Starting phenix.real_space_refine on Thu Jul 2 02:16:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jsp_61780/07_2026/9jsp_61780.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jsp_61780/07_2026/9jsp_61780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jsp_61780/07_2026/9jsp_61780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jsp_61780/07_2026/9jsp_61780.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jsp_61780/07_2026/9jsp_61780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jsp_61780/07_2026/9jsp_61780.map" } resolution = 3.34 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= -0.001 sd= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 22 5.49 5 Mg 1 5.21 5 S 20 5.16 5 C 3650 2.51 5 N 1030 2.21 5 O 1139 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5862 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3693 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 26, 'TRANS': 438} Chain breaks: 1 Chain: "B" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1705 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 11, 'TRANS': 196} Chain breaks: 3 Chain: "G" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 255 Classifications: {'RNA': 12} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 10} Chain: "T" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 208 Classifications: {'DNA': 10} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.50, per 1000 atoms: 0.26 Number of scatterers: 5862 At special positions: 0 Unit cell: (73.95, 74.8, 108.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 20 16.00 P 22 15.00 Mg 1 11.99 O 1139 8.00 N 1030 7.00 C 3650 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=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 316.5 milliseconds 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1248 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 9 sheets defined 34.0% alpha, 10.4% beta 10 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 Processing helix chain 'A' and resid 49 through 63 Processing helix chain 'A' and resid 105 through 113 removed outlier: 3.560A pdb=" N LEU A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 139 Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 181 through 191 removed outlier: 3.649A pdb=" N MET A 185 " --> pdb=" O ASN A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 206 removed outlier: 3.522A pdb=" N ASP A 206 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 242 Processing helix chain 'A' and resid 311 through 328 Processing helix chain 'A' and resid 343 through 357 Processing helix chain 'A' and resid 429 through 441 removed outlier: 3.531A pdb=" N LEU A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 removed outlier: 4.304A pdb=" N ALA A 461 " --> pdb=" O PRO A 457 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ARG A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 removed outlier: 4.468A pdb=" N TYR A 484 " --> pdb=" O ASP A 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'B' and resid 216 through 220 removed outlier: 3.576A pdb=" N THR B 219 " --> pdb=" O ASP B 216 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER B 220 " --> pdb=" O PRO B 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 216 through 220' Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 236 through 241 Processing helix chain 'B' and resid 245 through 263 Processing helix chain 'B' and resid 355 through 364 Processing helix chain 'B' and resid 371 through 384 removed outlier: 3.818A pdb=" N GLN B 384 " --> pdb=" O ARG B 380 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 4.338A pdb=" N GLU A 4 " --> pdb=" O ASP A 390 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 387 " --> pdb=" O TYR A 398 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 389 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY A 395 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 420 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 419 " --> pdb=" O GLN A 368 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL A 334 " --> pdb=" O ASP A 363 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N VAL A 365 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE A 336 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL A 367 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS A 338 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE A 335 " --> pdb=" O CYS A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 96 removed outlier: 6.009A pdb=" N ASP A 40 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLU A 95 " --> pdb=" O ASP A 40 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ILE A 42 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N VAL A 145 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LYS A 43 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE A 147 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLY A 45 " --> pdb=" O ILE A 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 261 through 262 Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 266 Processing sheet with id=AA5, first strand: chain 'B' and resid 171 through 172 removed outlier: 3.642A pdb=" N MET B 402 " --> pdb=" O THR B 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 211 through 213 Processing sheet with id=AA7, first strand: chain 'B' and resid 268 through 269 Processing sheet with id=AA8, first strand: chain 'B' and resid 322 through 323 Processing sheet with id=AA9, first strand: chain 'B' and resid 326 through 330 180 hydrogen bonds defined for protein. 501 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 0.84 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1752 1.34 - 1.46: 1295 1.46 - 1.58: 2921 1.58 - 1.70: 42 1.70 - 1.82: 36 Bond restraints: 6046 Sorted by residual: bond pdb=" C3' DG T 17 " pdb=" C2' DG T 17 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.41e+00 bond pdb=" C3' DG T 14 " pdb=" C2' DG T 14 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.53e+00 bond pdb=" C1' DT T 13 " pdb=" N1 DT T 13 " ideal model delta sigma weight residual 1.468 1.498 -0.030 1.40e-02 5.10e+03 4.60e+00 bond pdb=" C3' DG T 9 " pdb=" C2' DG T 9 " ideal model delta sigma weight residual 1.516 1.532 -0.016 8.00e-03 1.56e+04 4.16e+00 bond pdb=" CB TYR A 239 " pdb=" CG TYR A 239 " ideal model delta sigma weight residual 1.512 1.556 -0.044 2.20e-02 2.07e+03 4.04e+00 ... (remaining 6041 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 7956 1.98 - 3.97: 271 3.97 - 5.95: 40 5.95 - 7.93: 6 7.93 - 9.92: 4 Bond angle restraints: 8277 Sorted by residual: angle pdb=" N3 DT T 18 " pdb=" C4 DT T 18 " pdb=" O4 DT T 18 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT T 11 " pdb=" C4 DT T 11 " pdb=" O4 DT T 11 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.83e+01 angle pdb=" O4 DT T 11 " pdb=" C4 DT T 11 " pdb=" C5 DT T 11 " ideal model delta sigma weight residual 124.90 122.08 2.82 7.00e-01 2.04e+00 1.63e+01 angle pdb=" N3 DT T 13 " pdb=" C4 DT T 13 " pdb=" O4 DT T 13 " ideal model delta sigma weight residual 119.90 122.32 -2.42 6.00e-01 2.78e+00 1.62e+01 angle pdb=" O4 DT T 18 " pdb=" C4 DT T 18 " pdb=" C5 DT T 18 " ideal model delta sigma weight residual 124.90 122.13 2.77 7.00e-01 2.04e+00 1.57e+01 ... (remaining 8272 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.53: 3329 32.53 - 65.05: 244 65.05 - 97.58: 18 97.58 - 130.10: 0 130.10 - 162.63: 1 Dihedral angle restraints: 3592 sinusoidal: 1648 harmonic: 1944 Sorted by residual: dihedral pdb=" O4' U G 2 " pdb=" C1' U G 2 " pdb=" N1 U G 2 " pdb=" C2 U G 2 " ideal model delta sinusoidal sigma weight residual 200.00 37.37 162.63 1 1.50e+01 4.44e-03 8.34e+01 dihedral pdb=" CA HIS A 304 " pdb=" C HIS A 304 " pdb=" N PRO A 305 " pdb=" CA PRO A 305 " ideal model delta harmonic sigma weight residual 180.00 155.07 24.93 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA ASP B 244 " pdb=" C ASP B 244 " pdb=" N ILE B 245 " pdb=" CA ILE B 245 " ideal model delta harmonic sigma weight residual -180.00 -159.16 -20.84 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 3589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 740 0.060 - 0.120: 132 0.120 - 0.180: 20 0.180 - 0.240: 3 0.240 - 0.301: 2 Chirality restraints: 897 Sorted by residual: chirality pdb=" CB ILE A 456 " pdb=" CA ILE A 456 " pdb=" CG1 ILE A 456 " pdb=" CG2 ILE A 456 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CG LEU B 267 " pdb=" CB LEU B 267 " pdb=" CD1 LEU B 267 " pdb=" CD2 LEU B 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CB ILE A 96 " pdb=" CA ILE A 96 " pdb=" CG1 ILE A 96 " pdb=" CG2 ILE A 96 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 894 not shown) Planarity restraints: 990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 304 " -0.044 5.00e-02 4.00e+02 6.59e-02 6.96e+00 pdb=" N PRO A 305 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 305 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 305 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 198 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.78e+00 pdb=" C GLN A 198 " 0.038 2.00e-02 2.50e+03 pdb=" O GLN A 198 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE A 199 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 185 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO B 186 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 186 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 186 " 0.029 5.00e-02 4.00e+02 ... (remaining 987 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1172 2.78 - 3.31: 5119 3.31 - 3.84: 9706 3.84 - 4.37: 10662 4.37 - 4.90: 18460 Nonbonded interactions: 45119 Sorted by model distance: nonbonded pdb=" O LYS A 58 " pdb=" OG1 THR A 62 " model vdw 2.250 3.040 nonbonded pdb=" O HIS B 379 " pdb=" OG1 THR B 383 " model vdw 2.286 3.040 nonbonded pdb=" O THR A 52 " pdb=" OG1 THR A 56 " model vdw 2.297 3.040 nonbonded pdb=" O ARG A 301 " pdb=" NH1 ARG A 301 " model vdw 2.316 3.120 nonbonded pdb=" OG SER A 370 " pdb=" OP2 DC T 10 " model vdw 2.317 3.040 ... (remaining 45114 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: 1.280 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 7.550 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6128 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6046 Z= 0.231 Angle : 0.835 9.918 8277 Z= 0.492 Chirality : 0.050 0.301 897 Planarity : 0.006 0.066 990 Dihedral : 20.396 162.627 2344 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.80 % Favored : 88.20 % Rotamer: Outliers : 0.87 % Allowed : 35.08 % Favored : 64.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.83 (0.29), residues: 661 helix: -0.58 (0.33), residues: 203 sheet: -0.76 (0.47), residues: 119 loop : -3.26 (0.27), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 333 TYR 0.017 0.002 TYR B 335 PHE 0.026 0.002 PHE A 388 TRP 0.019 0.002 TRP A 366 HIS 0.006 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.23 ( 6046) covalent geometry : angle 0.83476 / 0.49 ( 8277) hydrogen bonds : bond 0.11996 / 9.06 ( 206) hydrogen bonds : angle 5.74979 / 4.18 ( 553) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: A 76 ASN cc_start: 0.5683 (m110) cc_final: 0.5354 (t0) REVERT: B 215 HIS cc_start: 0.6235 (p90) cc_final: 0.5977 (p90) REVERT: B 352 HIS cc_start: 0.5295 (OUTLIER) cc_final: 0.4156 (p90) outliers start: 5 outliers final: 1 residues processed: 78 average time/residue: 0.0926 time to fit residues: 9.2241 Evaluate side-chains 73 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain B residue 352 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0470 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 424 HIS B 215 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5123 r_free = 0.5123 target = 0.278311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.239038 restraints weight = 6739.526| |-----------------------------------------------------------------------------| r_work (start): 0.4814 rms_B_bonded: 3.10 r_work (final): 0.4814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6046 Z= 0.147 Angle : 0.624 7.202 8277 Z= 0.334 Chirality : 0.042 0.213 897 Planarity : 0.005 0.049 990 Dihedral : 14.211 179.347 1024 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 2.62 % Allowed : 34.03 % Favored : 63.35 % 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: -2.36 (0.30), residues: 661 helix: 0.22 (0.35), residues: 206 sheet: -0.87 (0.46), residues: 130 loop : -3.20 (0.27), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 341 TYR 0.010 0.001 TYR A 90 PHE 0.016 0.001 PHE A 342 TRP 0.020 0.002 TRP A 366 HIS 0.004 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 6046) covalent geometry : angle 0.62380 / 0.33 ( 8277) hydrogen bonds : bond 0.04819 / 3.32 ( 206) hydrogen bonds : angle 4.82974 / 3.32 ( 553) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 76 ASN cc_start: 0.6697 (m110) cc_final: 0.5871 (t0) REVERT: B 352 HIS cc_start: 0.6151 (OUTLIER) cc_final: 0.5284 (p90) outliers start: 15 outliers final: 10 residues processed: 86 average time/residue: 0.1032 time to fit residues: 11.1390 Evaluate side-chains 81 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 352 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 52 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN A 423 HIS ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5034 r_free = 0.5034 target = 0.268288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.223573 restraints weight = 6751.532| |-----------------------------------------------------------------------------| r_work (start): 0.4656 rms_B_bonded: 3.25 r_work: 0.4312 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.4312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 6046 Z= 0.268 Angle : 0.783 11.987 8277 Z= 0.407 Chirality : 0.047 0.298 897 Planarity : 0.006 0.060 990 Dihedral : 14.146 168.618 1024 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.67 % Favored : 85.33 % Rotamer: Outliers : 5.41 % Allowed : 32.81 % Favored : 61.78 % 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: -2.45 (0.30), residues: 661 helix: 0.31 (0.36), residues: 205 sheet: -1.32 (0.45), residues: 133 loop : -3.19 (0.28), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 303 TYR 0.023 0.002 TYR A 90 PHE 0.022 0.003 PHE A 342 TRP 0.040 0.003 TRP A 366 HIS 0.006 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.27 ( 6046) covalent geometry : angle 0.78286 / 0.41 ( 8277) hydrogen bonds : bond 0.06131 / 4.15 ( 206) hydrogen bonds : angle 5.16337 / 3.48 ( 553) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 71 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 TRP cc_start: 0.5509 (OUTLIER) cc_final: 0.1183 (t-100) REVERT: A 221 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6850 (ptm-80) REVERT: A 462 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.6710 (ttp-170) REVERT: B 202 PHE cc_start: 0.4789 (OUTLIER) cc_final: 0.4581 (t80) REVERT: B 352 HIS cc_start: 0.6781 (OUTLIER) cc_final: 0.6465 (p90) outliers start: 31 outliers final: 18 residues processed: 95 average time/residue: 0.0966 time to fit residues: 11.5071 Evaluate side-chains 91 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 159 TRP Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 352 HIS Chi-restraints excluded: chain B residue 358 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 16 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 7 optimal weight: 0.0970 chunk 18 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5073 r_free = 0.5073 target = 0.273203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.231233 restraints weight = 6704.024| |-----------------------------------------------------------------------------| r_work (start): 0.4738 rms_B_bonded: 3.10 r_work: 0.4402 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.4402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6046 Z= 0.148 Angle : 0.634 6.936 8277 Z= 0.336 Chirality : 0.042 0.234 897 Planarity : 0.005 0.054 990 Dihedral : 14.063 175.961 1024 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % Rotamer: Outliers : 4.71 % Allowed : 33.51 % Favored : 61.78 % 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: -2.25 (0.31), residues: 661 helix: 0.55 (0.36), residues: 207 sheet: -1.31 (0.47), residues: 121 loop : -3.04 (0.28), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 333 TYR 0.018 0.002 TYR A 239 PHE 0.015 0.001 PHE A 342 TRP 0.021 0.002 TRP A 366 HIS 0.005 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 6046) covalent geometry : angle 0.63413 / 0.34 ( 8277) hydrogen bonds : bond 0.04691 / 3.20 ( 206) hydrogen bonds : angle 4.80169 / 3.21 ( 553) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 345 GLU cc_start: 0.7781 (pm20) cc_final: 0.7495 (pm20) REVERT: A 462 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6799 (ttp-170) REVERT: B 352 HIS cc_start: 0.6708 (OUTLIER) cc_final: 0.6405 (p90) outliers start: 27 outliers final: 17 residues processed: 93 average time/residue: 0.0936 time to fit residues: 11.0689 Evaluate side-chains 92 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 352 HIS Chi-restraints excluded: chain B residue 358 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 54 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 48 optimal weight: 30.0000 chunk 18 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 424 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5075 r_free = 0.5075 target = 0.273730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.232368 restraints weight = 6789.610| |-----------------------------------------------------------------------------| r_work (start): 0.4743 rms_B_bonded: 3.09 r_work: 0.4401 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.4401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6046 Z= 0.137 Angle : 0.603 6.866 8277 Z= 0.320 Chirality : 0.041 0.221 897 Planarity : 0.004 0.052 990 Dihedral : 13.936 175.971 1024 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.35 % Favored : 88.65 % Rotamer: Outliers : 5.93 % Allowed : 32.11 % Favored : 61.95 % 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: -2.09 (0.31), residues: 661 helix: 0.69 (0.37), residues: 208 sheet: -1.14 (0.46), residues: 130 loop : -3.03 (0.28), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 333 TYR 0.018 0.002 TYR A 239 PHE 0.012 0.001 PHE A 282 TRP 0.019 0.001 TRP A 366 HIS 0.005 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 6046) covalent geometry : angle 0.60278 / 0.32 ( 8277) hydrogen bonds : bond 0.04418 / 3.02 ( 206) hydrogen bonds : angle 4.62471 / 3.10 ( 553) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 72 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6752 (ttp-170) REVERT: B 352 HIS cc_start: 0.6695 (OUTLIER) cc_final: 0.6396 (p90) outliers start: 34 outliers final: 21 residues processed: 101 average time/residue: 0.0861 time to fit residues: 11.2950 Evaluate side-chains 95 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 352 HIS Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 359 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 59 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5093 r_free = 0.5093 target = 0.275644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.234834 restraints weight = 6696.691| |-----------------------------------------------------------------------------| r_work (start): 0.4762 rms_B_bonded: 3.04 r_work: 0.4422 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.4422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6046 Z= 0.123 Angle : 0.595 9.611 8277 Z= 0.313 Chirality : 0.041 0.297 897 Planarity : 0.004 0.048 990 Dihedral : 13.895 177.853 1024 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 4.36 % Allowed : 32.81 % Favored : 62.83 % 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: -2.02 (0.31), residues: 661 helix: 0.79 (0.37), residues: 208 sheet: -1.16 (0.45), residues: 130 loop : -2.99 (0.28), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 333 TYR 0.020 0.001 TYR A 239 PHE 0.010 0.001 PHE A 342 TRP 0.016 0.001 TRP A 366 HIS 0.004 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 6046) covalent geometry : angle 0.59491 / 0.31 ( 8277) hydrogen bonds : bond 0.04081 / 2.78 ( 206) hydrogen bonds : angle 4.46998 / 2.99 ( 553) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 352 HIS cc_start: 0.6642 (OUTLIER) cc_final: 0.6299 (p90) REVERT: B 402 MET cc_start: 0.6875 (mmp) cc_final: 0.6576 (mpp) outliers start: 25 outliers final: 21 residues processed: 88 average time/residue: 0.0901 time to fit residues: 10.2912 Evaluate side-chains 91 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 352 HIS Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 359 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 50 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN A 446 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5046 r_free = 0.5046 target = 0.269950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.229033 restraints weight = 6667.821| |-----------------------------------------------------------------------------| r_work (start): 0.4708 rms_B_bonded: 2.99 r_work: 0.4361 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.4361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6046 Z= 0.194 Angle : 0.678 9.229 8277 Z= 0.354 Chirality : 0.044 0.267 897 Planarity : 0.005 0.053 990 Dihedral : 13.907 172.540 1022 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.01 % Favored : 86.99 % Rotamer: Outliers : 5.93 % Allowed : 31.94 % Favored : 62.13 % 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: -2.18 (0.31), residues: 661 helix: 0.63 (0.36), residues: 208 sheet: -1.39 (0.44), residues: 132 loop : -3.00 (0.29), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 309 TYR 0.020 0.002 TYR A 239 PHE 0.014 0.002 PHE A 282 TRP 0.024 0.002 TRP A 366 HIS 0.005 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 ( 6046) covalent geometry : angle 0.67778 / 0.35 ( 8277) hydrogen bonds : bond 0.04863 / 3.31 ( 206) hydrogen bonds : angle 4.69165 / 3.15 ( 553) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 69 time to evaluate : 0.244 Fit side-chains REVERT: A 77 MET cc_start: 0.5871 (mtt) cc_final: 0.5320 (ptt) REVERT: A 314 LYS cc_start: 0.7385 (tptp) cc_final: 0.6919 (ptmt) REVERT: A 341 ARG cc_start: 0.6272 (ptm-80) cc_final: 0.5934 (ptm-80) REVERT: A 345 GLU cc_start: 0.7727 (pm20) cc_final: 0.7478 (pm20) REVERT: A 446 ASN cc_start: 0.7471 (OUTLIER) cc_final: 0.5031 (t0) REVERT: A 462 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6765 (ttp-170) REVERT: B 171 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6215 (mp) REVERT: B 402 MET cc_start: 0.6836 (mmp) cc_final: 0.6564 (mpp) outliers start: 34 outliers final: 26 residues processed: 96 average time/residue: 0.0889 time to fit residues: 11.0184 Evaluate side-chains 96 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 67 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 446 ASN Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 352 HIS Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 359 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5060 r_free = 0.5060 target = 0.272058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.230044 restraints weight = 6625.489| |-----------------------------------------------------------------------------| r_work (start): 0.4719 rms_B_bonded: 3.09 r_work: 0.4379 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.4379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6046 Z= 0.143 Angle : 0.635 7.952 8277 Z= 0.334 Chirality : 0.042 0.241 897 Planarity : 0.005 0.053 990 Dihedral : 13.931 175.662 1022 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 4.89 % Allowed : 32.81 % Favored : 62.30 % 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: -2.12 (0.31), residues: 661 helix: 0.73 (0.36), residues: 208 sheet: -1.31 (0.45), residues: 129 loop : -3.03 (0.28), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 333 TYR 0.021 0.002 TYR A 239 PHE 0.011 0.001 PHE A 282 TRP 0.035 0.002 TRP A 247 HIS 0.004 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 6046) covalent geometry : angle 0.63497 / 0.33 ( 8277) hydrogen bonds : bond 0.04322 / 2.93 ( 206) hydrogen bonds : angle 4.47769 / 2.96 ( 553) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.231 Fit side-chains REVERT: A 77 MET cc_start: 0.5952 (mtt) cc_final: 0.5327 (ptt) REVERT: A 244 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6555 (ttp-170) REVERT: A 314 LYS cc_start: 0.7316 (tptp) cc_final: 0.6846 (ptmt) REVERT: A 341 ARG cc_start: 0.5912 (ptm-80) cc_final: 0.5558 (ptm-80) REVERT: A 345 GLU cc_start: 0.7749 (pm20) cc_final: 0.7501 (pm20) REVERT: A 462 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6749 (ttp-170) REVERT: B 171 LEU cc_start: 0.6863 (OUTLIER) cc_final: 0.6184 (mp) REVERT: B 402 MET cc_start: 0.6831 (mmp) cc_final: 0.6502 (mpp) outliers start: 28 outliers final: 24 residues processed: 91 average time/residue: 0.0956 time to fit residues: 11.0333 Evaluate side-chains 96 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 159 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 352 HIS Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 359 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 64 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 43 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 42 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5082 r_free = 0.5082 target = 0.274684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.232763 restraints weight = 6744.306| |-----------------------------------------------------------------------------| r_work (start): 0.4736 rms_B_bonded: 3.11 r_work: 0.4409 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.4409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6046 Z= 0.126 Angle : 0.614 7.509 8277 Z= 0.322 Chirality : 0.042 0.231 897 Planarity : 0.004 0.052 990 Dihedral : 13.896 178.006 1022 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 5.24 % Allowed : 32.64 % Favored : 62.13 % 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: -2.03 (0.31), residues: 661 helix: 0.88 (0.37), residues: 208 sheet: -1.32 (0.45), residues: 131 loop : -3.01 (0.28), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 333 TYR 0.017 0.001 TYR A 239 PHE 0.009 0.001 PHE A 342 TRP 0.034 0.002 TRP A 247 HIS 0.004 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 6046) covalent geometry : angle 0.61357 / 0.32 ( 8277) hydrogen bonds : bond 0.03998 / 2.69 ( 206) hydrogen bonds : angle 4.36083 / 2.89 ( 553) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 69 time to evaluate : 0.187 Fit side-chains REVERT: A 77 MET cc_start: 0.5924 (mtt) cc_final: 0.5334 (ptt) REVERT: A 244 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6640 (ttp-170) REVERT: A 314 LYS cc_start: 0.7174 (tptp) cc_final: 0.6782 (ptmt) REVERT: A 341 ARG cc_start: 0.5813 (ptm-80) cc_final: 0.5467 (ptm-80) REVERT: A 462 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.6691 (ttp-170) REVERT: B 171 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6072 (mp) REVERT: B 402 MET cc_start: 0.6844 (mmp) cc_final: 0.6471 (mpp) outliers start: 30 outliers final: 25 residues processed: 92 average time/residue: 0.0948 time to fit residues: 11.1789 Evaluate side-chains 97 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 159 TRP Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 352 HIS Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 359 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 2 optimal weight: 4.9990 chunk 28 optimal weight: 0.0060 chunk 20 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 62 optimal weight: 0.0870 chunk 55 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5084 r_free = 0.5084 target = 0.275029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.233172 restraints weight = 6723.297| |-----------------------------------------------------------------------------| r_work (start): 0.4746 rms_B_bonded: 3.10 r_work: 0.4409 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.4409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6046 Z= 0.124 Angle : 0.614 7.500 8277 Z= 0.322 Chirality : 0.041 0.219 897 Planarity : 0.004 0.053 990 Dihedral : 13.898 177.944 1022 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 4.89 % Allowed : 32.29 % Favored : 62.83 % 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: -1.97 (0.32), residues: 661 helix: 0.96 (0.37), residues: 208 sheet: -1.26 (0.46), residues: 131 loop : -3.00 (0.28), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 333 TYR 0.018 0.001 TYR A 239 PHE 0.010 0.001 PHE A 342 TRP 0.028 0.002 TRP A 247 HIS 0.004 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 6046) covalent geometry : angle 0.61392 / 0.32 ( 8277) hydrogen bonds : bond 0.03920 / 2.65 ( 206) hydrogen bonds : angle 4.32226 / 2.87 ( 553) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 77 MET cc_start: 0.5812 (mtt) cc_final: 0.5343 (ptt) REVERT: A 244 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6268 (ptp-170) REVERT: A 341 ARG cc_start: 0.5700 (ptm-80) cc_final: 0.5419 (ptm-80) REVERT: A 462 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.6758 (ttp-170) REVERT: B 171 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6271 (mp) REVERT: B 402 MET cc_start: 0.6772 (mmp) cc_final: 0.6527 (mpp) outliers start: 28 outliers final: 25 residues processed: 91 average time/residue: 0.0935 time to fit residues: 10.9266 Evaluate side-chains 97 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 159 TRP Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 352 HIS Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 359 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 13 optimal weight: 6.9990 chunk 67 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5075 r_free = 0.5075 target = 0.273786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.231754 restraints weight = 6661.232| |-----------------------------------------------------------------------------| r_work (start): 0.4728 rms_B_bonded: 3.09 r_work: 0.4383 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.4383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6046 Z= 0.138 Angle : 0.627 7.511 8277 Z= 0.328 Chirality : 0.042 0.230 897 Planarity : 0.005 0.056 990 Dihedral : 13.897 176.386 1022 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer: Outliers : 5.24 % Allowed : 32.29 % Favored : 62.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.99 (0.31), residues: 661 helix: 0.96 (0.37), residues: 208 sheet: -1.30 (0.45), residues: 131 loop : -3.01 (0.28), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 333 TYR 0.018 0.002 TYR A 239 PHE 0.010 0.001 PHE A 282 TRP 0.024 0.002 TRP A 247 HIS 0.004 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 6046) covalent geometry : angle 0.62707 / 0.33 ( 8277) hydrogen bonds : bond 0.04025 / 2.73 ( 206) hydrogen bonds : angle 4.39073 / 2.93 ( 553) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1427.94 seconds wall clock time: 25 minutes 16.97 seconds (1516.97 seconds total)