Starting phenix.real_space_refine on Tue Feb 11 11:10:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b2z_44118/02_2025/9b2z_44118.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b2z_44118/02_2025/9b2z_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_44118/02_2025/9b2z_44118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b2z_44118/02_2025/9b2z_44118.map" model { file = "/net/cci-nas-00/data/ceres_data/9b2z_44118/02_2025/9b2z_44118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b2z_44118/02_2025/9b2z_44118.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.036 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 2} 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 Classifications: {'RNA': 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: 3.98, per 1000 atoms: 0.72 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: 1.73 Conformation dependent library (CDL) restraints added in 881.6 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: 0.77 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: 1.70 Time building geometry restraints manager: 1.87 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.620 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 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 5625 Z= 0.446 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (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 TRP 0.016 0.002 TRP A 295 HIS 0.003 0.001 HIS B 101 PHE 0.013 0.002 PHE A 86 TYR 0.023 0.001 TYR A 299 ARG 0.007 0.001 ARG A 119 *********************** 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 : 0.533 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 1.0439 time to fit residues: 89.0990 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 : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4148 r_free = 0.4148 target = 0.165474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.138305 restraints weight = 5619.453| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 1.62 r_work: 0.3752 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5625 Z= 0.213 Angle : 0.564 7.408 7650 Z= 0.283 Chirality : 0.042 0.143 881 Planarity : 0.004 0.036 967 Dihedral : 13.084 161.001 849 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.88 % Allowed : 8.14 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.32), residues: 705 helix: 0.29 (0.27), residues: 367 sheet: -0.85 (0.71), residues: 55 loop : -0.28 (0.39), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 295 HIS 0.003 0.001 HIS B 101 PHE 0.010 0.001 PHE B 31 TYR 0.018 0.001 TYR A 299 ARG 0.005 0.001 ARG A 119 *********************** 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 78 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.741 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 75 average time/residue: 0.9252 time to fit residues: 73.8450 Evaluate side-chains 70 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 70 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4112 r_free = 0.4112 target = 0.162888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.135511 restraints weight = 5718.466| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 1.62 r_work: 0.3738 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3618 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5625 Z= 0.316 Angle : 0.616 8.012 7650 Z= 0.309 Chirality : 0.044 0.165 881 Planarity : 0.004 0.035 967 Dihedral : 12.582 161.162 849 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.59 % Allowed : 10.80 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.32), residues: 705 helix: 0.13 (0.27), residues: 366 sheet: -0.81 (0.72), residues: 54 loop : -0.33 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 295 HIS 0.004 0.001 HIS A 305 PHE 0.014 0.002 PHE A 86 TYR 0.020 0.001 TYR A 299 ARG 0.004 0.001 ARG A 119 *********************** 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 74 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.632 Fit side-chains REVERT: B 72 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8235 (mt-10) REVERT: B 248 ILE cc_start: 0.7882 (pt) cc_final: 0.7480 (pt) outliers start: 9 outliers final: 4 residues processed: 70 average time/residue: 0.9092 time to fit residues: 67.8465 Evaluate side-chains 67 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 51 optimal weight: 0.5980 chunk 44 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4188 r_free = 0.4188 target = 0.169730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.142594 restraints weight = 5837.145| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 1.64 r_work: 0.3789 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3671 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5625 Z= 0.191 Angle : 0.538 7.618 7650 Z= 0.268 Chirality : 0.041 0.141 881 Planarity : 0.004 0.035 967 Dihedral : 12.328 163.324 849 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.59 % Allowed : 12.04 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.32), residues: 705 helix: 0.42 (0.27), residues: 373 sheet: -0.66 (0.73), residues: 54 loop : 0.01 (0.40), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 295 HIS 0.003 0.001 HIS B 101 PHE 0.008 0.001 PHE B 31 TYR 0.012 0.001 TYR A 299 ARG 0.002 0.000 ARG A 119 *********************** 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 78 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.653 Fit side-chains REVERT: B 72 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8133 (mm-30) REVERT: B 207 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6853 (mm-30) REVERT: B 248 ILE cc_start: 0.7892 (pt) cc_final: 0.7550 (pt) outliers start: 9 outliers final: 4 residues processed: 75 average time/residue: 0.9293 time to fit residues: 74.1001 Evaluate side-chains 72 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 72 GLU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 272 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 36 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4107 r_free = 0.4107 target = 0.162281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.134999 restraints weight = 5762.217| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.61 r_work: 0.3714 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5625 Z= 0.338 Angle : 0.616 8.065 7650 Z= 0.308 Chirality : 0.045 0.158 881 Planarity : 0.004 0.034 967 Dihedral : 12.711 168.860 849 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.83 % Allowed : 13.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.32), residues: 705 helix: 0.13 (0.26), residues: 372 sheet: -1.04 (0.68), residues: 60 loop : -0.19 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 295 HIS 0.004 0.001 HIS A 305 PHE 0.015 0.002 PHE A 86 TYR 0.014 0.001 TYR A 299 ARG 0.003 0.001 ARG A 119 *********************** 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 80 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.672 Fit side-chains REVERT: B 28 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7843 (mtm110) REVERT: B 72 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8261 (mt-10) REVERT: B 207 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6851 (mm-30) REVERT: B 248 ILE cc_start: 0.7909 (pt) cc_final: 0.7569 (pt) outliers start: 16 outliers final: 4 residues processed: 75 average time/residue: 1.0197 time to fit residues: 81.0351 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 : 0.666 ------------------------------------------------------------------------------- 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 72 GLU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 287 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 58 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 43 optimal weight: 0.1980 chunk 50 optimal weight: 0.9980 chunk 8 optimal weight: 0.0870 chunk 23 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.166889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.139669 restraints weight = 5674.607| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 1.62 r_work: 0.3778 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3659 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5625 Z= 0.178 Angle : 0.537 7.887 7650 Z= 0.265 Chirality : 0.041 0.140 881 Planarity : 0.004 0.033 967 Dihedral : 12.314 166.428 849 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.48 % Allowed : 14.16 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.32), residues: 705 helix: 0.48 (0.27), residues: 379 sheet: -0.92 (0.68), residues: 60 loop : 0.12 (0.41), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 295 HIS 0.003 0.001 HIS B 101 PHE 0.007 0.001 PHE A 366 TYR 0.009 0.001 TYR A 299 ARG 0.002 0.000 ARG A 119 *********************** 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 82 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.575 Fit side-chains REVERT: A 74 GLN cc_start: 0.6836 (OUTLIER) cc_final: 0.6632 (mp-120) REVERT: B 28 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7841 (mtm110) REVERT: B 72 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8121 (mm-30) REVERT: B 207 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6705 (mm-30) REVERT: B 248 ILE cc_start: 0.7839 (pt) cc_final: 0.7506 (pt) outliers start: 14 outliers final: 4 residues processed: 77 average time/residue: 0.9925 time to fit residues: 80.9973 Evaluate side-chains 76 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 28 ARG Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 287 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 0.0170 chunk 19 optimal weight: 0.8980 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4148 r_free = 0.4148 target = 0.165957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.138640 restraints weight = 5716.032| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 1.63 r_work: 0.3787 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3666 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5625 Z= 0.216 Angle : 0.555 8.741 7650 Z= 0.274 Chirality : 0.042 0.139 881 Planarity : 0.004 0.033 967 Dihedral : 12.313 166.513 849 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.12 % Allowed : 15.22 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.32), residues: 705 helix: 0.51 (0.27), residues: 379 sheet: -0.83 (0.65), residues: 66 loop : 0.16 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 295 HIS 0.003 0.001 HIS A 305 PHE 0.009 0.001 PHE B 31 TYR 0.010 0.001 TYR A 299 ARG 0.002 0.000 ARG A 119 *********************** 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 79 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.678 Fit side-chains REVERT: A 74 GLN cc_start: 0.6850 (OUTLIER) cc_final: 0.6626 (mp-120) REVERT: B 28 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7815 (mtm110) REVERT: B 72 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8229 (mt-10) REVERT: B 207 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6811 (mm-30) REVERT: B 248 ILE cc_start: 0.7916 (pt) cc_final: 0.7553 (pt) outliers start: 12 outliers final: 4 residues processed: 75 average time/residue: 1.0044 time to fit residues: 79.8953 Evaluate side-chains 75 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 28 ARG Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 287 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 48 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 38 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4151 r_free = 0.4151 target = 0.166440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.138537 restraints weight = 5615.951| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 1.66 r_work: 0.3803 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5625 Z= 0.170 Angle : 0.531 8.912 7650 Z= 0.259 Chirality : 0.041 0.135 881 Planarity : 0.004 0.033 967 Dihedral : 12.139 163.922 849 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.12 % Allowed : 15.22 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.32), residues: 705 helix: 0.72 (0.27), residues: 379 sheet: -0.81 (0.65), residues: 66 loop : 0.25 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 295 HIS 0.003 0.001 HIS B 101 PHE 0.007 0.001 PHE A 143 TYR 0.008 0.001 TYR A 348 ARG 0.002 0.000 ARG A 119 *********************** 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 78 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.602 Fit side-chains REVERT: A 74 GLN cc_start: 0.6790 (OUTLIER) cc_final: 0.6590 (mp-120) REVERT: A 146 LEU cc_start: 0.7636 (tp) cc_final: 0.7432 (tp) REVERT: B 28 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7816 (mtm110) REVERT: B 207 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6770 (mm-30) REVERT: B 248 ILE cc_start: 0.7896 (pt) cc_final: 0.7523 (pt) outliers start: 12 outliers final: 5 residues processed: 72 average time/residue: 1.0271 time to fit residues: 78.2402 Evaluate side-chains 71 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 28 ARG Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 287 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 67 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 14 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN B 59 GLN B 263 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 = 0.4153 r_free = 0.4153 target = 0.166607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.138683 restraints weight = 5591.951| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 1.66 r_work: 0.3802 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5625 Z= 0.176 Angle : 0.536 8.581 7650 Z= 0.262 Chirality : 0.041 0.137 881 Planarity : 0.004 0.033 967 Dihedral : 12.103 162.803 849 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.12 % Allowed : 15.22 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.32), residues: 705 helix: 0.79 (0.27), residues: 379 sheet: -0.67 (0.66), residues: 66 loop : 0.30 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 295 HIS 0.003 0.001 HIS B 101 PHE 0.007 0.001 PHE B 31 TYR 0.008 0.001 TYR A 348 ARG 0.002 0.000 ARG A 119 *********************** 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: 12 poor density : 63 time to evaluate : 0.622 Fit side-chains REVERT: A 74 GLN cc_start: 0.6799 (OUTLIER) cc_final: 0.6583 (mp-120) REVERT: B 28 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7818 (mtm110) REVERT: B 207 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6785 (mm-30) REVERT: B 248 ILE cc_start: 0.7884 (pt) cc_final: 0.7521 (pt) outliers start: 12 outliers final: 4 residues processed: 72 average time/residue: 0.9782 time to fit residues: 74.8832 Evaluate side-chains 69 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 28 ARG Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 287 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 13 optimal weight: 3.9990 chunk 62 optimal weight: 0.0570 chunk 33 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 68 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4194 r_free = 0.4194 target = 0.170288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.142401 restraints weight = 5637.185| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 1.68 r_work: 0.3822 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3700 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5625 Z= 0.156 Angle : 0.525 9.080 7650 Z= 0.256 Chirality : 0.041 0.135 881 Planarity : 0.004 0.033 967 Dihedral : 11.982 162.913 849 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.42 % Allowed : 15.58 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.32), residues: 705 helix: 0.96 (0.27), residues: 380 sheet: -0.64 (0.66), residues: 66 loop : 0.41 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 295 HIS 0.003 0.001 HIS B 101 PHE 0.007 0.001 PHE A 143 TYR 0.008 0.001 TYR A 348 ARG 0.002 0.000 ARG A 119 ********************** 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 69 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.754 Fit side-chains REVERT: B 28 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7784 (mtm110) REVERT: B 59 GLN cc_start: 0.5463 (OUTLIER) cc_final: 0.4938 (tt0) REVERT: B 248 ILE cc_start: 0.7916 (pt) cc_final: 0.7515 (pt) outliers start: 8 outliers final: 3 residues processed: 67 average time/residue: 1.0422 time to fit residues: 74.1644 Evaluate side-chains 63 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 59 GLN Chi-restraints excluded: chain B residue 287 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 3 optimal weight: 0.0570 chunk 57 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4175 r_free = 0.4175 target = 0.168516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.140347 restraints weight = 5742.227| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 1.69 r_work: 0.3796 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3673 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5625 Z= 0.182 Angle : 0.543 9.563 7650 Z= 0.263 Chirality : 0.041 0.135 881 Planarity : 0.004 0.032 967 Dihedral : 11.950 165.568 849 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.88 % Allowed : 16.64 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.32), residues: 705 helix: 0.93 (0.27), residues: 380 sheet: -0.52 (0.63), residues: 71 loop : 0.45 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 295 HIS 0.003 0.001 HIS B 101 PHE 0.008 0.001 PHE B 31 TYR 0.008 0.001 TYR A 299 ARG 0.002 0.000 ARG B 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4982.29 seconds wall clock time: 88 minutes 51.00 seconds (5331.00 seconds total)