Starting phenix.real_space_refine on Tue Feb 3 19:35:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ue6_64077/02_2026/9ue6_64077.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ue6_64077/02_2026/9ue6_64077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ue6_64077/02_2026/9ue6_64077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ue6_64077/02_2026/9ue6_64077.map" model { file = "/net/cci-nas-00/data/ceres_data/9ue6_64077/02_2026/9ue6_64077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ue6_64077/02_2026/9ue6_64077.cif" } resolution = 2.9 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= -0.026 sd= 0.354 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: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4107 2.51 5 N 1063 2.21 5 O 1198 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6405 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1560 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 181} Chain: "B" Number of atoms: 4845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4845 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 27, 'TRANS': 566} Time building chain proxies: 1.26, per 1000 atoms: 0.20 Number of scatterers: 6405 At special positions: 0 Unit cell: (82.016, 83.88, 114.636, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1198 8.00 N 1063 7.00 C 4107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 542 " distance=2.03 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: 0.56 Conformation dependent library (CDL) restraints added in 236.3 milliseconds 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1488 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 7 sheets defined 57.8% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.990A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.516A pdb=" N PHE A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.964A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.747A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'B' and resid 20 through 53 removed outlier: 3.540A pdb=" N GLN B 24 " --> pdb=" O THR B 20 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 80 Processing helix chain 'B' and resid 81 through 83 No H-bonds generated for 'chain 'B' and resid 81 through 83' Processing helix chain 'B' and resid 84 through 88 Processing helix chain 'B' and resid 90 through 101 Processing helix chain 'B' and resid 103 through 107 removed outlier: 3.678A pdb=" N VAL B 107 " --> pdb=" O GLY B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 130 Processing helix chain 'B' and resid 147 through 155 Processing helix chain 'B' and resid 157 through 172 removed outlier: 3.755A pdb=" N ARG B 169 " --> pdb=" O TRP B 165 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 172 " --> pdb=" O TRP B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 194 removed outlier: 4.167A pdb=" N GLU B 182 " --> pdb=" O PRO B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 218 through 252 removed outlier: 3.790A pdb=" N LEU B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) Proline residue: B 235 - end of helix Processing helix chain 'B' and resid 275 through 281 removed outlier: 4.062A pdb=" N SER B 280 " --> pdb=" O ASN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 300 Processing helix chain 'B' and resid 303 through 318 removed outlier: 3.644A pdb=" N VAL B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 331 Processing helix chain 'B' and resid 365 through 385 removed outlier: 3.540A pdb=" N TYR B 385 " --> pdb=" O TYR B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 388 No H-bonds generated for 'chain 'B' and resid 386 through 388' Processing helix chain 'B' and resid 389 through 393 Processing helix chain 'B' and resid 399 through 413 removed outlier: 3.517A pdb=" N MET B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 421 Processing helix chain 'B' and resid 431 through 447 Processing helix chain 'B' and resid 448 through 465 removed outlier: 4.413A pdb=" N PHE B 452 " --> pdb=" O GLY B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 485 Processing helix chain 'B' and resid 499 through 502 Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 512 through 533 removed outlier: 4.178A pdb=" N TYR B 516 " --> pdb=" O PHE B 512 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 559 removed outlier: 3.947A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 564 removed outlier: 3.568A pdb=" N SER B 563 " --> pdb=" O LEU B 560 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU B 564 " --> pdb=" O GLY B 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 560 through 564' Processing helix chain 'B' and resid 565 through 574 Processing helix chain 'B' and resid 581 through 588 Processing helix chain 'B' and resid 588 through 600 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.582A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.765A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'B' and resid 132 through 133 Processing sheet with id=AA6, first strand: chain 'B' and resid 262 through 263 removed outlier: 6.089A pdb=" N LEU B 262 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 347 through 352 removed outlier: 5.886A pdb=" N ASP B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) 324 hydrogen bonds defined for protein. 909 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.96 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2055 1.34 - 1.46: 1639 1.46 - 1.58: 2840 1.58 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 6592 Sorted by residual: bond pdb=" N ILE A 410 " pdb=" CA ILE A 410 " ideal model delta sigma weight residual 1.474 1.458 0.017 1.57e-02 4.06e+03 1.11e+00 bond pdb=" C LYS B 288 " pdb=" O LYS B 288 " ideal model delta sigma weight residual 1.249 1.242 0.007 8.50e-03 1.38e+04 6.77e-01 bond pdb=" CA GLY B 561 " pdb=" C GLY B 561 " ideal model delta sigma weight residual 1.520 1.512 0.009 1.06e-02 8.90e+03 6.66e-01 bond pdb=" CA GLU B 145 " pdb=" C GLU B 145 " ideal model delta sigma weight residual 1.521 1.530 -0.009 1.08e-02 8.57e+03 6.33e-01 bond pdb=" CA CYS B 344 " pdb=" C CYS B 344 " ideal model delta sigma weight residual 1.531 1.523 0.008 1.12e-02 7.97e+03 5.33e-01 ... (remaining 6587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 8620 1.01 - 2.03: 275 2.03 - 3.04: 47 3.04 - 4.06: 11 4.06 - 5.07: 8 Bond angle restraints: 8961 Sorted by residual: angle pdb=" N VAL B 318 " pdb=" CA VAL B 318 " pdb=" C VAL B 318 " ideal model delta sigma weight residual 113.07 109.41 3.66 1.37e+00 5.33e-01 7.14e+00 angle pdb=" N GLN B 175 " pdb=" CA GLN B 175 " pdb=" C GLN B 175 " ideal model delta sigma weight residual 114.04 110.93 3.11 1.24e+00 6.50e-01 6.29e+00 angle pdb=" N ILE A 468 " pdb=" CA ILE A 468 " pdb=" C ILE A 468 " ideal model delta sigma weight residual 111.77 109.56 2.21 1.04e+00 9.25e-01 4.50e+00 angle pdb=" N ILE B 484 " pdb=" CA ILE B 484 " pdb=" CB ILE B 484 " ideal model delta sigma weight residual 111.57 109.48 2.09 9.90e-01 1.02e+00 4.46e+00 angle pdb=" CA ILE A 410 " pdb=" C ILE A 410 " pdb=" O ILE A 410 " ideal model delta sigma weight residual 122.63 120.87 1.76 8.70e-01 1.32e+00 4.09e+00 ... (remaining 8956 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.64: 3611 11.64 - 23.27: 215 23.27 - 34.91: 51 34.91 - 46.55: 9 46.55 - 58.18: 3 Dihedral angle restraints: 3889 sinusoidal: 1572 harmonic: 2317 Sorted by residual: dihedral pdb=" CA LYS B 470 " pdb=" C LYS B 470 " pdb=" N ASP B 471 " pdb=" CA ASP B 471 " ideal model delta harmonic sigma weight residual -180.00 -159.98 -20.02 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA LEU B 144 " pdb=" C LEU B 144 " pdb=" N GLU B 145 " pdb=" CA GLU B 145 " ideal model delta harmonic sigma weight residual 180.00 -164.39 -15.61 0 5.00e+00 4.00e-02 9.74e+00 dihedral pdb=" N GLN B 388 " pdb=" CA GLN B 388 " pdb=" CB GLN B 388 " pdb=" CG GLN B 388 " ideal model delta sinusoidal sigma weight residual -60.00 -118.18 58.18 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 3886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 637 0.030 - 0.061: 202 0.061 - 0.091: 59 0.091 - 0.121: 34 0.121 - 0.151: 1 Chirality restraints: 933 Sorted by residual: chirality pdb=" CA ILE B 468 " pdb=" N ILE B 468 " pdb=" C ILE B 468 " pdb=" CB ILE B 468 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.73e-01 chirality pdb=" CA ILE B 256 " pdb=" N ILE B 256 " pdb=" C ILE B 256 " pdb=" CB ILE B 256 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA PRO B 469 " pdb=" N PRO B 469 " pdb=" C PRO B 469 " pdb=" CB PRO B 469 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.50e-01 ... (remaining 930 not shown) Planarity restraints: 1161 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 336 " 0.029 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO A 337 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 582 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO B 583 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 583 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 583 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 234 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO B 235 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 235 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 235 " -0.017 5.00e-02 4.00e+02 ... (remaining 1158 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1079 2.76 - 3.29: 6146 3.29 - 3.83: 10956 3.83 - 4.36: 12827 4.36 - 4.90: 22480 Nonbonded interactions: 53488 Sorted by model distance: nonbonded pdb=" OG SER B 607 " pdb=" OD1 ASP B 609 " model vdw 2.223 3.040 nonbonded pdb=" OD1 ASP B 494 " pdb=" OG1 THR B 496 " model vdw 2.272 3.040 nonbonded pdb=" OG1 THR A 500 " pdb=" OH TYR B 41 " model vdw 2.317 3.040 nonbonded pdb=" OH TYR B 237 " pdb=" O VAL B 485 " model vdw 2.318 3.040 nonbonded pdb=" OH TYR B 217 " pdb=" OD2 ASP B 225 " model vdw 2.318 3.040 ... (remaining 53483 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: 4.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 6.340 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:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 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 : 0.002 0.018 6598 Z= 0.104 Angle : 0.458 5.070 8973 Z= 0.280 Chirality : 0.037 0.151 933 Planarity : 0.003 0.045 1161 Dihedral : 8.071 58.184 2383 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.01 % Allowed : 3.46 % Favored : 95.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.28), residues: 785 helix: 0.55 (0.25), residues: 387 sheet: 0.01 (0.68), residues: 50 loop : -1.15 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 518 TYR 0.011 0.001 TYR B 385 PHE 0.012 0.001 PHE B 369 TRP 0.005 0.001 TRP B 168 HIS 0.002 0.001 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00169 ( 6592) covalent geometry : angle 0.45818 ( 8961) SS BOND : bond 0.00204 ( 6) SS BOND : angle 0.56574 ( 12) hydrogen bonds : bond 0.16559 ( 324) hydrogen bonds : angle 5.38489 ( 909) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 172 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 LYS cc_start: 0.7723 (mtpp) cc_final: 0.6461 (tttp) REVERT: B 167 SER cc_start: 0.8478 (t) cc_final: 0.8222 (p) outliers start: 7 outliers final: 0 residues processed: 177 average time/residue: 0.5966 time to fit residues: 110.2939 Evaluate side-chains 109 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.0020 chunk 74 optimal weight: 0.4980 overall best weight: 0.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN B 53 ASN B 61 ASN B 96 GLN B 102 GLN B 250 ASN B 373 HIS B 388 GLN ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.063061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.052262 restraints weight = 15323.594| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 1.67 r_work: 0.2581 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2484 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 6598 Z= 0.123 Angle : 0.546 9.992 8973 Z= 0.276 Chirality : 0.042 0.158 933 Planarity : 0.004 0.041 1161 Dihedral : 3.605 19.708 855 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 4.03 % Allowed : 12.97 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.30), residues: 785 helix: 1.36 (0.26), residues: 393 sheet: 0.14 (0.69), residues: 48 loop : -0.57 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 161 TYR 0.017 0.001 TYR B 202 PHE 0.014 0.001 PHE B 369 TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 6592) covalent geometry : angle 0.53958 ( 8961) SS BOND : bond 0.00807 ( 6) SS BOND : angle 2.29194 ( 12) hydrogen bonds : bond 0.04379 ( 324) hydrogen bonds : angle 4.43124 ( 909) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8526 (p0) cc_final: 0.8205 (p0) REVERT: A 516 GLU cc_start: 0.8715 (tt0) cc_final: 0.8336 (pt0) REVERT: B 150 GLU cc_start: 0.8395 (tp30) cc_final: 0.8192 (tp30) REVERT: B 154 ASN cc_start: 0.8790 (m-40) cc_final: 0.8471 (m110) REVERT: B 568 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8811 (tt) outliers start: 28 outliers final: 9 residues processed: 147 average time/residue: 0.5053 time to fit residues: 77.9721 Evaluate side-chains 126 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 568 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 31 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 66 optimal weight: 0.0870 chunk 46 optimal weight: 0.4980 chunk 50 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 ASN B 239 HIS B 397 ASN ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.058472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.047694 restraints weight = 15606.338| |-----------------------------------------------------------------------------| r_work (start): 0.2561 rms_B_bonded: 1.69 r_work: 0.2463 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2364 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 6598 Z= 0.165 Angle : 0.610 16.417 8973 Z= 0.308 Chirality : 0.045 0.275 933 Planarity : 0.004 0.043 1161 Dihedral : 4.036 20.641 855 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 4.47 % Allowed : 13.83 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.30), residues: 785 helix: 1.30 (0.26), residues: 400 sheet: 0.49 (0.72), residues: 47 loop : -0.47 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 357 TYR 0.020 0.002 TYR B 385 PHE 0.016 0.002 PHE B 369 TRP 0.008 0.001 TRP B 328 HIS 0.005 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 6592) covalent geometry : angle 0.60462 ( 8961) SS BOND : bond 0.00981 ( 6) SS BOND : angle 2.25658 ( 12) hydrogen bonds : bond 0.04981 ( 324) hydrogen bonds : angle 4.51421 ( 909) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8631 (p0) cc_final: 0.8414 (p0) REVERT: B 150 GLU cc_start: 0.8384 (tp30) cc_final: 0.8149 (tp30) REVERT: B 154 ASN cc_start: 0.8836 (m-40) cc_final: 0.8520 (m110) REVERT: B 163 TRP cc_start: 0.8807 (t60) cc_final: 0.8462 (t-100) REVERT: B 383 MET cc_start: 0.8989 (mtp) cc_final: 0.8777 (mtm) REVERT: B 568 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8774 (tt) outliers start: 31 outliers final: 11 residues processed: 139 average time/residue: 0.5523 time to fit residues: 80.4244 Evaluate side-chains 120 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 568 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 26 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 51 optimal weight: 0.0010 chunk 16 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN B 159 ASN B 250 ASN B 397 ASN B 472 GLN B 493 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.058094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.047148 restraints weight = 15667.954| |-----------------------------------------------------------------------------| r_work (start): 0.2545 rms_B_bonded: 1.69 r_work: 0.2447 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2348 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 6598 Z= 0.166 Angle : 0.625 14.963 8973 Z= 0.312 Chirality : 0.045 0.271 933 Planarity : 0.004 0.043 1161 Dihedral : 4.181 19.831 855 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.60 % Allowed : 15.56 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.30), residues: 785 helix: 1.19 (0.26), residues: 407 sheet: 0.59 (0.68), residues: 57 loop : -0.30 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 357 TYR 0.038 0.002 TYR B 158 PHE 0.015 0.001 PHE B 369 TRP 0.008 0.001 TRP A 436 HIS 0.004 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 6592) covalent geometry : angle 0.62028 ( 8961) SS BOND : bond 0.01077 ( 6) SS BOND : angle 2.21978 ( 12) hydrogen bonds : bond 0.04915 ( 324) hydrogen bonds : angle 4.55895 ( 909) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 154 ASN cc_start: 0.8856 (m-40) cc_final: 0.8578 (m110) REVERT: B 163 TRP cc_start: 0.8813 (t60) cc_final: 0.8528 (t-100) outliers start: 25 outliers final: 11 residues processed: 127 average time/residue: 0.5193 time to fit residues: 68.9148 Evaluate side-chains 123 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 589 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 45 optimal weight: 0.0070 chunk 53 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN B 159 ASN B 472 GLN B 493 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.056822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.045931 restraints weight = 15750.506| |-----------------------------------------------------------------------------| r_work (start): 0.2513 rms_B_bonded: 1.69 r_work: 0.2416 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2318 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 6598 Z= 0.192 Angle : 0.639 13.892 8973 Z= 0.326 Chirality : 0.046 0.267 933 Planarity : 0.005 0.043 1161 Dihedral : 4.351 19.614 855 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.89 % Allowed : 15.71 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.30), residues: 785 helix: 1.21 (0.26), residues: 402 sheet: 0.66 (0.68), residues: 57 loop : -0.36 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 357 TYR 0.041 0.002 TYR B 158 PHE 0.016 0.002 PHE B 369 TRP 0.009 0.002 TRP B 594 HIS 0.005 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 6592) covalent geometry : angle 0.63415 ( 8961) SS BOND : bond 0.01060 ( 6) SS BOND : angle 2.26985 ( 12) hydrogen bonds : bond 0.05237 ( 324) hydrogen bonds : angle 4.64268 ( 909) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 150 GLU cc_start: 0.8360 (tp30) cc_final: 0.8120 (tp30) REVERT: B 154 ASN cc_start: 0.8855 (m-40) cc_final: 0.8571 (m-40) REVERT: B 163 TRP cc_start: 0.8767 (t60) cc_final: 0.8509 (t-100) REVERT: B 568 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8861 (tt) outliers start: 27 outliers final: 14 residues processed: 138 average time/residue: 0.4971 time to fit residues: 71.9604 Evaluate side-chains 129 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 522 GLN Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 589 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN B 325 GLN B 397 ASN ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.056457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.045603 restraints weight = 15811.588| |-----------------------------------------------------------------------------| r_work (start): 0.2505 rms_B_bonded: 1.69 r_work: 0.2406 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2308 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 6598 Z= 0.203 Angle : 0.651 12.448 8973 Z= 0.334 Chirality : 0.046 0.256 933 Planarity : 0.005 0.043 1161 Dihedral : 4.444 19.649 855 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.03 % Allowed : 16.43 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.30), residues: 785 helix: 1.17 (0.26), residues: 400 sheet: 0.67 (0.66), residues: 57 loop : -0.36 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 357 TYR 0.040 0.002 TYR B 158 PHE 0.015 0.002 PHE B 308 TRP 0.010 0.002 TRP B 594 HIS 0.007 0.002 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 6592) covalent geometry : angle 0.64648 ( 8961) SS BOND : bond 0.01009 ( 6) SS BOND : angle 2.24969 ( 12) hydrogen bonds : bond 0.05345 ( 324) hydrogen bonds : angle 4.69249 ( 909) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 150 GLU cc_start: 0.8387 (tp30) cc_final: 0.8115 (tp30) REVERT: B 154 ASN cc_start: 0.8866 (m-40) cc_final: 0.8548 (m-40) REVERT: B 163 TRP cc_start: 0.8782 (t60) cc_final: 0.8528 (t-100) REVERT: B 482 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8709 (mtt180) REVERT: B 568 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8842 (tt) outliers start: 28 outliers final: 14 residues processed: 134 average time/residue: 0.5886 time to fit residues: 82.6223 Evaluate side-chains 127 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 482 ARG Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 589 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 1.9990 chunk 51 optimal weight: 0.0670 chunk 38 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 44 optimal weight: 0.0060 chunk 63 optimal weight: 0.4980 chunk 30 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 ASN B 397 ASN ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.058088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.047083 restraints weight = 15649.459| |-----------------------------------------------------------------------------| r_work (start): 0.2543 rms_B_bonded: 1.71 r_work: 0.2445 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2346 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 6598 Z= 0.149 Angle : 0.618 14.327 8973 Z= 0.314 Chirality : 0.044 0.250 933 Planarity : 0.004 0.043 1161 Dihedral : 4.315 18.180 855 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.75 % Allowed : 16.86 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.30), residues: 785 helix: 1.35 (0.26), residues: 395 sheet: 0.65 (0.69), residues: 53 loop : -0.35 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 192 TYR 0.036 0.002 TYR B 158 PHE 0.013 0.001 PHE B 369 TRP 0.014 0.001 TRP B 168 HIS 0.007 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 6592) covalent geometry : angle 0.61306 ( 8961) SS BOND : bond 0.01063 ( 6) SS BOND : angle 2.16068 ( 12) hydrogen bonds : bond 0.04700 ( 324) hydrogen bonds : angle 4.57275 ( 909) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 ASN cc_start: 0.8754 (OUTLIER) cc_final: 0.8497 (t0) REVERT: A 428 ASP cc_start: 0.8839 (p0) cc_final: 0.8638 (p0) REVERT: B 150 GLU cc_start: 0.8361 (tp30) cc_final: 0.8072 (tp30) REVERT: B 154 ASN cc_start: 0.8805 (m-40) cc_final: 0.8475 (m110) REVERT: B 163 TRP cc_start: 0.8738 (t60) cc_final: 0.8464 (t-100) REVERT: B 176 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8487 (mt) REVERT: B 383 MET cc_start: 0.9033 (mtp) cc_final: 0.8796 (mtm) REVERT: B 568 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8774 (tt) outliers start: 26 outliers final: 11 residues processed: 133 average time/residue: 0.5730 time to fit residues: 79.8602 Evaluate side-chains 131 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 589 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 58 optimal weight: 0.0980 chunk 75 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 0.0010 chunk 59 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 ASN ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.058262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.047331 restraints weight = 15535.446| |-----------------------------------------------------------------------------| r_work (start): 0.2549 rms_B_bonded: 1.65 r_work: 0.2452 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2355 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 6598 Z= 0.148 Angle : 0.624 14.110 8973 Z= 0.316 Chirality : 0.044 0.241 933 Planarity : 0.004 0.043 1161 Dihedral : 4.290 17.961 855 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.88 % Allowed : 18.73 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.30), residues: 785 helix: 1.34 (0.26), residues: 397 sheet: 0.66 (0.70), residues: 53 loop : -0.32 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 357 TYR 0.032 0.002 TYR B 158 PHE 0.013 0.001 PHE B 369 TRP 0.021 0.001 TRP B 168 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 6592) covalent geometry : angle 0.61953 ( 8961) SS BOND : bond 0.01034 ( 6) SS BOND : angle 2.13960 ( 12) hydrogen bonds : bond 0.04677 ( 324) hydrogen bonds : angle 4.52967 ( 909) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 ASN cc_start: 0.8783 (OUTLIER) cc_final: 0.8523 (t0) REVERT: A 428 ASP cc_start: 0.8759 (p0) cc_final: 0.8540 (p0) REVERT: B 149 ASN cc_start: 0.8534 (m-40) cc_final: 0.8306 (m-40) REVERT: B 150 GLU cc_start: 0.8327 (tp30) cc_final: 0.8051 (tp30) REVERT: B 154 ASN cc_start: 0.8663 (m-40) cc_final: 0.8370 (m-40) REVERT: B 163 TRP cc_start: 0.8779 (t60) cc_final: 0.8545 (t-100) REVERT: B 176 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8504 (mt) REVERT: B 383 MET cc_start: 0.9011 (mtp) cc_final: 0.8806 (mtm) REVERT: B 568 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8849 (tt) outliers start: 20 outliers final: 12 residues processed: 129 average time/residue: 0.5470 time to fit residues: 73.9376 Evaluate side-chains 130 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 589 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 61 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 14 optimal weight: 0.2980 chunk 9 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 0.0060 chunk 8 optimal weight: 0.0980 chunk 45 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 ASN B 325 GLN ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.059042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.047991 restraints weight = 15605.589| |-----------------------------------------------------------------------------| r_work (start): 0.2567 rms_B_bonded: 1.72 r_work: 0.2469 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2369 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 6598 Z= 0.138 Angle : 0.621 13.694 8973 Z= 0.315 Chirality : 0.044 0.234 933 Planarity : 0.004 0.043 1161 Dihedral : 4.241 17.744 855 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.88 % Allowed : 18.59 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.30), residues: 785 helix: 1.40 (0.26), residues: 395 sheet: 0.63 (0.70), residues: 53 loop : -0.33 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 357 TYR 0.029 0.001 TYR B 158 PHE 0.013 0.001 PHE B 369 TRP 0.025 0.001 TRP B 168 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 6592) covalent geometry : angle 0.61707 ( 8961) SS BOND : bond 0.00971 ( 6) SS BOND : angle 2.03504 ( 12) hydrogen bonds : bond 0.04490 ( 324) hydrogen bonds : angle 4.47108 ( 909) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 ASN cc_start: 0.8770 (OUTLIER) cc_final: 0.8497 (t0) REVERT: A 428 ASP cc_start: 0.8726 (p0) cc_final: 0.8516 (p0) REVERT: B 176 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8360 (mt) REVERT: B 383 MET cc_start: 0.8985 (mtp) cc_final: 0.8750 (mtm) REVERT: B 568 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8796 (tt) REVERT: B 589 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8524 (tp30) outliers start: 20 outliers final: 10 residues processed: 129 average time/residue: 0.5128 time to fit residues: 69.2657 Evaluate side-chains 130 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 589 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 0.0870 chunk 32 optimal weight: 0.0870 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 64 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN B 325 GLN ** B 472 GLN ** 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 = 0.2838 r_free = 0.2838 target = 0.058423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.047559 restraints weight = 15293.349| |-----------------------------------------------------------------------------| r_work (start): 0.2557 rms_B_bonded: 1.65 r_work: 0.2461 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2364 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 6598 Z= 0.155 Angle : 0.660 13.763 8973 Z= 0.336 Chirality : 0.046 0.294 933 Planarity : 0.004 0.044 1161 Dihedral : 4.329 18.218 855 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.45 % Allowed : 19.60 % Favored : 77.95 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.30), residues: 785 helix: 1.35 (0.26), residues: 395 sheet: 0.66 (0.70), residues: 53 loop : -0.34 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 357 TYR 0.027 0.002 TYR B 158 PHE 0.014 0.001 PHE B 369 TRP 0.034 0.002 TRP B 168 HIS 0.005 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 6592) covalent geometry : angle 0.65643 ( 8961) SS BOND : bond 0.01019 ( 6) SS BOND : angle 2.10443 ( 12) hydrogen bonds : bond 0.04723 ( 324) hydrogen bonds : angle 4.50481 ( 909) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8483 (t0) REVERT: A 428 ASP cc_start: 0.8719 (p0) cc_final: 0.8501 (p0) REVERT: B 152 MET cc_start: 0.8160 (mtp) cc_final: 0.7905 (mtm) REVERT: B 176 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8374 (mt) REVERT: B 325 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.8061 (tm-30) REVERT: B 568 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8853 (tt) outliers start: 17 outliers final: 11 residues processed: 128 average time/residue: 0.5273 time to fit residues: 70.7816 Evaluate side-chains 127 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 325 GLN Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 589 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 35 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 0.0040 chunk 60 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 18 optimal weight: 0.0570 chunk 61 optimal weight: 0.9990 overall best weight: 0.3910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 ASN B 325 GLN ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.058691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.047701 restraints weight = 15555.410| |-----------------------------------------------------------------------------| r_work (start): 0.2561 rms_B_bonded: 1.67 r_work: 0.2465 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2368 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 6598 Z= 0.152 Angle : 0.672 13.573 8973 Z= 0.340 Chirality : 0.045 0.252 933 Planarity : 0.005 0.044 1161 Dihedral : 4.350 19.853 855 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.45 % Allowed : 20.03 % Favored : 77.52 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.30), residues: 785 helix: 1.40 (0.26), residues: 395 sheet: 0.67 (0.70), residues: 53 loop : -0.35 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 357 TYR 0.028 0.001 TYR B 158 PHE 0.014 0.001 PHE B 285 TRP 0.045 0.002 TRP B 168 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 6592) covalent geometry : angle 0.66766 ( 8961) SS BOND : bond 0.00987 ( 6) SS BOND : angle 2.07727 ( 12) hydrogen bonds : bond 0.04607 ( 324) hydrogen bonds : angle 4.51594 ( 909) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2296.30 seconds wall clock time: 39 minutes 49.32 seconds (2389.32 seconds total)