - 0.471: 0 0.471 - 0.589: 1 Chirality restraints: 881 Sorted by residual: chirality pdb=" C16 LAB B 401 " pdb=" C15 LAB B 401 " pdb=" C17 LAB B 401 " pdb=" N1 LAB B 401 " both_signs ideal model delta sigma weight residual False 2.52 3.11 -0.59 2.00e-01 2.50e+01 8.68e+00 chirality pdb=" C15 LAB B 401 " pdb=" C14 LAB B 401 " pdb=" C16 LAB B 401 " pdb=" O3 LAB B 401 " both_signs ideal model delta sigma weight residual False 2.52 2.82 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C13 LAB B 401 " pdb=" C12 LAB B 401 " pdb=" C14 LAB B 401 " pdb=" O2 LAB B 401 " both_signs ideal model delta sigma weight residual False 2.29 2.57 -0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 878 not shown) Planarity restraints: 967 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5 LAB B 401 " 0.097 2.00e-02 2.50e+03 2.31e-01 5.36e+02 pdb=" C6 LAB B 401 " -0.308 2.00e-02 2.50e+03 pdb=" C7 LAB B 401 " 0.315 2.00e-02 2.50e+03 pdb=" C8 LAB B 401 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 LAB B 401 " -0.242 2.00e-02 2.50e+03 2.03e-01 5.14e+02 pdb=" C19 LAB B 401 " -0.158 2.00e-02 2.50e+03 pdb=" C2 LAB B 401 " 0.344 2.00e-02 2.50e+03 pdb=" C3 LAB B 401 " 0.062 2.00e-02 2.50e+03 pdb=" C4 LAB B 401 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 229 " 0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO A 230 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 230 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 230 " 0.022 5.00e-02 4.00e+02 ... (remaining 964 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 452 2.74 - 3.28: 5621 3.28 - 3.82: 9343 3.82 - 4.36: 11808 4.36 - 4.90: 19779 Nonbonded interactions: 47003 Sorted by model distance: nonbonded pdb=" O PHE A 174 " pdb=" OG SER A 177 " model vdw 2.200 3.040 nonbonded pdb=" O ALA B 174 " pdb=" OG SER B 281 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR B 160 " pdb=" O LEU B 180 " model vdw 2.243 3.040 nonbonded pdb=" OD2 ASP B 157 " pdb=" O3' ATP B 402 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR A 307 " pdb=" O TYR A 332 " model vdw 2.253 3.040 ... (remaining 46998 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.200 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: 0.010 Load rotamer database and sin/cos tables:9.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 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 : 0.007 0.202 5626 Z= 0.441 Angle : 0.820 16.257 7650 Z= 0.519 Chirality : 0.051 0.589 881 Planarity : 0.011 0.231 967 Dihedral : 15.828 157.363 2086 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.18 % Allowed : 0.88 % Favored : 98.94 % 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: -0.65 (0.31), residues: 705 helix: -0.11 (0.27), residues: 362 sheet: -0.99 (0.71), residues: 55 loop : -0.53 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 119 TYR 0.023 0.001 TYR A 299 PHE 0.013 0.002 PHE A 86 TRP 0.016 0.002 TRP A 295 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00705 / 0.43 ( 5625) covalent geometry : angle 0.81997 / 0.52 ( 7650) hydrogen bonds : bond 0.14541 / 9.34 ( 287) hydrogen bonds : angle 6.24492 / 4.31 ( 780) Misc. bond : bond 0.05451 / 2.87 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.226 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.4337 time to fit residues: 36.9706 Evaluate side-chains 65 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 363 GLN B 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.163033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.135720 restraints weight = 5754.228| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 1.64 r_work: 0.3704 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5626 Z= 0.182 Angle : 0.607 8.203 7650 Z= 0.305 Chirality : 0.044 0.173 881 Planarity : 0.005 0.037 967 Dihedral : 13.110 159.399 849 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.88 % Allowed : 9.56 % Favored : 89.56 % 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: -0.40 (0.32), residues: 705 helix: 0.06 (0.27), residues: 367 sheet: -0.97 (0.74), residues: 49 loop : -0.37 (0.39), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 119 TYR 0.023 0.001 TYR A 299 PHE 0.013 0.002 PHE B 31 TRP 0.014 0.002 TRP A 295 HIS 0.004 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.18 ( 5625) covalent geometry : angle 0.60716 / 0.31 ( 7650) hydrogen bonds : bond 0.04240 / 2.87 ( 287) hydrogen bonds : angle 4.96855 / 3.39 ( 780) Misc. bond : bond 0.00317 / 0.17 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.130 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 74 average time/residue: 0.3261 time to fit residues: 25.5684 Evaluate side-chains 69 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain B residue 272 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 31 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 GLN A 363 GLN B 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.165365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.137868 restraints weight = 5714.740| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.64 r_work: 0.3514 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5626 Z= 0.125 Angle : 0.542 7.564 7650 Z= 0.271 Chirality : 0.041 0.140 881 Planarity : 0.004 0.035 967 Dihedral : 12.283 164.621 849 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.59 % Allowed : 10.62 % Favored : 87.79 % 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: 0.02 (0.32), residues: 705 helix: 0.34 (0.27), residues: 373 sheet: -0.74 (0.73), residues: 54 loop : -0.06 (0.40), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 119 TYR 0.013 0.001 TYR A 299 PHE 0.008 0.001 PHE B 31 TRP 0.011 0.002 TRP A 295 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 5625) covalent geometry : angle 0.54155 / 0.27 ( 7650) hydrogen bonds : bond 0.03644 / 2.48 ( 287) hydrogen bonds : angle 4.55275 / 3.11 ( 780) Misc. bond : bond 0.00089 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.212 Fit side-chains REVERT: B 72 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8205 (mm-30) REVERT: B 248 ILE cc_start: 0.7768 (pt) cc_final: 0.7360 (pt) outliers start: 9 outliers final: 4 residues processed: 74 average time/residue: 0.3244 time to fit residues: 25.6650 Evaluate side-chains 70 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 287 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 0.0670 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 31 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 363 GLN B 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.166984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.139223 restraints weight = 5741.908| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 1.67 r_work: 0.3810 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3691 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5626 Z= 0.104 Angle : 0.510 7.470 7650 Z= 0.253 Chirality : 0.040 0.137 881 Planarity : 0.004 0.033 967 Dihedral : 12.108 163.587 849 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.06 % Allowed : 12.74 % Favored : 86.19 % 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: 0.36 (0.33), residues: 705 helix: 0.64 (0.27), residues: 379 sheet: -0.52 (0.73), residues: 55 loop : 0.04 (0.40), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 119 TYR 0.010 0.001 TYR A 299 PHE 0.007 0.001 PHE A 366 TRP 0.009 0.001 TRP A 295 HIS 0.003 0.000 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 ( 5625) covalent geometry : angle 0.50966 / 0.25 ( 7650) hydrogen bonds : bond 0.03202 / 2.17 ( 287) hydrogen bonds : angle 4.29995 / 2.94 ( 780) Misc. bond : bond 0.00051 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.139 Fit side-chains REVERT: B 207 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6803 (mm-30) REVERT: B 248 ILE cc_start: 0.7910 (pt) cc_final: 0.7561 (pt) outliers start: 6 outliers final: 3 residues processed: 68 average time/residue: 0.3232 time to fit residues: 23.3778 Evaluate side-chains 68 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain B residue 207 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 70 optimal weight: 2.9990 chunk 58 optimal weight: 0.0010 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.1980 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 59 optimal weight: 0.0060 overall best weight: 0.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 363 GLN B 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.170234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.142652 restraints weight = 5817.772| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 1.68 r_work: 0.3847 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5626 Z= 0.093 Angle : 0.491 7.651 7650 Z= 0.243 Chirality : 0.040 0.131 881 Planarity : 0.003 0.031 967 Dihedral : 11.958 163.397 849 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.95 % Allowed : 12.74 % Favored : 85.31 % 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: 0.77 (0.33), residues: 705 helix: 0.97 (0.27), residues: 381 sheet: -0.38 (0.75), residues: 55 loop : 0.25 (0.40), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 201 TYR 0.009 0.001 TYR A 348 PHE 0.027 0.001 PHE A 72 TRP 0.009 0.001 TRP A 295 HIS 0.002 0.000 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 ( 5625) covalent geometry : angle 0.49069 / 0.24 ( 7650) hydrogen bonds : bond 0.02944 / 2.00 ( 287) hydrogen bonds : angle 4.11348 / 2.82 ( 780) Misc. bond : bond 0.00026 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.214 Fit side-chains REVERT: B 28 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7904 (mtm110) outliers start: 11 outliers final: 3 residues processed: 72 average time/residue: 0.3518 time to fit residues: 26.8914 Evaluate side-chains 64 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 272 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 70 optimal weight: 0.0980 chunk 13 optimal weight: 0.0470 chunk 48 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 0.3980 chunk 18 optimal weight: 2.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN A 363 GLN B 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.169808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.142115 restraints weight = 5650.544| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 1.67 r_work: 0.3878 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5626 Z= 0.099 Angle : 0.492 7.751 7650 Z= 0.242 Chirality : 0.040 0.133 881 Planarity : 0.003 0.029 967 Dihedral : 12.127 174.884 849 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.77 % Allowed : 13.63 % Favored : 84.60 % 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: 0.93 (0.33), residues: 705 helix: 1.09 (0.27), residues: 381 sheet: -0.75 (0.73), residues: 55 loop : 0.45 (0.40), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 256 TYR 0.009 0.001 TYR A 299 PHE 0.007 0.001 PHE A 143 TRP 0.009 0.001 TRP A 295 HIS 0.002 0.000 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 5625) covalent geometry : angle 0.49238 / 0.24 ( 7650) hydrogen bonds : bond 0.03000 / 2.04 ( 287) hydrogen bonds : angle 4.07392 / 2.79 ( 780) Misc. bond : bond 0.00031 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.150 Fit side-chains REVERT: B 66 THR cc_start: 0.8515 (m) cc_final: 0.8175 (p) outliers start: 10 outliers final: 5 residues processed: 68 average time/residue: 0.3418 time to fit residues: 24.6750 Evaluate side-chains 66 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 358 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 67 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN A 363 GLN B 59 GLN B 296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.168379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.140368 restraints weight = 5721.188| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 1.68 r_work: 0.3834 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3716 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5626 Z= 0.118 Angle : 0.519 7.903 7650 Z= 0.255 Chirality : 0.041 0.134 881 Planarity : 0.003 0.029 967 Dihedral : 12.273 179.739 849 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.48 % Allowed : 12.74 % Favored : 84.78 % 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: 0.93 (0.33), residues: 705 helix: 1.02 (0.27), residues: 381 sheet: -0.54 (0.70), residues: 60 loop : 0.53 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 147 TYR 0.010 0.001 TYR A 299 PHE 0.027 0.002 PHE A 42 TRP 0.011 0.001 TRP A 295 HIS 0.003 0.001 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 5625) covalent geometry : angle 0.51906 / 0.26 ( 7650) hydrogen bonds : bond 0.03199 / 2.17 ( 287) hydrogen bonds : angle 4.16707 / 2.84 ( 780) Misc. bond : bond 0.00041 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.149 Fit side-chains REVERT: A 322 ILE cc_start: 0.6817 (OUTLIER) cc_final: 0.5987 (mp) REVERT: B 28 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7862 (mtm110) REVERT: B 66 THR cc_start: 0.8535 (m) cc_final: 0.8210 (p) REVERT: B 248 ILE cc_start: 0.7954 (pt) cc_final: 0.7698 (pt) outliers start: 14 outliers final: 5 residues processed: 76 average time/residue: 0.3309 time to fit residues: 26.7199 Evaluate side-chains 72 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 358 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 46 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 3 optimal weight: 0.3980 chunk 28 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 363 GLN B 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.167950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.139640 restraints weight = 5674.697| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 1.69 r_work: 0.3773 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5626 Z= 0.122 Angle : 0.527 8.114 7650 Z= 0.260 Chirality : 0.041 0.135 881 Planarity : 0.004 0.031 967 Dihedral : 12.297 170.619 849 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.12 % Allowed : 13.45 % Favored : 84.42 % 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: 0.88 (0.33), residues: 705 helix: 0.94 (0.27), residues: 381 sheet: -0.50 (0.69), residues: 60 loop : 0.58 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 147 TYR 0.010 0.001 TYR A 299 PHE 0.020 0.001 PHE A 42 TRP 0.012 0.002 TRP A 295 HIS 0.003 0.001 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 5625) covalent geometry : angle 0.52749 / 0.26 ( 7650) hydrogen bonds : bond 0.03323 / 2.26 ( 287) hydrogen bonds : angle 4.25103 / 2.90 ( 780) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.232 Fit side-chains REVERT: B 28 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7809 (mtm110) REVERT: B 66 THR cc_start: 0.8524 (m) cc_final: 0.8212 (p) outliers start: 12 outliers final: 5 residues processed: 71 average time/residue: 0.3707 time to fit residues: 27.9603 Evaluate side-chains 71 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 358 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 52 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 363 GLN B 59 GLN B 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.167944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.139532 restraints weight = 5698.053| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.69 r_work: 0.3785 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3661 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5626 Z= 0.128 Angle : 0.551 9.065 7650 Z= 0.270 Chirality : 0.042 0.138 881 Planarity : 0.004 0.030 967 Dihedral : 12.305 164.486 849 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.77 % Allowed : 14.34 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.79 (0.32), residues: 705 helix: 0.91 (0.27), residues: 380 sheet: -0.56 (0.68), residues: 60 loop : 0.46 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 147 TYR 0.010 0.001 TYR A 299 PHE 0.012 0.001 PHE A 42 TRP 0.012 0.002 TRP A 295 HIS 0.003 0.001 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 5625) covalent geometry : angle 0.55130 / 0.27 ( 7650) hydrogen bonds : bond 0.03379 / 2.30 ( 287) hydrogen bonds : angle 4.29047 / 2.93 ( 780) Misc. bond : bond 0.00034 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.210 Fit side-chains REVERT: A 338 THR cc_start: 0.7098 (OUTLIER) cc_final: 0.6825 (m) REVERT: B 28 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7812 (mtm110) REVERT: B 66 THR cc_start: 0.8526 (m) cc_final: 0.8213 (p) outliers start: 10 outliers final: 5 residues processed: 72 average time/residue: 0.3554 time to fit residues: 27.1855 Evaluate side-chains 70 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 358 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 8 optimal weight: 0.0970 chunk 23 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 20 optimal weight: 0.0980 chunk 47 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 363 GLN B 59 GLN B 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.169876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.141467 restraints weight = 5703.141| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 1.71 r_work: 0.3826 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3703 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5626 Z= 0.102 Angle : 0.529 9.189 7650 Z= 0.257 Chirality : 0.041 0.141 881 Planarity : 0.003 0.030 967 Dihedral : 12.135 158.847 849 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.77 % Allowed : 14.51 % Favored : 83.72 % 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: 1.04 (0.33), residues: 705 helix: 1.11 (0.27), residues: 381 sheet: -0.75 (0.71), residues: 55 loop : 0.63 (0.40), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 119 TYR 0.008 0.001 TYR A 348 PHE 0.006 0.001 PHE A 366 TRP 0.010 0.001 TRP A 295 HIS 0.002 0.000 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 ( 5625) covalent geometry : angle 0.52889 / 0.26 ( 7650) hydrogen bonds : bond 0.03071 / 2.08 ( 287) hydrogen bonds : angle 4.13168 / 2.83 ( 780) Misc. bond : bond 0.00033 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.212 Fit side-chains REVERT: A 338 THR cc_start: 0.7052 (OUTLIER) cc_final: 0.6758 (m) REVERT: B 28 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7824 (mtm110) REVERT: B 66 THR cc_start: 0.8518 (m) cc_final: 0.8224 (p) REVERT: B 311 ASP cc_start: 0.6448 (t0) cc_final: 0.5997 (m-30) outliers start: 10 outliers final: 5 residues processed: 68 average time/residue: 0.3488 time to fit residues: 25.2244 Evaluate side-chains 67 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 358 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 69 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.1980 chunk 54 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 363 GLN B 59 GLN B 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.169506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.141202 restraints weight = 5670.015| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 1.69 r_work: 0.3818 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5626 Z= 0.113 Angle : 0.550 9.153 7650 Z= 0.266 Chirality : 0.041 0.135 881 Planarity : 0.004 0.029 967 Dihedral : 12.027 158.409 849 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.42 % Allowed : 14.69 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.04 (0.33), residues: 705 helix: 1.06 (0.27), residues: 381 sheet: -0.55 (0.68), residues: 60 loop : 0.69 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 119 TYR 0.009 0.001 TYR A 299 PHE 0.007 0.001 PHE B 31 TRP 0.011 0.001 TRP A 295 HIS 0.002 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 5625) covalent geometry : angle 0.54967 / 0.27 ( 7650) hydrogen bonds : bond 0.03218 / 2.18 ( 287) hydrogen bonds : angle 4.17413 / 2.85 ( 780) Misc. bond : bond 0.00033 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2048.54 seconds wall clock time: 35 minutes 29.96 seconds (2129.96 seconds total)