Starting phenix.real_space_refine on Fri Sep 11 03:09:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6l47_0831/09_2026/6l47_0831.cif Found real_map, /net/cci-nas-00/data/ceres_data/6l47_0831/09_2026/6l47_0831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6l47_0831/09_2026/6l47_0831.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6l47_0831/09_2026/6l47_0831.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6l47_0831/09_2026/6l47_0831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6l47_0831/09_2026/6l47_0831.map" model { file = "/net/cci-nas-00/data/ceres_data/6l47_0831/09_2026/6l47_0831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6l47_0831/09_2026/6l47_0831.cif" } resolution = 3.5 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= 0.015 sd= 0.713 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 38 5.16 5 C 4796 2.51 5 N 1066 2.21 5 O 1100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7000 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3444 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 19, 'TRANS': 396} Chain breaks: 2 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 5, 'GLU:plan': 2, 'PHE:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 1, 'E5L': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 2.73, per 1000 atoms: 0.39 Number of scatterers: 7000 At special positions: 0 Unit cell: (141.075, 86.735, 76.285, 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 38 16.00 O 1100 8.00 N 1066 7.00 C 4796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 516 " distance=2.06 Simple disulfide: pdb=" SG CYS A 528 " - pdb=" SG CYS A 548 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 516 " distance=2.06 Simple disulfide: pdb=" SG CYS B 528 " - pdb=" SG CYS B 548 " 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: 0.78 Conformation dependent library (CDL) restraints added in 343.0 milliseconds 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1604 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 76.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 135 through 165 Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 180 through 213 Proline residue: A 199 - end of helix removed outlier: 4.092A pdb=" N SER A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 247 removed outlier: 3.870A pdb=" N GLY A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.637A pdb=" N VAL A 243 " --> pdb=" O PRO A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 285 removed outlier: 3.676A pdb=" N PHE A 254 " --> pdb=" O PRO A 250 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Proline residue: A 276 - end of helix Processing helix chain 'A' and resid 293 through 301 removed outlier: 3.573A pdb=" N TYR A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 346 removed outlier: 3.658A pdb=" N PHE A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 369 Processing helix chain 'A' and resid 369 through 395 Processing helix chain 'A' and resid 412 through 419 Processing helix chain 'A' and resid 421 through 439 Processing helix chain 'A' and resid 446 through 467 removed outlier: 4.618A pdb=" N LEU A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N CYS A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 487 Processing helix chain 'A' and resid 498 through 528 removed outlier: 3.642A pdb=" N CYS A 528 " --> pdb=" O ALA A 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 133 Processing helix chain 'B' and resid 135 through 165 Processing helix chain 'B' and resid 172 through 178 Processing helix chain 'B' and resid 180 through 213 Proline residue: B 199 - end of helix removed outlier: 4.092A pdb=" N SER B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 247 removed outlier: 3.870A pdb=" N GLY B 238 " --> pdb=" O VAL B 234 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.636A pdb=" N VAL B 243 " --> pdb=" O PRO B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 285 removed outlier: 3.675A pdb=" N PHE B 254 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE B 256 " --> pdb=" O SER B 252 " (cutoff:3.500A) Proline residue: B 276 - end of helix Processing helix chain 'B' and resid 293 through 301 removed outlier: 3.573A pdb=" N TYR B 297 " --> pdb=" O THR B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 346 removed outlier: 3.658A pdb=" N PHE B 335 " --> pdb=" O PHE B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 369 Processing helix chain 'B' and resid 369 through 395 Processing helix chain 'B' and resid 412 through 419 Processing helix chain 'B' and resid 421 through 439 Processing helix chain 'B' and resid 446 through 467 removed outlier: 4.618A pdb=" N LEU B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL B 452 " --> pdb=" O ALA B 448 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N CYS B 467 " --> pdb=" O ALA B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 487 Processing helix chain 'B' and resid 498 through 528 removed outlier: 3.642A pdb=" N CYS B 528 " --> pdb=" O ALA B 524 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1428 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: 0.98 Time building geometry restraints manager: 0.96 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: 1940 1.34 - 1.46: 2208 1.46 - 1.58: 3064 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 7272 Sorted by residual: bond pdb=" C E5L A1001 " pdb=" C2 E5L A1001 " ideal model delta sigma weight residual 1.394 1.482 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C E5L B1001 " pdb=" C2 E5L B1001 " ideal model delta sigma weight residual 1.394 1.482 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C E5L B1001 " pdb=" C1 E5L B1001 " ideal model delta sigma weight residual 1.399 1.485 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C E5L A1001 " pdb=" C1 E5L A1001 " ideal model delta sigma weight residual 1.399 1.485 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" N E5L A1001 " pdb=" C E5L A1001 " ideal model delta sigma weight residual 1.407 1.353 0.054 2.00e-02 2.50e+03 7.34e+00 ... (remaining 7267 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 9603 1.80 - 3.59: 249 3.59 - 5.39: 66 5.39 - 7.18: 14 7.18 - 8.98: 2 Bond angle restraints: 9934 Sorted by residual: angle pdb=" C HIS A 386 " pdb=" N CYS A 387 " pdb=" CA CYS A 387 " ideal model delta sigma weight residual 120.68 115.11 5.57 1.70e+00 3.46e-01 1.07e+01 angle pdb=" C HIS B 386 " pdb=" N CYS B 387 " pdb=" CA CYS B 387 " ideal model delta sigma weight residual 120.68 115.11 5.57 1.70e+00 3.46e-01 1.07e+01 angle pdb=" C17 CLR B1002 " pdb=" C20 CLR B1002 " pdb=" C21 CLR B1002 " ideal model delta sigma weight residual 113.17 104.19 8.98 3.00e+00 1.11e-01 8.96e+00 angle pdb=" C17 CLR A1002 " pdb=" C20 CLR A1002 " pdb=" C21 CLR A1002 " ideal model delta sigma weight residual 113.17 104.22 8.95 3.00e+00 1.11e-01 8.91e+00 angle pdb=" N VAL A 198 " pdb=" CA VAL A 198 " pdb=" C VAL A 198 " ideal model delta sigma weight residual 108.88 114.15 -5.27 2.16e+00 2.14e-01 5.95e+00 ... (remaining 9929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.43: 3577 14.43 - 28.86: 361 28.86 - 43.29: 96 43.29 - 57.72: 16 57.72 - 72.15: 4 Dihedral angle restraints: 4054 sinusoidal: 1568 harmonic: 2486 Sorted by residual: dihedral pdb=" CA ARG A 309 " pdb=" C ARG A 309 " pdb=" N ASP A 310 " pdb=" CA ASP A 310 " ideal model delta harmonic sigma weight residual 180.00 -158.38 -21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA ARG B 309 " pdb=" C ARG B 309 " pdb=" N ASP B 310 " pdb=" CA ASP B 310 " ideal model delta harmonic sigma weight residual -180.00 -158.40 -21.60 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA LYS A 212 " pdb=" C LYS A 212 " pdb=" N SER A 213 " pdb=" CA SER A 213 " ideal model delta harmonic sigma weight residual -180.00 -159.15 -20.85 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 4051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 890 0.057 - 0.115: 164 0.115 - 0.172: 12 0.172 - 0.230: 2 0.230 - 0.287: 2 Chirality restraints: 1070 Sorted by residual: chirality pdb=" C17 CLR A1002 " pdb=" C13 CLR A1002 " pdb=" C16 CLR A1002 " pdb=" C20 CLR A1002 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C17 CLR B1002 " pdb=" C13 CLR B1002 " pdb=" C16 CLR B1002 " pdb=" C20 CLR B1002 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C20 CLR A1002 " pdb=" C17 CLR A1002 " pdb=" C21 CLR A1002 " pdb=" C22 CLR A1002 " both_signs ideal model delta sigma weight residual False 2.59 2.81 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1067 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N E5L A1001 " 0.201 2.00e-02 2.50e+03 1.26e-01 2.00e+02 pdb=" C E5L A1001 " -0.158 2.00e-02 2.50e+03 pdb=" C3 E5L A1001 " 0.045 2.00e-02 2.50e+03 pdb=" C4 E5L A1001 " -0.110 2.00e-02 2.50e+03 pdb=" O3 E5L A1001 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N E5L B1001 " -0.201 2.00e-02 2.50e+03 1.26e-01 2.00e+02 pdb=" C E5L B1001 " 0.157 2.00e-02 2.50e+03 pdb=" C3 E5L B1001 " -0.046 2.00e-02 2.50e+03 pdb=" C4 E5L B1001 " 0.110 2.00e-02 2.50e+03 pdb=" O3 E5L B1001 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 385 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.67e+00 pdb=" C LEU B 385 " 0.045 2.00e-02 2.50e+03 pdb=" O LEU B 385 " -0.017 2.00e-02 2.50e+03 pdb=" N HIS B 386 " -0.015 2.00e-02 2.50e+03 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1864 2.79 - 3.32: 6882 3.32 - 3.85: 11886 3.85 - 4.37: 12772 4.37 - 4.90: 21603 Nonbonded interactions: 55007 Sorted by model distance: nonbonded pdb=" OE1 GLU B 284 " pdb=" OG SER B 286 " model vdw 2.266 3.040 nonbonded pdb=" OE1 GLU A 284 " pdb=" OG SER A 286 " model vdw 2.266 3.040 nonbonded pdb=" O THR B 419 " pdb=" OG1 THR B 419 " model vdw 2.279 3.040 nonbonded pdb=" O THR A 419 " pdb=" OG1 THR A 419 " model vdw 2.279 3.040 nonbonded pdb=" OH TYR B 299 " pdb=" O LEU B 396 " model vdw 2.370 3.040 ... (remaining 55002 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' 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 group one per residue 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: 0.670 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.920 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 7276 Z= 0.212 Angle : 0.763 8.981 9942 Z= 0.388 Chirality : 0.045 0.287 1070 Planarity : 0.008 0.126 1180 Dihedral : 12.665 72.148 2438 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 3.34 % Allowed : 10.58 % Favored : 86.07 % 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: -3.09 (0.26), residues: 820 helix: -1.17 (0.19), residues: 586 sheet: None (None), residues: 0 loop : -4.15 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 418 TYR 0.016 0.002 TYR A 308 PHE 0.020 0.002 PHE B 230 TRP 0.011 0.001 TRP B 407 HIS 0.004 0.001 HIS A 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.21 ( 7272) covalent geometry : angle 0.76081 / 0.39 ( 9934) SS BOND : bond 0.02212 / 1.14 ( 4) SS BOND : angle 1.97082 / 1.11 ( 8) hydrogen bonds : bond 0.12137 / 8.13 ( 476) hydrogen bonds : angle 7.08949 / 5.04 ( 1428) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 235 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 LYS cc_start: 0.8063 (ptpt) cc_final: 0.7802 (ptpp) REVERT: A 273 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8152 (tm-30) REVERT: A 339 TYR cc_start: 0.8713 (m-80) cc_final: 0.8279 (m-80) REVERT: A 342 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7278 (tm-30) REVERT: A 371 LEU cc_start: 0.8659 (tm) cc_final: 0.7920 (mm) REVERT: A 422 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8447 (p) REVERT: A 426 ASP cc_start: 0.8348 (m-30) cc_final: 0.8025 (m-30) REVERT: B 223 HIS cc_start: 0.8844 (m90) cc_final: 0.8627 (m170) REVERT: B 273 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8215 (tm-30) REVERT: B 339 TYR cc_start: 0.8716 (m-80) cc_final: 0.8278 (m-80) REVERT: B 342 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7268 (tm-30) REVERT: B 371 LEU cc_start: 0.8656 (tm) cc_final: 0.7906 (mm) REVERT: B 422 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8440 (p) REVERT: B 426 ASP cc_start: 0.8360 (m-30) cc_final: 0.8051 (m-30) outliers start: 24 outliers final: 10 residues processed: 251 average time/residue: 0.0883 time to fit residues: 29.3661 Evaluate side-chains 177 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 548 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 460 HIS B 460 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.123167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.102449 restraints weight = 16457.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.105899 restraints weight = 8124.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.108108 restraints weight = 5161.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.109484 restraints weight = 3828.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.110923 restraints weight = 3151.517| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7276 Z= 0.161 Angle : 0.705 8.517 9942 Z= 0.363 Chirality : 0.042 0.160 1070 Planarity : 0.006 0.054 1180 Dihedral : 7.747 47.080 998 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % Rotamer: Outliers : 6.41 % Allowed : 15.60 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.29), residues: 820 helix: -0.08 (0.20), residues: 600 sheet: None (None), residues: 0 loop : -3.76 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 272 TYR 0.033 0.002 TYR A 308 PHE 0.027 0.002 PHE B 270 TRP 0.014 0.001 TRP A 438 HIS 0.003 0.001 HIS B 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 ( 7272) covalent geometry : angle 0.70488 / 0.36 ( 9934) SS BOND : bond 0.00260 / 0.13 ( 4) SS BOND : angle 1.04045 / 0.58 ( 8) hydrogen bonds : bond 0.04306 / 2.84 ( 476) hydrogen bonds : angle 5.80999 / 4.16 ( 1428) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.9195 (t0) cc_final: 0.8990 (t0) REVERT: A 180 LYS cc_start: 0.8030 (mttt) cc_final: 0.7613 (mtmm) REVERT: A 201 PHE cc_start: 0.8700 (t80) cc_final: 0.8482 (t80) REVERT: A 259 GLU cc_start: 0.8608 (tp30) cc_final: 0.8325 (tp30) REVERT: A 260 GLN cc_start: 0.9258 (pt0) cc_final: 0.8702 (tt0) REVERT: A 327 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8396 (m-80) REVERT: A 342 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7560 (tm-30) REVERT: A 396 LEU cc_start: 0.9536 (tp) cc_final: 0.9320 (tp) REVERT: A 418 ARG cc_start: 0.8090 (ttm-80) cc_final: 0.7598 (ttp-110) REVERT: A 453 PHE cc_start: 0.8350 (m-10) cc_final: 0.7957 (m-80) REVERT: A 471 PHE cc_start: 0.7058 (p90) cc_final: 0.6296 (m-80) REVERT: A 475 LEU cc_start: 0.8443 (tt) cc_final: 0.8210 (tt) REVERT: A 503 MET cc_start: 0.8924 (ttp) cc_final: 0.8711 (ttp) REVERT: B 180 LYS cc_start: 0.8033 (mttt) cc_final: 0.7616 (mtmm) REVERT: B 201 PHE cc_start: 0.8734 (t80) cc_final: 0.8473 (t80) REVERT: B 259 GLU cc_start: 0.8645 (tp30) cc_final: 0.8387 (tp30) REVERT: B 327 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.8342 (m-80) REVERT: B 342 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7558 (tm-30) REVERT: B 387 CYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8444 (p) REVERT: B 418 ARG cc_start: 0.8081 (ttm-80) cc_final: 0.7610 (ttp-110) REVERT: B 422 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8320 (p) REVERT: B 426 ASP cc_start: 0.8487 (m-30) cc_final: 0.8160 (m-30) REVERT: B 453 PHE cc_start: 0.8392 (m-10) cc_final: 0.8077 (m-80) REVERT: B 471 PHE cc_start: 0.7042 (p90) cc_final: 0.6258 (m-80) REVERT: B 475 LEU cc_start: 0.8426 (tt) cc_final: 0.8189 (tt) REVERT: B 503 MET cc_start: 0.8920 (ttp) cc_final: 0.8703 (ttp) outliers start: 46 outliers final: 30 residues processed: 194 average time/residue: 0.0732 time to fit residues: 19.8489 Evaluate side-chains 184 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 526 GLN Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 405 LYS Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 526 GLN Chi-restraints excluded: chain B residue 548 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 17 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 28 optimal weight: 0.0170 chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.120256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.101214 restraints weight = 16146.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.104260 restraints weight = 7764.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.106405 restraints weight = 4919.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.107950 restraints weight = 3617.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.108911 restraints weight = 2893.784| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7276 Z= 0.191 Angle : 0.689 7.074 9942 Z= 0.357 Chirality : 0.042 0.176 1070 Planarity : 0.006 0.051 1180 Dihedral : 7.261 56.779 995 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 6.13 % Allowed : 19.50 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.96 (0.30), residues: 820 helix: 0.42 (0.21), residues: 612 sheet: None (None), residues: 0 loop : -3.88 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 262 TYR 0.030 0.002 TYR A 308 PHE 0.032 0.002 PHE B 270 TRP 0.013 0.001 TRP A 438 HIS 0.006 0.001 HIS B 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 ( 7272) covalent geometry : angle 0.68893 / 0.36 ( 9934) SS BOND : bond 0.00380 / 0.19 ( 4) SS BOND : angle 1.07806 / 0.60 ( 8) hydrogen bonds : bond 0.04186 / 2.75 ( 476) hydrogen bonds : angle 5.70193 / 4.08 ( 1428) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8708 (tt) REVERT: A 180 LYS cc_start: 0.8013 (mttt) cc_final: 0.7618 (mtmm) REVERT: A 201 PHE cc_start: 0.8742 (t80) cc_final: 0.8522 (t80) REVERT: A 327 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8388 (m-80) REVERT: A 342 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7640 (tm-30) REVERT: A 402 MET cc_start: 0.8392 (ppp) cc_final: 0.7656 (ppp) REVERT: A 418 ARG cc_start: 0.8124 (ttm-80) cc_final: 0.7807 (ttp-110) REVERT: A 462 TYR cc_start: 0.9046 (t80) cc_final: 0.8715 (t80) REVERT: A 471 PHE cc_start: 0.7361 (p90) cc_final: 0.6706 (m-80) REVERT: B 132 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8707 (tt) REVERT: B 180 LYS cc_start: 0.8030 (mttt) cc_final: 0.7635 (mtmm) REVERT: B 201 PHE cc_start: 0.8748 (t80) cc_final: 0.8495 (t80) REVERT: B 273 GLU cc_start: 0.8514 (tm-30) cc_final: 0.7619 (tm-30) REVERT: B 327 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8421 (m-80) REVERT: B 342 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7617 (tm-30) REVERT: B 418 ARG cc_start: 0.8141 (ttm-80) cc_final: 0.7840 (ttp-110) REVERT: B 462 TYR cc_start: 0.9042 (t80) cc_final: 0.8718 (t80) outliers start: 44 outliers final: 30 residues processed: 189 average time/residue: 0.0751 time to fit residues: 19.8608 Evaluate side-chains 185 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 514 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 34 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 329 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.116111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.098135 restraints weight = 16230.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.101303 restraints weight = 7312.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.103514 restraints weight = 4408.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.104992 restraints weight = 3116.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.105875 restraints weight = 2440.604| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 7276 Z= 0.211 Angle : 0.723 11.248 9942 Z= 0.369 Chirality : 0.043 0.178 1070 Planarity : 0.006 0.043 1180 Dihedral : 6.677 45.871 992 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 7.52 % Allowed : 18.66 % Favored : 73.82 % 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: -0.63 (0.30), residues: 820 helix: 0.65 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -3.83 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 262 TYR 0.035 0.002 TYR A 308 PHE 0.030 0.002 PHE B 270 TRP 0.013 0.001 TRP A 438 HIS 0.006 0.001 HIS A 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.21 ( 7272) covalent geometry : angle 0.72280 / 0.37 ( 9934) SS BOND : bond 0.00489 / 0.24 ( 4) SS BOND : angle 1.01496 / 0.58 ( 8) hydrogen bonds : bond 0.04162 / 2.73 ( 476) hydrogen bonds : angle 5.71873 / 4.10 ( 1428) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 166 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8508 (tt) REVERT: A 160 ASP cc_start: 0.8597 (t0) cc_final: 0.8366 (t0) REVERT: A 180 LYS cc_start: 0.8132 (mttt) cc_final: 0.7801 (mtmm) REVERT: A 201 PHE cc_start: 0.8753 (t80) cc_final: 0.8380 (t80) REVERT: A 253 ARG cc_start: 0.8658 (mtt90) cc_final: 0.8405 (mmt90) REVERT: A 265 MET cc_start: 0.8304 (ttm) cc_final: 0.7957 (ttm) REVERT: A 279 LEU cc_start: 0.9661 (OUTLIER) cc_final: 0.9386 (tt) REVERT: A 327 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.8433 (m-80) REVERT: A 342 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7619 (tm-30) REVERT: A 365 CYS cc_start: 0.7627 (t) cc_final: 0.7332 (t) REVERT: A 402 MET cc_start: 0.8671 (ppp) cc_final: 0.7602 (ppp) REVERT: A 462 TYR cc_start: 0.9043 (t80) cc_final: 0.8716 (t80) REVERT: B 132 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8519 (tt) REVERT: B 160 ASP cc_start: 0.8563 (t0) cc_final: 0.8339 (t0) REVERT: B 180 LYS cc_start: 0.8125 (mttt) cc_final: 0.7801 (mtmm) REVERT: B 201 PHE cc_start: 0.8779 (t80) cc_final: 0.8523 (t80) REVERT: B 253 ARG cc_start: 0.8630 (mtt90) cc_final: 0.8398 (mmt90) REVERT: B 265 MET cc_start: 0.8440 (ttm) cc_final: 0.8070 (ttm) REVERT: B 273 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8429 (tm-30) REVERT: B 279 LEU cc_start: 0.9655 (OUTLIER) cc_final: 0.9388 (tt) REVERT: B 308 TYR cc_start: 0.7982 (t80) cc_final: 0.7677 (t80) REVERT: B 327 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8376 (m-80) REVERT: B 342 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7621 (tm-30) REVERT: B 365 CYS cc_start: 0.7597 (t) cc_final: 0.7296 (t) REVERT: B 462 TYR cc_start: 0.9042 (t80) cc_final: 0.8723 (t80) outliers start: 54 outliers final: 38 residues processed: 196 average time/residue: 0.0713 time to fit residues: 19.3591 Evaluate side-chains 195 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 151 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 514 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 15 optimal weight: 0.4980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.119827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.101554 restraints weight = 15798.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.104976 restraints weight = 7025.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.107219 restraints weight = 4180.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.108798 restraints weight = 2942.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.109771 restraints weight = 2287.036| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7276 Z= 0.138 Angle : 0.661 9.164 9942 Z= 0.333 Chirality : 0.042 0.165 1070 Planarity : 0.006 0.067 1180 Dihedral : 6.421 48.875 992 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 5.43 % Allowed : 22.42 % Favored : 72.14 % 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 (0.30), residues: 820 helix: 0.87 (0.21), residues: 614 sheet: None (None), residues: 0 loop : -3.75 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 272 TYR 0.031 0.002 TYR A 308 PHE 0.027 0.001 PHE B 270 TRP 0.016 0.001 TRP A 438 HIS 0.005 0.001 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 7272) covalent geometry : angle 0.66038 / 0.33 ( 9934) SS BOND : bond 0.00253 / 0.13 ( 4) SS BOND : angle 0.86903 / 0.50 ( 8) hydrogen bonds : bond 0.03863 / 2.55 ( 476) hydrogen bonds : angle 5.54358 / 3.98 ( 1428) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8554 (tt) REVERT: A 253 ARG cc_start: 0.8674 (mtt90) cc_final: 0.8109 (mtt-85) REVERT: A 259 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8233 (mp0) REVERT: A 265 MET cc_start: 0.8314 (ttm) cc_final: 0.7872 (ttm) REVERT: A 327 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.8228 (m-80) REVERT: A 342 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7564 (tm-30) REVERT: A 402 MET cc_start: 0.8603 (ppp) cc_final: 0.7919 (ppp) REVERT: A 426 ASP cc_start: 0.8366 (m-30) cc_final: 0.8133 (m-30) REVERT: A 471 PHE cc_start: 0.7246 (p90) cc_final: 0.6801 (m-80) REVERT: B 132 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8499 (tt) REVERT: B 253 ARG cc_start: 0.8663 (mtt90) cc_final: 0.8461 (mmt90) REVERT: B 259 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8274 (mp0) REVERT: B 273 GLU cc_start: 0.8489 (tm-30) cc_final: 0.7892 (tm-30) REVERT: B 327 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8137 (m-80) REVERT: B 342 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7569 (tm-30) REVERT: B 390 ASN cc_start: 0.8234 (m-40) cc_final: 0.7949 (m-40) REVERT: B 426 ASP cc_start: 0.8368 (m-30) cc_final: 0.8106 (m-30) outliers start: 39 outliers final: 28 residues processed: 193 average time/residue: 0.0746 time to fit residues: 19.8873 Evaluate side-chains 179 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 514 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 27 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 5 optimal weight: 0.0570 chunk 63 optimal weight: 0.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 274 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.121000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.102725 restraints weight = 15968.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.106116 restraints weight = 7274.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.108396 restraints weight = 4374.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.109981 restraints weight = 3088.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.111126 restraints weight = 2402.764| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7276 Z= 0.134 Angle : 0.680 11.140 9942 Z= 0.338 Chirality : 0.043 0.192 1070 Planarity : 0.006 0.062 1180 Dihedral : 6.274 49.535 992 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 5.15 % Allowed : 22.98 % Favored : 71.87 % 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: -0.35 (0.30), residues: 820 helix: 0.86 (0.21), residues: 614 sheet: None (None), residues: 0 loop : -3.68 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 262 TYR 0.024 0.002 TYR A 308 PHE 0.027 0.001 PHE B 270 TRP 0.013 0.001 TRP A 438 HIS 0.009 0.001 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 7272) covalent geometry : angle 0.67946 / 0.34 ( 9934) SS BOND : bond 0.00228 / 0.12 ( 4) SS BOND : angle 0.81097 / 0.46 ( 8) hydrogen bonds : bond 0.03799 / 2.50 ( 476) hydrogen bonds : angle 5.53041 / 3.97 ( 1428) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8551 (tt) REVERT: A 180 LYS cc_start: 0.8049 (mttt) cc_final: 0.7711 (mtmm) REVERT: A 259 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8217 (mp0) REVERT: A 265 MET cc_start: 0.8250 (ttm) cc_final: 0.7797 (ttm) REVERT: A 279 LEU cc_start: 0.9639 (OUTLIER) cc_final: 0.9372 (tt) REVERT: A 327 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.8207 (m-80) REVERT: A 342 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7601 (tm-30) REVERT: A 402 MET cc_start: 0.8466 (ppp) cc_final: 0.7780 (ppp) REVERT: A 471 PHE cc_start: 0.7318 (p90) cc_final: 0.6842 (m-80) REVERT: A 472 TYR cc_start: 0.7952 (t80) cc_final: 0.7517 (t80) REVERT: B 132 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8486 (tt) REVERT: B 180 LYS cc_start: 0.8026 (mttt) cc_final: 0.7691 (mtmm) REVERT: B 259 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8248 (mp0) REVERT: B 265 MET cc_start: 0.8404 (ttm) cc_final: 0.7878 (ttm) REVERT: B 279 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9377 (tt) REVERT: B 327 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.8096 (m-80) REVERT: B 342 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7609 (tm-30) REVERT: B 390 ASN cc_start: 0.8217 (m-40) cc_final: 0.7904 (m-40) REVERT: B 395 MET cc_start: 0.8225 (ttt) cc_final: 0.7957 (tmm) REVERT: B 422 VAL cc_start: 0.8869 (OUTLIER) cc_final: 0.8147 (p) REVERT: B 426 ASP cc_start: 0.8346 (m-30) cc_final: 0.8018 (m-30) REVERT: B 471 PHE cc_start: 0.7275 (p90) cc_final: 0.6663 (t80) REVERT: B 472 TYR cc_start: 0.7898 (t80) cc_final: 0.7552 (t80) outliers start: 37 outliers final: 20 residues processed: 176 average time/residue: 0.0775 time to fit residues: 18.7180 Evaluate side-chains 175 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 422 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 80 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 0.0370 chunk 53 optimal weight: 0.4980 chunk 17 optimal weight: 0.0020 chunk 61 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 overall best weight: 0.6868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 526 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.125724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.107910 restraints weight = 15777.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.111299 restraints weight = 7132.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.113386 restraints weight = 4239.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.115082 restraints weight = 3052.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.116102 restraints weight = 2305.212| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7276 Z= 0.132 Angle : 0.681 11.801 9942 Z= 0.333 Chirality : 0.043 0.224 1070 Planarity : 0.006 0.052 1180 Dihedral : 6.193 49.552 992 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 5.43 % Allowed : 22.98 % Favored : 71.59 % 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: -0.24 (0.31), residues: 820 helix: 0.93 (0.21), residues: 614 sheet: None (None), residues: 0 loop : -3.62 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 253 TYR 0.026 0.002 TYR A 308 PHE 0.027 0.001 PHE B 270 TRP 0.013 0.001 TRP B 438 HIS 0.008 0.001 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 7272) covalent geometry : angle 0.68085 / 0.33 ( 9934) SS BOND : bond 0.00232 / 0.12 ( 4) SS BOND : angle 0.86077 / 0.49 ( 8) hydrogen bonds : bond 0.03800 / 2.48 ( 476) hydrogen bonds : angle 5.49685 / 3.96 ( 1428) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8522 (tt) REVERT: A 180 LYS cc_start: 0.8082 (mttt) cc_final: 0.7807 (mtmm) REVERT: A 259 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8178 (mp0) REVERT: A 265 MET cc_start: 0.8258 (ttm) cc_final: 0.7804 (ttm) REVERT: A 279 LEU cc_start: 0.9657 (OUTLIER) cc_final: 0.9381 (tt) REVERT: A 327 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.8184 (m-80) REVERT: A 342 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7668 (tm-30) REVERT: A 395 MET cc_start: 0.8195 (ttt) cc_final: 0.7951 (tmm) REVERT: A 402 MET cc_start: 0.8366 (ppp) cc_final: 0.7752 (ppp) REVERT: A 471 PHE cc_start: 0.7291 (p90) cc_final: 0.6864 (m-80) REVERT: A 472 TYR cc_start: 0.7850 (t80) cc_final: 0.7245 (t80) REVERT: B 132 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8532 (tt) REVERT: B 180 LYS cc_start: 0.8085 (mttt) cc_final: 0.7794 (mtmm) REVERT: B 265 MET cc_start: 0.8380 (ttm) cc_final: 0.7892 (ttm) REVERT: B 273 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8367 (tm-30) REVERT: B 279 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.9389 (tt) REVERT: B 308 TYR cc_start: 0.7912 (t80) cc_final: 0.7688 (t80) REVERT: B 327 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.8064 (m-80) REVERT: B 342 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7636 (tm-30) REVERT: B 390 ASN cc_start: 0.8106 (m-40) cc_final: 0.7902 (m-40) REVERT: B 395 MET cc_start: 0.8251 (ttt) cc_final: 0.7981 (tmm) REVERT: B 422 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8187 (p) REVERT: B 426 ASP cc_start: 0.8258 (m-30) cc_final: 0.7997 (m-30) REVERT: B 471 PHE cc_start: 0.7245 (p90) cc_final: 0.6600 (t80) REVERT: B 472 TYR cc_start: 0.7860 (t80) cc_final: 0.7420 (t80) outliers start: 39 outliers final: 24 residues processed: 190 average time/residue: 0.0776 time to fit residues: 20.0340 Evaluate side-chains 176 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 526 GLN Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 474 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 11 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 44 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 274 ASN A 415 ASN B 415 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.121472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.103119 restraints weight = 15852.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.106438 restraints weight = 7311.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.108811 restraints weight = 4442.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.110324 restraints weight = 3125.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.111181 restraints weight = 2440.218| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7276 Z= 0.150 Angle : 0.718 13.079 9942 Z= 0.353 Chirality : 0.044 0.255 1070 Planarity : 0.006 0.043 1180 Dihedral : 6.267 48.838 992 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 5.01 % Allowed : 24.79 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.31), residues: 820 helix: 0.88 (0.21), residues: 614 sheet: None (None), residues: 0 loop : -3.71 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 253 TYR 0.029 0.002 TYR B 322 PHE 0.027 0.001 PHE B 270 TRP 0.013 0.001 TRP A 438 HIS 0.011 0.002 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 7272) covalent geometry : angle 0.71779 / 0.35 ( 9934) SS BOND : bond 0.00224 / 0.11 ( 4) SS BOND : angle 0.84018 / 0.48 ( 8) hydrogen bonds : bond 0.03973 / 2.60 ( 476) hydrogen bonds : angle 5.52073 / 3.98 ( 1428) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8572 (tt) REVERT: A 180 LYS cc_start: 0.8051 (mttt) cc_final: 0.7800 (mtmm) REVERT: A 259 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8194 (mp0) REVERT: A 265 MET cc_start: 0.8352 (ttm) cc_final: 0.7908 (ttm) REVERT: A 279 LEU cc_start: 0.9657 (OUTLIER) cc_final: 0.9377 (tt) REVERT: A 327 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.8271 (m-80) REVERT: A 342 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7722 (tm-30) REVERT: A 395 MET cc_start: 0.8176 (ttt) cc_final: 0.7934 (tmm) REVERT: A 402 MET cc_start: 0.8456 (ppp) cc_final: 0.7913 (ppp) REVERT: A 471 PHE cc_start: 0.7306 (p90) cc_final: 0.6853 (m-80) REVERT: A 472 TYR cc_start: 0.7735 (t80) cc_final: 0.7253 (t80) REVERT: B 132 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8549 (tt) REVERT: B 180 LYS cc_start: 0.8087 (mttt) cc_final: 0.7801 (mtmm) REVERT: B 265 MET cc_start: 0.8472 (ttm) cc_final: 0.8011 (ttm) REVERT: B 273 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8386 (tm-30) REVERT: B 279 LEU cc_start: 0.9662 (OUTLIER) cc_final: 0.9398 (tt) REVERT: B 308 TYR cc_start: 0.7996 (t80) cc_final: 0.7773 (t80) REVERT: B 327 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.8135 (m-80) REVERT: B 342 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7624 (tm-30) REVERT: B 390 ASN cc_start: 0.8098 (m-40) cc_final: 0.7895 (m-40) REVERT: B 395 MET cc_start: 0.8270 (ttt) cc_final: 0.7996 (tmm) REVERT: B 422 VAL cc_start: 0.8958 (OUTLIER) cc_final: 0.8223 (p) REVERT: B 426 ASP cc_start: 0.8326 (m-30) cc_final: 0.8052 (m-30) REVERT: B 471 PHE cc_start: 0.7228 (p90) cc_final: 0.6489 (t80) REVERT: B 472 TYR cc_start: 0.7814 (t80) cc_final: 0.7443 (t80) outliers start: 36 outliers final: 27 residues processed: 166 average time/residue: 0.0759 time to fit residues: 17.3904 Evaluate side-chains 171 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 514 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 30 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 526 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.122579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.104596 restraints weight = 15570.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.107945 restraints weight = 7252.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.110119 restraints weight = 4369.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.111696 restraints weight = 3100.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.112528 restraints weight = 2404.605| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7276 Z= 0.140 Angle : 0.709 14.179 9942 Z= 0.347 Chirality : 0.043 0.240 1070 Planarity : 0.005 0.042 1180 Dihedral : 6.300 49.482 992 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 4.32 % Allowed : 25.21 % Favored : 70.47 % 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: -0.32 (0.31), residues: 820 helix: 0.87 (0.21), residues: 612 sheet: None (None), residues: 0 loop : -3.57 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 253 TYR 0.029 0.002 TYR B 322 PHE 0.025 0.001 PHE B 270 TRP 0.013 0.001 TRP A 438 HIS 0.012 0.002 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 7272) covalent geometry : angle 0.70871 / 0.35 ( 9934) SS BOND : bond 0.00199 / 0.10 ( 4) SS BOND : angle 0.80406 / 0.46 ( 8) hydrogen bonds : bond 0.03957 / 2.58 ( 476) hydrogen bonds : angle 5.48516 / 3.96 ( 1428) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8657 (tt) REVERT: A 180 LYS cc_start: 0.8048 (mttt) cc_final: 0.7829 (mtmm) REVERT: A 260 GLN cc_start: 0.9415 (pt0) cc_final: 0.8854 (tt0) REVERT: A 265 MET cc_start: 0.8412 (ttm) cc_final: 0.7946 (ttm) REVERT: A 279 LEU cc_start: 0.9648 (OUTLIER) cc_final: 0.9358 (tt) REVERT: A 327 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.8349 (m-80) REVERT: A 342 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7667 (tm-30) REVERT: A 395 MET cc_start: 0.8140 (ttt) cc_final: 0.7917 (tmm) REVERT: A 402 MET cc_start: 0.8404 (ppp) cc_final: 0.7863 (ppp) REVERT: A 471 PHE cc_start: 0.7163 (p90) cc_final: 0.6872 (m-80) REVERT: A 472 TYR cc_start: 0.7673 (t80) cc_final: 0.7280 (t80) REVERT: A 484 MET cc_start: 0.6919 (ttt) cc_final: 0.6665 (ttm) REVERT: B 132 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8648 (tt) REVERT: B 180 LYS cc_start: 0.8090 (mttt) cc_final: 0.7841 (mtmm) REVERT: B 260 GLN cc_start: 0.9441 (pt0) cc_final: 0.8861 (tt0) REVERT: B 265 MET cc_start: 0.8540 (ttm) cc_final: 0.8054 (ttm) REVERT: B 273 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8347 (tm-30) REVERT: B 279 LEU cc_start: 0.9655 (OUTLIER) cc_final: 0.9378 (tt) REVERT: B 327 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.8122 (m-80) REVERT: B 342 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7702 (tm-30) REVERT: B 390 ASN cc_start: 0.8154 (m-40) cc_final: 0.7882 (m-40) REVERT: B 395 MET cc_start: 0.8209 (ttt) cc_final: 0.7992 (tmm) REVERT: B 422 VAL cc_start: 0.9011 (OUTLIER) cc_final: 0.8280 (p) REVERT: B 426 ASP cc_start: 0.8076 (m-30) cc_final: 0.7811 (m-30) REVERT: B 471 PHE cc_start: 0.7138 (p90) cc_final: 0.6772 (m-80) REVERT: B 472 TYR cc_start: 0.7794 (t80) cc_final: 0.7408 (t80) REVERT: B 484 MET cc_start: 0.6896 (ttt) cc_final: 0.6651 (ttm) outliers start: 31 outliers final: 24 residues processed: 166 average time/residue: 0.0703 time to fit residues: 16.3261 Evaluate side-chains 171 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 526 GLN Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 474 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 33 optimal weight: 0.6980 chunk 4 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 526 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.122145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.104049 restraints weight = 15598.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.107381 restraints weight = 7227.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.109590 restraints weight = 4372.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.111195 restraints weight = 3097.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.112106 restraints weight = 2406.004| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7276 Z= 0.141 Angle : 0.720 14.852 9942 Z= 0.350 Chirality : 0.044 0.243 1070 Planarity : 0.005 0.040 1180 Dihedral : 6.272 50.090 992 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 5.01 % Allowed : 25.21 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.31), residues: 820 helix: 0.85 (0.21), residues: 612 sheet: None (None), residues: 0 loop : -3.50 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 253 TYR 0.031 0.002 TYR B 322 PHE 0.030 0.001 PHE B 270 TRP 0.013 0.001 TRP B 438 HIS 0.013 0.002 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 7272) covalent geometry : angle 0.72015 / 0.35 ( 9934) SS BOND : bond 0.00237 / 0.12 ( 4) SS BOND : angle 0.85511 / 0.49 ( 8) hydrogen bonds : bond 0.03890 / 2.55 ( 476) hydrogen bonds : angle 5.47799 / 3.97 ( 1428) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8533 (tt) REVERT: A 180 LYS cc_start: 0.8015 (mttt) cc_final: 0.7790 (mtmm) REVERT: A 260 GLN cc_start: 0.9459 (OUTLIER) cc_final: 0.8910 (tt0) REVERT: A 265 MET cc_start: 0.8377 (ttm) cc_final: 0.7931 (ttm) REVERT: A 279 LEU cc_start: 0.9657 (OUTLIER) cc_final: 0.9369 (tt) REVERT: A 327 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.8276 (m-80) REVERT: A 342 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7678 (tm-30) REVERT: A 365 CYS cc_start: 0.7557 (t) cc_final: 0.7146 (t) REVERT: A 395 MET cc_start: 0.8200 (ttt) cc_final: 0.7950 (tmm) REVERT: A 402 MET cc_start: 0.8435 (ppp) cc_final: 0.7882 (ppp) REVERT: A 471 PHE cc_start: 0.7282 (p90) cc_final: 0.6891 (m-80) REVERT: A 472 TYR cc_start: 0.7682 (t80) cc_final: 0.7238 (t80) REVERT: A 484 MET cc_start: 0.6917 (ttt) cc_final: 0.6636 (ttm) REVERT: B 132 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8532 (tt) REVERT: B 180 LYS cc_start: 0.8062 (mttt) cc_final: 0.7803 (mtmm) REVERT: B 260 GLN cc_start: 0.9473 (pt0) cc_final: 0.8923 (tt0) REVERT: B 265 MET cc_start: 0.8392 (ttm) cc_final: 0.7969 (ttm) REVERT: B 273 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8391 (tm-30) REVERT: B 279 LEU cc_start: 0.9656 (OUTLIER) cc_final: 0.9390 (tt) REVERT: B 327 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.8077 (m-80) REVERT: B 342 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7714 (tm-30) REVERT: B 390 ASN cc_start: 0.8151 (m-40) cc_final: 0.7877 (m-40) REVERT: B 395 MET cc_start: 0.8268 (ttt) cc_final: 0.8000 (tmm) REVERT: B 422 VAL cc_start: 0.8971 (OUTLIER) cc_final: 0.8218 (p) REVERT: B 426 ASP cc_start: 0.8154 (m-30) cc_final: 0.7863 (m-30) REVERT: B 471 PHE cc_start: 0.7259 (p90) cc_final: 0.6618 (t80) REVERT: B 472 TYR cc_start: 0.7700 (t80) cc_final: 0.7272 (t80) REVERT: B 484 MET cc_start: 0.6900 (ttt) cc_final: 0.6644 (ttm) outliers start: 36 outliers final: 25 residues processed: 167 average time/residue: 0.0735 time to fit residues: 17.0072 Evaluate side-chains 172 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 526 GLN Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 502 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 63 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 78 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 chunk 17 optimal weight: 0.6980 chunk 57 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 526 GLN B 526 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.123234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.105180 restraints weight = 15656.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.108529 restraints weight = 7315.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.110701 restraints weight = 4418.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.112317 restraints weight = 3138.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.113132 restraints weight = 2427.911| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7276 Z= 0.138 Angle : 0.725 14.865 9942 Z= 0.350 Chirality : 0.043 0.238 1070 Planarity : 0.005 0.040 1180 Dihedral : 5.847 47.126 988 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 4.46 % Allowed : 25.63 % Favored : 69.92 % 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: -0.34 (0.31), residues: 820 helix: 0.81 (0.21), residues: 618 sheet: None (None), residues: 0 loop : -3.57 (0.46), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 253 TYR 0.030 0.001 TYR B 322 PHE 0.029 0.001 PHE B 270 TRP 0.013 0.001 TRP A 438 HIS 0.013 0.002 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 7272) covalent geometry : angle 0.72527 / 0.35 ( 9934) SS BOND : bond 0.00208 / 0.11 ( 4) SS BOND : angle 0.83101 / 0.48 ( 8) hydrogen bonds : bond 0.03864 / 2.53 ( 476) hydrogen bonds : angle 5.44949 / 3.94 ( 1428) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1194.60 seconds wall clock time: 21 minutes 30.11 seconds (1290.11 seconds total)