Starting phenix.real_space_refine on Tue Feb 3 16:26:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i8j_52727/02_2026/9i8j_52727.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i8j_52727/02_2026/9i8j_52727.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 { model { file = "/net/cci-nas-00/data/ceres_data/9i8j_52727/02_2026/9i8j_52727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i8j_52727/02_2026/9i8j_52727.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i8j_52727/02_2026/9i8j_52727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i8j_52727/02_2026/9i8j_52727.map" } 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 ------------------------------------------------------------------------------- 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= 0.005 sd= 0.029 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 12 5.16 5 C 3138 2.51 5 N 845 2.21 5 O 963 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 4958 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2481 Classifications: {'peptide': 340} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 310} Chain: "B" Number of atoms: 2477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2477 Classifications: {'peptide': 339} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 309} Time building chain proxies: 1.19, per 1000 atoms: 0.24 Number of scatterers: 4958 At special positions: 0 Unit cell: (77.0307, 75.9457, 92.2198, 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 12 16.00 O 963 8.00 N 845 7.00 C 3138 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: 0.42 Conformation dependent library (CDL) restraints added in 421.0 milliseconds 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1188 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 8 sheets defined 3.5% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 244 through 248 removed outlier: 3.607A pdb=" N VAL A 247 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU A 248 " --> pdb=" O THR A 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 244 through 248' Processing helix chain 'A' and resid 491 through 500 removed outlier: 4.043A pdb=" N LEU A 500 " --> pdb=" O ILE A 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 499 Processing sheet with id=AA1, first strand: chain 'A' and resid 485 through 488 removed outlier: 5.218A pdb=" N PHE A 534 " --> pdb=" O ILE A 461 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 557 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLN A 516 " --> pdb=" O PRO A 555 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 545 through 546 removed outlier: 7.650A pdb=" N ILE A 261 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N VAL A 466 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A 263 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N PHE A 534 " --> pdb=" O ILE A 461 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN A 568 " --> pdb=" O PHE A 523 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 294 through 297 removed outlier: 5.561A pdb=" N PHE A 357 " --> pdb=" O MET A 421 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE A 360 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR A 372 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 11.399A pdb=" N ASN A 362 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 10.874A pdb=" N VAL A 370 " --> pdb=" O ASN A 362 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 294 through 297 removed outlier: 5.561A pdb=" N PHE A 357 " --> pdb=" O MET A 421 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE A 360 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR A 372 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 11.399A pdb=" N ASN A 362 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 10.874A pdb=" N VAL A 370 " --> pdb=" O ASN A 362 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 485 through 488 removed outlier: 5.066A pdb=" N PHE B 534 " --> pdb=" O ILE B 461 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE B 526 " --> pdb=" O TRP B 515 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N GLN B 516 " --> pdb=" O PRO B 555 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR B 518 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL B 553 " --> pdb=" O THR B 518 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 545 through 546 removed outlier: 7.797A pdb=" N ILE B 261 " --> pdb=" O VAL B 466 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL B 466 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY B 263 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N PHE B 534 " --> pdb=" O ILE B 461 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE B 526 " --> pdb=" O TRP B 515 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 294 through 296 removed outlier: 5.714A pdb=" N PHE B 357 " --> pdb=" O MET B 421 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N TRP B 354 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE B 360 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N THR B 372 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 11.914A pdb=" N ASN B 362 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 11.080A pdb=" N VAL B 370 " --> pdb=" O ASN B 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 294 through 296 removed outlier: 5.714A pdb=" N PHE B 357 " --> pdb=" O MET B 421 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N TRP B 354 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE B 360 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N THR B 372 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 11.914A pdb=" N ASN B 362 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 11.080A pdb=" N VAL B 370 " --> pdb=" O ASN B 362 " (cutoff:3.500A) 154 hydrogen bonds defined for protein. 414 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: 0.74 Time building geometry restraints manager: 0.59 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: 1591 1.34 - 1.46: 1101 1.46 - 1.58: 2384 1.58 - 1.70: 0 1.70 - 1.82: 22 Bond restraints: 5098 Sorted by residual: bond pdb=" N ASN B 481 " pdb=" CA ASN B 481 " ideal model delta sigma weight residual 1.457 1.502 -0.045 1.29e-02 6.01e+03 1.22e+01 bond pdb=" N ILE B 434 " pdb=" CA ILE B 434 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.25e-02 6.40e+03 1.17e+01 bond pdb=" N LEU A 492 " pdb=" CA LEU A 492 " ideal model delta sigma weight residual 1.462 1.489 -0.027 8.50e-03 1.38e+04 1.02e+01 bond pdb=" N ASP B 294 " pdb=" CA ASP B 294 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.16e-02 7.43e+03 8.97e+00 bond pdb=" N ILE B 295 " pdb=" CA ILE B 295 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.24e-02 6.50e+03 8.04e+00 ... (remaining 5093 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 6748 2.56 - 5.11: 213 5.11 - 7.67: 30 7.67 - 10.23: 8 10.23 - 12.78: 6 Bond angle restraints: 7005 Sorted by residual: angle pdb=" CA THR B 245 " pdb=" C THR B 245 " pdb=" N PRO B 246 " ideal model delta sigma weight residual 118.44 124.71 -6.27 1.59e+00 3.96e-01 1.56e+01 angle pdb=" N THR B 245 " pdb=" CA THR B 245 " pdb=" C THR B 245 " ideal model delta sigma weight residual 109.81 118.39 -8.58 2.21e+00 2.05e-01 1.51e+01 angle pdb=" C SER A 288 " pdb=" N SER A 289 " pdb=" CA SER A 289 " ideal model delta sigma weight residual 120.51 126.14 -5.63 1.45e+00 4.76e-01 1.51e+01 angle pdb=" C ALA A 480 " pdb=" N ASN A 481 " pdb=" CA ASN A 481 " ideal model delta sigma weight residual 121.54 128.92 -7.38 1.91e+00 2.74e-01 1.49e+01 angle pdb=" C LYS A 232 " pdb=" N THR A 233 " pdb=" CA THR A 233 " ideal model delta sigma weight residual 121.54 128.86 -7.32 1.91e+00 2.74e-01 1.47e+01 ... (remaining 7000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 2533 17.74 - 35.49: 307 35.49 - 53.23: 63 53.23 - 70.97: 20 70.97 - 88.71: 10 Dihedral angle restraints: 2933 sinusoidal: 1048 harmonic: 1885 Sorted by residual: dihedral pdb=" CA LEU B 280 " pdb=" C LEU B 280 " pdb=" N ASN B 281 " pdb=" CA ASN B 281 " ideal model delta harmonic sigma weight residual 180.00 159.60 20.40 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA ALA A 293 " pdb=" C ALA A 293 " pdb=" N ASP A 294 " pdb=" CA ASP A 294 " ideal model delta harmonic sigma weight residual -180.00 -161.23 -18.77 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA GLY A 263 " pdb=" C GLY A 263 " pdb=" N LEU A 264 " pdb=" CA LEU A 264 " ideal model delta harmonic sigma weight residual 180.00 161.30 18.70 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 2930 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 543 0.053 - 0.106: 167 0.106 - 0.159: 59 0.159 - 0.211: 10 0.211 - 0.264: 9 Chirality restraints: 788 Sorted by residual: chirality pdb=" CG LEU A 547 " pdb=" CB LEU A 547 " pdb=" CD1 LEU A 547 " pdb=" CD2 LEU A 547 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA THR B 245 " pdb=" N THR B 245 " pdb=" C THR B 245 " pdb=" CB THR B 245 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CG LEU B 418 " pdb=" CB LEU B 418 " pdb=" CD1 LEU B 418 " pdb=" CD2 LEU B 418 " both_signs ideal model delta sigma weight residual False -2.59 -2.84 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 785 not shown) Planarity restraints: 931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 439 " -0.051 5.00e-02 4.00e+02 7.72e-02 9.54e+00 pdb=" N PRO A 440 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 440 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 440 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 267 " 0.016 2.00e-02 2.50e+03 3.07e-02 9.40e+00 pdb=" C VAL A 267 " -0.053 2.00e-02 2.50e+03 pdb=" O VAL A 267 " 0.020 2.00e-02 2.50e+03 pdb=" N PRO A 268 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 439 " 0.050 5.00e-02 4.00e+02 7.55e-02 9.13e+00 pdb=" N PRO B 440 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO B 440 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 440 " 0.042 5.00e-02 4.00e+02 ... (remaining 928 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 2506 3.02 - 3.49: 4717 3.49 - 3.96: 7516 3.96 - 4.43: 8201 4.43 - 4.90: 14388 Nonbonded interactions: 37328 Sorted by model distance: nonbonded pdb=" N THR A 435 " pdb=" O THR A 435 " model vdw 2.554 2.496 nonbonded pdb=" O LEU A 492 " pdb=" N THR A 495 " model vdw 2.597 3.120 nonbonded pdb=" N SER A 430 " pdb=" O SER A 430 " model vdw 2.597 2.496 nonbonded pdb=" N VAL B 234 " pdb=" O VAL B 234 " model vdw 2.615 2.496 nonbonded pdb=" N THR A 428 " pdb=" OG1 THR A 428 " model vdw 2.624 2.496 ... (remaining 37323 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 232 through 570) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.000 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.680 Find NCS groups from input model: 0.080 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:8.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 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 : 0.006 0.063 5098 Z= 0.331 Angle : 1.097 12.784 7005 Z= 0.589 Chirality : 0.063 0.264 788 Planarity : 0.009 0.077 931 Dihedral : 17.298 88.714 1745 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.33 % Favored : 90.37 % Rotamer: Outliers : 6.82 % Allowed : 26.52 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -3.57 (0.27), residues: 675 helix: -1.64 (1.01), residues: 18 sheet: -1.62 (0.40), residues: 147 loop : -2.88 (0.23), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 442 TYR 0.017 0.001 TYR B 304 PHE 0.036 0.002 PHE A 380 TRP 0.023 0.003 TRP A 287 HIS 0.002 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00581 ( 5098) covalent geometry : angle 1.09689 ( 7005) hydrogen bonds : bond 0.18585 ( 116) hydrogen bonds : angle 8.24408 ( 414) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 76 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 SER cc_start: 0.7259 (p) cc_final: 0.6938 (t) REVERT: A 326 ASN cc_start: 0.6555 (t0) cc_final: 0.6281 (t0) REVERT: A 360 ILE cc_start: 0.5993 (OUTLIER) cc_final: 0.5740 (mp) REVERT: A 382 THR cc_start: 0.6859 (OUTLIER) cc_final: 0.6399 (p) REVERT: A 398 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.7041 (pt0) outliers start: 36 outliers final: 22 residues processed: 101 average time/residue: 0.3032 time to fit residues: 32.7989 Evaluate side-chains 99 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 257 TRP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 402 LYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 550 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 50.0000 chunk 62 optimal weight: 50.0000 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 ASN A 516 GLN B 345 ASN B 369 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.217709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.181398 restraints weight = 6159.104| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 2.57 r_work: 0.4011 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 5098 Z= 0.317 Angle : 0.795 9.295 7005 Z= 0.401 Chirality : 0.049 0.187 788 Planarity : 0.007 0.066 931 Dihedral : 9.626 59.971 762 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.22 % Favored : 89.63 % Rotamer: Outliers : 10.98 % Allowed : 21.78 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -3.42 (0.28), residues: 675 helix: -1.57 (0.94), residues: 24 sheet: -1.16 (0.42), residues: 149 loop : -2.91 (0.23), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 276 TYR 0.015 0.002 TYR B 376 PHE 0.030 0.002 PHE A 512 TRP 0.020 0.003 TRP A 287 HIS 0.006 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00767 ( 5098) covalent geometry : angle 0.79518 ( 7005) hydrogen bonds : bond 0.04875 ( 116) hydrogen bonds : angle 6.17026 ( 414) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 78 time to evaluate : 0.110 Fit side-chains revert: symmetry clash REVERT: A 326 ASN cc_start: 0.6141 (t0) cc_final: 0.5889 (t0) REVERT: A 515 TRP cc_start: 0.8473 (m-90) cc_final: 0.8217 (m-90) REVERT: B 294 ASP cc_start: 0.6852 (p0) cc_final: 0.6522 (p0) REVERT: B 372 THR cc_start: 0.4045 (OUTLIER) cc_final: 0.3144 (p) REVERT: B 442 ARG cc_start: 0.6645 (OUTLIER) cc_final: 0.6202 (mmm160) outliers start: 58 outliers final: 35 residues processed: 119 average time/residue: 0.3048 time to fit residues: 38.8817 Evaluate side-chains 116 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 79 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 402 LYS Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 257 TRP Chi-restraints excluded: chain B residue 298 ARG Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 507 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 58 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 chunk 49 optimal weight: 30.0000 chunk 34 optimal weight: 50.0000 chunk 59 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN A 393 ASN A 502 ASN B 281 ASN B 311 ASN B 345 ASN B 369 ASN B 393 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.220179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.185162 restraints weight = 5937.113| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 2.44 r_work: 0.4038 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3870 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 5098 Z= 0.274 Angle : 0.763 9.298 7005 Z= 0.380 Chirality : 0.047 0.182 788 Planarity : 0.006 0.063 931 Dihedral : 9.136 59.683 748 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.96 % Favored : 88.89 % Rotamer: Outliers : 10.23 % Allowed : 23.30 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -3.36 (0.28), residues: 675 helix: -0.83 (1.09), residues: 24 sheet: -1.10 (0.43), residues: 142 loop : -2.89 (0.23), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 276 TYR 0.013 0.002 TYR A 485 PHE 0.025 0.002 PHE A 512 TRP 0.018 0.003 TRP A 287 HIS 0.004 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00671 ( 5098) covalent geometry : angle 0.76297 ( 7005) hydrogen bonds : bond 0.04434 ( 116) hydrogen bonds : angle 5.88435 ( 414) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 78 time to evaluate : 0.127 Fit side-chains REVERT: A 504 SER cc_start: 0.7767 (p) cc_final: 0.7520 (m) REVERT: A 515 TRP cc_start: 0.8455 (m-90) cc_final: 0.8218 (m-90) REVERT: A 516 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7015 (tm-30) REVERT: A 565 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7391 (mt) REVERT: B 294 ASP cc_start: 0.7114 (p0) cc_final: 0.6808 (p0) REVERT: B 326 ASN cc_start: 0.7955 (t0) cc_final: 0.7605 (t0) outliers start: 54 outliers final: 33 residues processed: 119 average time/residue: 0.3007 time to fit residues: 38.4670 Evaluate side-chains 114 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 79 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 257 TRP Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 494 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 34 optimal weight: 50.0000 chunk 37 optimal weight: 5.9990 chunk 64 optimal weight: 40.0000 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN B 311 ASN B 345 ASN B 369 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.218445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.182978 restraints weight = 6020.734| |-----------------------------------------------------------------------------| r_work (start): 0.4158 rms_B_bonded: 2.54 r_work: 0.4057 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5098 Z= 0.222 Angle : 0.718 8.754 7005 Z= 0.355 Chirality : 0.046 0.178 788 Planarity : 0.006 0.059 931 Dihedral : 8.375 58.743 741 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.81 % Favored : 88.89 % Rotamer: Outliers : 10.80 % Allowed : 23.86 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -3.14 (0.29), residues: 675 helix: -0.52 (1.09), residues: 25 sheet: -0.89 (0.43), residues: 148 loop : -2.79 (0.23), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 442 TYR 0.011 0.002 TYR A 485 PHE 0.023 0.002 PHE A 512 TRP 0.017 0.002 TRP A 287 HIS 0.003 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 5098) covalent geometry : angle 0.71827 ( 7005) hydrogen bonds : bond 0.04018 ( 116) hydrogen bonds : angle 5.65256 ( 414) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 76 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 317 TYR cc_start: 0.6544 (OUTLIER) cc_final: 0.6086 (p90) REVERT: A 504 SER cc_start: 0.7533 (p) cc_final: 0.7314 (m) REVERT: A 516 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.6896 (tm-30) REVERT: B 294 ASP cc_start: 0.6782 (p0) cc_final: 0.6458 (p0) REVERT: B 326 ASN cc_start: 0.7832 (t0) cc_final: 0.7487 (t0) REVERT: B 466 VAL cc_start: 0.7770 (p) cc_final: 0.7512 (t) outliers start: 57 outliers final: 34 residues processed: 118 average time/residue: 0.2947 time to fit residues: 37.3748 Evaluate side-chains 111 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 75 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 257 TRP Chi-restraints excluded: chain B residue 298 ARG Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 5 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 65 optimal weight: 50.0000 chunk 49 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 1 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN A 502 ASN B 311 ASN B 345 ASN B 369 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.220816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.185814 restraints weight = 6119.255| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 2.58 r_work: 0.4074 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5098 Z= 0.144 Angle : 0.678 8.266 7005 Z= 0.326 Chirality : 0.044 0.168 788 Planarity : 0.006 0.057 931 Dihedral : 7.518 58.502 735 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.07 % Favored : 89.63 % Rotamer: Outliers : 9.09 % Allowed : 25.95 % Favored : 64.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -2.87 (0.29), residues: 675 helix: 1.14 (1.31), residues: 19 sheet: -0.66 (0.43), residues: 150 loop : -2.66 (0.24), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 299 TYR 0.008 0.001 TYR A 485 PHE 0.021 0.001 PHE A 512 TRP 0.016 0.001 TRP A 287 HIS 0.002 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 5098) covalent geometry : angle 0.67770 ( 7005) hydrogen bonds : bond 0.03395 ( 116) hydrogen bonds : angle 5.32266 ( 414) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 74 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: A 339 MET cc_start: 0.6340 (mpp) cc_final: 0.6110 (mpp) REVERT: A 504 SER cc_start: 0.7482 (p) cc_final: 0.7273 (m) REVERT: B 294 ASP cc_start: 0.6608 (p0) cc_final: 0.6267 (p0) REVERT: B 326 ASN cc_start: 0.7772 (t0) cc_final: 0.7467 (t0) REVERT: B 338 ASP cc_start: 0.6945 (p0) cc_final: 0.6572 (p0) REVERT: B 372 THR cc_start: 0.4372 (OUTLIER) cc_final: 0.3405 (p) REVERT: B 466 VAL cc_start: 0.7728 (p) cc_final: 0.7495 (t) outliers start: 48 outliers final: 33 residues processed: 110 average time/residue: 0.2500 time to fit residues: 29.6852 Evaluate side-chains 110 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 76 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 257 TRP Chi-restraints excluded: chain B residue 298 ARG Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 507 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 64 optimal weight: 30.0000 chunk 60 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 61 optimal weight: 40.0000 chunk 8 optimal weight: 7.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 369 ASN A 502 ASN A 516 GLN B 311 ASN B 345 ASN B 369 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.218203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.182547 restraints weight = 6203.673| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 2.58 r_work: 0.4031 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5098 Z= 0.215 Angle : 0.720 8.868 7005 Z= 0.351 Chirality : 0.046 0.190 788 Planarity : 0.006 0.056 931 Dihedral : 7.771 59.290 735 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.41 % Favored : 88.30 % Rotamer: Outliers : 10.42 % Allowed : 25.19 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -2.92 (0.29), residues: 675 helix: -0.33 (1.10), residues: 25 sheet: -0.76 (0.43), residues: 148 loop : -2.62 (0.24), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 469 TYR 0.010 0.001 TYR A 485 PHE 0.024 0.002 PHE A 512 TRP 0.021 0.002 TRP A 287 HIS 0.003 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00528 ( 5098) covalent geometry : angle 0.72041 ( 7005) hydrogen bonds : bond 0.03969 ( 116) hydrogen bonds : angle 5.49444 ( 414) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 73 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: A 317 TYR cc_start: 0.6570 (OUTLIER) cc_final: 0.6176 (p90) REVERT: A 339 MET cc_start: 0.6430 (mpp) cc_final: 0.6212 (mpp) REVERT: A 504 SER cc_start: 0.7510 (p) cc_final: 0.7294 (m) REVERT: B 294 ASP cc_start: 0.6706 (p0) cc_final: 0.6358 (p0) REVERT: B 326 ASN cc_start: 0.7848 (t0) cc_final: 0.7523 (t0) REVERT: B 338 ASP cc_start: 0.7058 (p0) cc_final: 0.6643 (p0) REVERT: B 466 VAL cc_start: 0.7733 (p) cc_final: 0.7515 (t) outliers start: 55 outliers final: 44 residues processed: 115 average time/residue: 0.2438 time to fit residues: 29.9886 Evaluate side-chains 118 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 73 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 257 TRP Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 298 ARG Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 507 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 65 optimal weight: 50.0000 chunk 50 optimal weight: 20.0000 chunk 57 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 9 optimal weight: 0.4980 chunk 37 optimal weight: 7.9990 chunk 61 optimal weight: 30.0000 chunk 54 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 22 optimal weight: 0.7980 chunk 63 optimal weight: 50.0000 overall best weight: 4.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN A 502 ASN A 516 GLN B 311 ASN B 345 ASN B 369 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.218139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.183207 restraints weight = 6077.352| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 2.48 r_work: 0.4044 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5098 Z= 0.204 Angle : 0.714 9.545 7005 Z= 0.348 Chirality : 0.045 0.179 788 Planarity : 0.006 0.057 931 Dihedral : 7.738 59.564 735 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.26 % Favored : 88.44 % Rotamer: Outliers : 10.80 % Allowed : 25.76 % Favored : 63.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -2.90 (0.30), residues: 675 helix: -0.29 (1.11), residues: 25 sheet: -0.81 (0.43), residues: 148 loop : -2.58 (0.24), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 276 TYR 0.009 0.001 TYR A 485 PHE 0.024 0.002 PHE A 512 TRP 0.022 0.002 TRP A 287 HIS 0.003 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 5098) covalent geometry : angle 0.71388 ( 7005) hydrogen bonds : bond 0.03835 ( 116) hydrogen bonds : angle 5.45553 ( 414) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 72 time to evaluate : 0.106 Fit side-chains revert: symmetry clash REVERT: A 339 MET cc_start: 0.6363 (mpp) cc_final: 0.6158 (mpp) REVERT: A 504 SER cc_start: 0.7498 (p) cc_final: 0.7281 (m) REVERT: B 294 ASP cc_start: 0.6668 (p0) cc_final: 0.6314 (p0) REVERT: B 326 ASN cc_start: 0.7894 (t0) cc_final: 0.7569 (t0) REVERT: B 338 ASP cc_start: 0.7084 (p0) cc_final: 0.6600 (p0) REVERT: B 466 VAL cc_start: 0.7736 (p) cc_final: 0.7507 (t) outliers start: 57 outliers final: 45 residues processed: 115 average time/residue: 0.2281 time to fit residues: 28.3262 Evaluate side-chains 118 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 73 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 257 TRP Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 298 ARG Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 507 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 11 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 46 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 3 optimal weight: 0.0060 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 ASN A 516 GLN B 260 GLN B 311 ASN B 345 ASN B 369 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.224845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.190903 restraints weight = 6030.253| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 2.45 r_work: 0.4100 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3935 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5098 Z= 0.111 Angle : 0.663 10.064 7005 Z= 0.313 Chirality : 0.044 0.164 788 Planarity : 0.005 0.054 931 Dihedral : 7.148 59.884 735 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.33 % Favored : 90.37 % Rotamer: Outliers : 7.20 % Allowed : 29.36 % Favored : 63.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -2.67 (0.30), residues: 675 helix: 1.38 (1.33), residues: 19 sheet: -0.90 (0.42), residues: 159 loop : -2.39 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 299 TYR 0.008 0.001 TYR A 436 PHE 0.017 0.001 PHE A 512 TRP 0.024 0.001 TRP A 287 HIS 0.002 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 5098) covalent geometry : angle 0.66311 ( 7005) hydrogen bonds : bond 0.02928 ( 116) hydrogen bonds : angle 5.04858 ( 414) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 73 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: A 504 SER cc_start: 0.7642 (p) cc_final: 0.7426 (m) REVERT: B 326 ASN cc_start: 0.7814 (t0) cc_final: 0.7533 (t0) REVERT: B 338 ASP cc_start: 0.6777 (p0) cc_final: 0.6487 (p0) REVERT: B 372 THR cc_start: 0.4519 (OUTLIER) cc_final: 0.3472 (p) outliers start: 38 outliers final: 24 residues processed: 102 average time/residue: 0.2686 time to fit residues: 29.4952 Evaluate side-chains 97 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 257 TRP Chi-restraints excluded: chain B residue 298 ARG Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 507 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 11 optimal weight: 10.0000 chunk 44 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 55 optimal weight: 40.0000 chunk 34 optimal weight: 40.0000 chunk 52 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 49 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 GLN B 311 ASN B 345 ASN B 369 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.220273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.185051 restraints weight = 6125.320| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 2.57 r_work: 0.4061 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5098 Z= 0.156 Angle : 0.689 9.872 7005 Z= 0.329 Chirality : 0.045 0.172 788 Planarity : 0.005 0.055 931 Dihedral : 7.235 59.783 734 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.78 % Favored : 89.93 % Rotamer: Outliers : 7.20 % Allowed : 29.92 % Favored : 62.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -2.61 (0.31), residues: 675 helix: 1.43 (1.33), residues: 19 sheet: -0.89 (0.41), residues: 161 loop : -2.35 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 469 TYR 0.010 0.001 TYR B 405 PHE 0.026 0.002 PHE A 512 TRP 0.026 0.002 TRP A 287 HIS 0.003 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 5098) covalent geometry : angle 0.68899 ( 7005) hydrogen bonds : bond 0.03285 ( 116) hydrogen bonds : angle 5.17776 ( 414) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 74 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: A 504 SER cc_start: 0.7494 (p) cc_final: 0.7276 (m) REVERT: A 523 PHE cc_start: 0.8199 (p90) cc_final: 0.7993 (p90) REVERT: B 326 ASN cc_start: 0.7787 (t0) cc_final: 0.7451 (t0) REVERT: B 338 ASP cc_start: 0.6638 (p0) cc_final: 0.6373 (p0) REVERT: B 405 TYR cc_start: 0.6223 (m-10) cc_final: 0.5940 (m-80) outliers start: 38 outliers final: 30 residues processed: 102 average time/residue: 0.3004 time to fit residues: 32.8402 Evaluate side-chains 103 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 73 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 257 TRP Chi-restraints excluded: chain B residue 298 ARG Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 402 LYS Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 507 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 17 optimal weight: 30.0000 chunk 18 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 35 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 65 optimal weight: 50.0000 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN A 502 ASN A 516 GLN B 260 GLN B 311 ASN B 345 ASN B 369 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.219610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.184547 restraints weight = 6090.163| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 2.53 r_work: 0.4056 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5098 Z= 0.173 Angle : 0.710 10.567 7005 Z= 0.341 Chirality : 0.045 0.215 788 Planarity : 0.005 0.055 931 Dihedral : 7.430 58.643 734 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.37 % Favored : 89.33 % Rotamer: Outliers : 7.20 % Allowed : 29.55 % Favored : 63.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -2.62 (0.30), residues: 675 helix: 1.54 (1.33), residues: 19 sheet: -0.79 (0.42), residues: 151 loop : -2.38 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 469 TYR 0.008 0.001 TYR B 376 PHE 0.027 0.002 PHE A 512 TRP 0.030 0.002 TRP A 287 HIS 0.003 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 5098) covalent geometry : angle 0.71016 ( 7005) hydrogen bonds : bond 0.03516 ( 116) hydrogen bonds : angle 5.25842 ( 414) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 75 time to evaluate : 0.175 Fit side-chains revert: symmetry clash REVERT: A 504 SER cc_start: 0.7449 (p) cc_final: 0.7241 (m) REVERT: A 523 PHE cc_start: 0.8222 (p90) cc_final: 0.7961 (p90) REVERT: B 294 ASP cc_start: 0.6517 (p0) cc_final: 0.6161 (p0) REVERT: B 326 ASN cc_start: 0.7815 (t0) cc_final: 0.7498 (t0) REVERT: B 338 ASP cc_start: 0.6726 (p0) cc_final: 0.6427 (p0) REVERT: B 405 TYR cc_start: 0.6248 (m-10) cc_final: 0.6005 (m-10) REVERT: B 442 ARG cc_start: 0.6591 (OUTLIER) cc_final: 0.6074 (mmm160) outliers start: 38 outliers final: 31 residues processed: 103 average time/residue: 0.2465 time to fit residues: 27.2372 Evaluate side-chains 107 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 75 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 257 TRP Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 257 TRP Chi-restraints excluded: chain B residue 298 ARG Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 402 LYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 507 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 55 optimal weight: 50.0000 chunk 14 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 66 optimal weight: 50.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN A 502 ASN A 516 GLN B 311 ASN B 345 ASN B 369 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.220230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.185253 restraints weight = 6185.872| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 2.54 r_work: 0.4098 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5098 Z= 0.144 Angle : 0.704 10.647 7005 Z= 0.331 Chirality : 0.045 0.191 788 Planarity : 0.005 0.054 931 Dihedral : 7.283 58.655 734 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.52 % Favored : 89.19 % Rotamer: Outliers : 7.01 % Allowed : 29.73 % Favored : 63.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -2.58 (0.30), residues: 675 helix: 1.65 (1.33), residues: 19 sheet: -0.87 (0.41), residues: 161 loop : -2.34 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 469 TYR 0.007 0.001 TYR A 485 PHE 0.025 0.001 PHE A 512 TRP 0.027 0.002 TRP A 287 HIS 0.002 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 5098) covalent geometry : angle 0.70384 ( 7005) hydrogen bonds : bond 0.03233 ( 116) hydrogen bonds : angle 5.12036 ( 414) =============================================================================== Job complete usr+sys time: 1534.88 seconds wall clock time: 26 minutes 57.08 seconds (1617.08 seconds total)