Starting phenix.real_space_refine on Tue Mar 3 13:38:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sl8_25194/03_2026/7sl8_25194_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sl8_25194/03_2026/7sl8_25194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sl8_25194/03_2026/7sl8_25194_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sl8_25194/03_2026/7sl8_25194_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sl8_25194/03_2026/7sl8_25194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sl8_25194/03_2026/7sl8_25194.map" } resolution = 3.4 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= 0.000 sd= 0.003 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 34 5.16 5 C 3493 2.51 5 N 844 2.21 5 O 924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5295 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4362 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 22, 'TRANS': 559} Chain breaks: 2 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 6, 'PHE:plan': 2, 'TYR:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 92 Chain: "B" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 905 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.47, per 1000 atoms: 0.28 Number of scatterers: 5295 At special positions: 0 Unit cell: (109.18, 78.44, 90.1, 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 34 16.00 O 924 8.00 N 844 7.00 C 3493 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 511 " distance=2.04 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 351 " distance=2.02 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 97 " 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: 0.29 Conformation dependent library (CDL) restraints added in 289.6 milliseconds 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1284 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 3 sheets defined 63.6% alpha, 5.1% 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 25 through 49 removed outlier: 4.188A pdb=" N ILE A 29 " --> pdb=" O ASN A 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 76 removed outlier: 3.900A pdb=" N SER A 73 " --> pdb=" O PRO A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.734A pdb=" N TRP A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 123 removed outlier: 3.540A pdb=" N ALA A 123 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 138 through 157 removed outlier: 4.599A pdb=" N GLN A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 174 Processing helix chain 'A' and resid 176 through 195 removed outlier: 3.613A pdb=" N SER A 180 " --> pdb=" O ASN A 176 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY A 195 " --> pdb=" O TYR A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 227 removed outlier: 3.727A pdb=" N GLY A 227 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 238 removed outlier: 3.582A pdb=" N TYR A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET A 237 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 4.397A pdb=" N TYR A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 294 removed outlier: 3.779A pdb=" N CYS A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP A 294 " --> pdb=" O TYR A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 303 removed outlier: 3.572A pdb=" N ALA A 303 " --> pdb=" O GLN A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 321 Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.853A pdb=" N VAL A 329 " --> pdb=" O MET A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 removed outlier: 3.699A pdb=" N MET A 333 " --> pdb=" O VAL A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 355 removed outlier: 4.692A pdb=" N LYS A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.598A pdb=" N LEU A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 409 removed outlier: 3.569A pdb=" N LEU A 383 " --> pdb=" O ARG A 379 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN A 399 " --> pdb=" O THR A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'A' and resid 418 through 440 removed outlier: 3.504A pdb=" N ALA A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 445 removed outlier: 3.532A pdb=" N VAL A 444 " --> pdb=" O TRP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 477 removed outlier: 3.991A pdb=" N SER A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) Proline residue: A 465 - end of helix removed outlier: 3.555A pdb=" N TRP A 477 " --> pdb=" O LEU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 505 removed outlier: 3.863A pdb=" N TRP A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 523 Processing helix chain 'A' and resid 527 through 548 Processing helix chain 'A' and resid 552 through 556 removed outlier: 3.901A pdb=" N HIS A 555 " --> pdb=" O PRO A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 666 Processing sheet with id=AA1, first strand: chain 'A' and resid 245 through 246 Processing sheet with id=AA2, first strand: chain 'B' and resid 5 through 9 removed outlier: 3.575A pdb=" N GLN B 5 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 23 " --> pdb=" O SER B 9 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 13 through 15 removed outlier: 6.728A pdb=" N VAL B 14 " --> pdb=" O SER B 119 " (cutoff:3.500A) 309 hydrogen bonds defined for protein. 912 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: 0.86 Time building geometry restraints manager: 0.46 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: 1579 1.34 - 1.46: 1073 1.46 - 1.58: 2721 1.58 - 1.69: 0 1.69 - 1.81: 53 Bond restraints: 5426 Sorted by residual: bond pdb=" C LEU A 323 " pdb=" N PRO A 324 " ideal model delta sigma weight residual 1.334 1.405 -0.071 2.34e-02 1.83e+03 9.11e+00 bond pdb=" C TRP A 276 " pdb=" N PRO A 277 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.96e+00 bond pdb=" C13 CLR A 701 " pdb=" C17 CLR A 701 " ideal model delta sigma weight residual 1.550 1.517 0.033 2.00e-02 2.50e+03 2.70e+00 bond pdb=" C10 CLR A 701 " pdb=" C9 CLR A 701 " ideal model delta sigma weight residual 1.551 1.519 0.032 2.00e-02 2.50e+03 2.50e+00 bond pdb=" C VAL A 117 " pdb=" N PRO A 118 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.28e-02 6.10e+03 2.27e+00 ... (remaining 5421 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 7106 2.17 - 4.34: 251 4.34 - 6.51: 40 6.51 - 8.68: 14 8.68 - 10.85: 1 Bond angle restraints: 7412 Sorted by residual: angle pdb=" N VAL A 359 " pdb=" CA VAL A 359 " pdb=" C VAL A 359 " ideal model delta sigma weight residual 108.12 118.97 -10.85 1.44e+00 4.82e-01 5.68e+01 angle pdb=" N VAL A 329 " pdb=" CA VAL A 329 " pdb=" C VAL A 329 " ideal model delta sigma weight residual 113.71 109.05 4.66 9.50e-01 1.11e+00 2.40e+01 angle pdb=" N LEU A 527 " pdb=" CA LEU A 527 " pdb=" C LEU A 527 " ideal model delta sigma weight residual 113.55 108.18 5.37 1.26e+00 6.30e-01 1.82e+01 angle pdb=" N LYS A 358 " pdb=" CA LYS A 358 " pdb=" C LYS A 358 " ideal model delta sigma weight residual 111.28 115.50 -4.22 1.09e+00 8.42e-01 1.50e+01 angle pdb=" N ALA A 464 " pdb=" CA ALA A 464 " pdb=" C ALA A 464 " ideal model delta sigma weight residual 109.81 118.33 -8.52 2.21e+00 2.05e-01 1.49e+01 ... (remaining 7407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 2754 15.96 - 31.92: 332 31.92 - 47.87: 83 47.87 - 63.83: 8 63.83 - 79.79: 4 Dihedral angle restraints: 3181 sinusoidal: 1172 harmonic: 2009 Sorted by residual: dihedral pdb=" CA PRO A 518 " pdb=" C PRO A 518 " pdb=" N THR A 519 " pdb=" CA THR A 519 " ideal model delta harmonic sigma weight residual -180.00 -158.39 -21.61 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA TYR B 101 " pdb=" C TYR B 101 " pdb=" N THR B 102 " pdb=" CA THR B 102 " 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 TYR B 61 " pdb=" C TYR B 61 " pdb=" N ALA B 62 " pdb=" CA ALA B 62 " ideal model delta harmonic sigma weight residual 180.00 158.68 21.32 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 3178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 652 0.055 - 0.109: 180 0.109 - 0.164: 38 0.164 - 0.218: 12 0.218 - 0.273: 2 Chirality restraints: 884 Sorted by residual: chirality pdb=" C13 CLR A 701 " pdb=" C12 CLR A 701 " pdb=" C14 CLR A 701 " pdb=" C17 CLR A 701 " both_signs ideal model delta sigma weight residual False -2.93 -2.66 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA CYS A 361 " pdb=" N CYS A 361 " pdb=" C CYS A 361 " pdb=" CB CYS A 361 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB VAL A 98 " pdb=" CA VAL A 98 " pdb=" CG1 VAL A 98 " pdb=" CG2 VAL A 98 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 881 not shown) Planarity restraints: 902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 465 " 0.044 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO A 466 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 466 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 466 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 330 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO A 331 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 331 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 331 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 102 " 0.037 5.00e-02 4.00e+02 5.66e-02 5.12e+00 pdb=" N PRO B 103 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 103 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 103 " 0.032 5.00e-02 4.00e+02 ... (remaining 899 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1750 2.83 - 3.35: 4902 3.35 - 3.87: 8745 3.87 - 4.38: 9429 4.38 - 4.90: 16804 Nonbonded interactions: 41630 Sorted by model distance: nonbonded pdb=" OE2 GLU A 234 " pdb=" OH TYR B 101 " model vdw 2.316 3.040 nonbonded pdb=" O SER A 446 " pdb=" OG SER A 446 " model vdw 2.321 3.040 nonbonded pdb=" O LEU A 152 " pdb=" OG1 THR A 156 " model vdw 2.327 3.040 nonbonded pdb=" CD2 TYR A 319 " pdb=" C24 CLR A 701 " model vdw 2.330 3.740 nonbonded pdb=" O LEU A 190 " pdb=" OG1 THR A 194 " model vdw 2.342 3.040 ... (remaining 41625 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.70 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.850 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 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 : 0.005 0.071 5431 Z= 0.248 Angle : 0.967 10.854 7422 Z= 0.543 Chirality : 0.057 0.273 884 Planarity : 0.008 0.066 902 Dihedral : 14.662 79.791 1882 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 0.92 % Allowed : 11.28 % Favored : 87.80 % 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: -4.09 (0.25), residues: 692 helix: -2.46 (0.19), residues: 413 sheet: -2.41 (0.66), residues: 49 loop : -2.90 (0.36), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 68 TYR 0.010 0.002 TYR A 144 PHE 0.016 0.002 PHE B 49 TRP 0.016 0.002 TRP A 68 HIS 0.003 0.001 HIS A 525 Details of bonding type rmsd covalent geometry : bond 0.00549 ( 5426) covalent geometry : angle 0.96779 ( 7412) SS BOND : bond 0.00477 ( 5) SS BOND : angle 0.62533 ( 10) hydrogen bonds : bond 0.18103 ( 309) hydrogen bonds : angle 7.34049 ( 912) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 126 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 333 MET cc_start: 0.8007 (mtm) cc_final: 0.7754 (mtm) REVERT: B 7 GLN cc_start: 0.7438 (mp10) cc_final: 0.7085 (mp10) outliers start: 5 outliers final: 2 residues processed: 131 average time/residue: 0.0799 time to fit residues: 13.4008 Evaluate side-chains 97 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 357 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 142 GLN A 525 HIS A 648 ASN A 666 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.126492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.106386 restraints weight = 10141.555| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.75 r_work: 0.3554 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3570 r_free = 0.3570 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3569 r_free = 0.3569 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5431 Z= 0.139 Angle : 0.654 7.300 7422 Z= 0.341 Chirality : 0.041 0.156 884 Planarity : 0.005 0.051 902 Dihedral : 6.193 59.349 814 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.33 % Allowed : 16.45 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.30), residues: 692 helix: -0.53 (0.24), residues: 412 sheet: -1.81 (0.69), residues: 48 loop : -2.73 (0.36), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.020 0.001 TYR B 61 PHE 0.013 0.001 PHE A 432 TRP 0.012 0.001 TRP A 276 HIS 0.002 0.000 HIS B 121 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 5426) covalent geometry : angle 0.65325 ( 7412) SS BOND : bond 0.00428 ( 5) SS BOND : angle 0.91669 ( 10) hydrogen bonds : bond 0.04311 ( 309) hydrogen bonds : angle 5.18265 ( 912) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 ARG cc_start: 0.7097 (tpt170) cc_final: 0.6876 (tpp80) REVERT: B 22 LEU cc_start: 0.9482 (mt) cc_final: 0.9216 (mp) REVERT: B 87 LEU cc_start: 0.7843 (mm) cc_final: 0.7498 (mm) REVERT: B 90 GLU cc_start: 0.7508 (pm20) cc_final: 0.6911 (pm20) outliers start: 18 outliers final: 13 residues processed: 116 average time/residue: 0.0664 time to fit residues: 10.3134 Evaluate side-chains 105 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 71 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 29 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.126740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.106416 restraints weight = 10110.619| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.74 r_work: 0.3563 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5431 Z= 0.133 Angle : 0.606 7.655 7422 Z= 0.315 Chirality : 0.040 0.145 884 Planarity : 0.005 0.046 902 Dihedral : 5.886 59.197 814 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.81 % Allowed : 18.11 % Favored : 77.08 % 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: -1.15 (0.32), residues: 692 helix: 0.28 (0.26), residues: 411 sheet: -1.23 (0.70), residues: 48 loop : -2.51 (0.38), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 47 TYR 0.016 0.001 TYR B 61 PHE 0.012 0.001 PHE A 432 TRP 0.011 0.001 TRP A 487 HIS 0.002 0.001 HIS B 121 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 5426) covalent geometry : angle 0.60546 ( 7412) SS BOND : bond 0.00452 ( 5) SS BOND : angle 0.84816 ( 10) hydrogen bonds : bond 0.03796 ( 309) hydrogen bonds : angle 4.77661 ( 912) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8198 (mmm) cc_final: 0.7737 (mtt) REVERT: A 133 ARG cc_start: 0.7116 (tpt170) cc_final: 0.6891 (tpp80) REVERT: A 349 SER cc_start: 0.9152 (m) cc_final: 0.8816 (p) REVERT: A 525 HIS cc_start: 0.8398 (OUTLIER) cc_final: 0.7829 (t70) REVERT: B 84 MET cc_start: 0.8022 (ptp) cc_final: 0.7672 (ptp) REVERT: B 88 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8641 (pttm) outliers start: 26 outliers final: 17 residues processed: 125 average time/residue: 0.0638 time to fit residues: 10.7190 Evaluate side-chains 110 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 88 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 17 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS A 666 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.127117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.107176 restraints weight = 9148.251| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.56 r_work: 0.3495 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5431 Z= 0.146 Angle : 0.639 8.475 7422 Z= 0.327 Chirality : 0.041 0.148 884 Planarity : 0.005 0.046 902 Dihedral : 5.826 59.015 813 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 6.65 % Allowed : 19.41 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.66 (0.32), residues: 692 helix: 0.71 (0.27), residues: 406 sheet: -1.03 (0.70), residues: 48 loop : -2.34 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 47 TYR 0.013 0.001 TYR B 61 PHE 0.012 0.001 PHE B 69 TRP 0.011 0.001 TRP A 487 HIS 0.006 0.001 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 5426) covalent geometry : angle 0.63783 ( 7412) SS BOND : bond 0.00484 ( 5) SS BOND : angle 1.11262 ( 10) hydrogen bonds : bond 0.03741 ( 309) hydrogen bonds : angle 4.70907 ( 912) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 94 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8169 (mmm) cc_final: 0.7717 (mtt) REVERT: A 133 ARG cc_start: 0.7108 (tpt170) cc_final: 0.6876 (tpp80) REVERT: A 347 VAL cc_start: 0.8921 (OUTLIER) cc_final: 0.8671 (m) REVERT: A 349 SER cc_start: 0.9123 (m) cc_final: 0.8809 (p) REVERT: A 525 HIS cc_start: 0.8475 (OUTLIER) cc_final: 0.8038 (t70) REVERT: B 88 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8646 (pttm) outliers start: 36 outliers final: 23 residues processed: 121 average time/residue: 0.0636 time to fit residues: 10.4763 Evaluate side-chains 115 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 88 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 53 optimal weight: 0.0020 chunk 43 optimal weight: 0.7980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS A 363 ASN A 648 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.131539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.111078 restraints weight = 9315.849| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.61 r_work: 0.3547 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5431 Z= 0.117 Angle : 0.619 11.331 7422 Z= 0.314 Chirality : 0.041 0.336 884 Planarity : 0.004 0.046 902 Dihedral : 5.478 57.415 811 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 6.10 % Allowed : 20.89 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.33), residues: 692 helix: 1.01 (0.27), residues: 406 sheet: -0.78 (0.72), residues: 48 loop : -2.28 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 47 TYR 0.019 0.001 TYR A 229 PHE 0.018 0.001 PHE B 69 TRP 0.009 0.001 TRP A 68 HIS 0.006 0.001 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 5426) covalent geometry : angle 0.61903 ( 7412) SS BOND : bond 0.00375 ( 5) SS BOND : angle 0.86564 ( 10) hydrogen bonds : bond 0.03465 ( 309) hydrogen bonds : angle 4.53979 ( 912) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8115 (mmm) cc_final: 0.7702 (mtt) REVERT: A 133 ARG cc_start: 0.7110 (tpt170) cc_final: 0.6859 (tpp80) REVERT: A 233 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8330 (mtt) REVERT: A 347 VAL cc_start: 0.8925 (OUTLIER) cc_final: 0.8676 (m) REVERT: A 349 SER cc_start: 0.9130 (m) cc_final: 0.8814 (p) REVERT: A 373 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8266 (tt) REVERT: A 525 HIS cc_start: 0.8476 (OUTLIER) cc_final: 0.8105 (t70) REVERT: B 88 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8620 (pttm) outliers start: 33 outliers final: 21 residues processed: 120 average time/residue: 0.0625 time to fit residues: 10.1596 Evaluate side-chains 117 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 88 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 22 optimal weight: 0.0070 chunk 41 optimal weight: 0.0040 chunk 18 optimal weight: 0.6980 chunk 64 optimal weight: 0.0170 chunk 63 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 overall best weight: 0.3048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.132579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.112665 restraints weight = 9131.849| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.54 r_work: 0.3592 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5431 Z= 0.109 Angle : 0.614 10.824 7422 Z= 0.305 Chirality : 0.040 0.280 884 Planarity : 0.004 0.048 902 Dihedral : 5.393 55.801 811 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 5.18 % Allowed : 22.00 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.33), residues: 692 helix: 1.18 (0.27), residues: 411 sheet: -0.52 (0.73), residues: 48 loop : -2.28 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 47 TYR 0.016 0.001 TYR A 229 PHE 0.011 0.001 PHE A 432 TRP 0.008 0.001 TRP A 289 HIS 0.014 0.002 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 5426) covalent geometry : angle 0.61351 ( 7412) SS BOND : bond 0.00295 ( 5) SS BOND : angle 0.73306 ( 10) hydrogen bonds : bond 0.03285 ( 309) hydrogen bonds : angle 4.46882 ( 912) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8027 (mmm) cc_final: 0.7671 (mtt) REVERT: A 133 ARG cc_start: 0.7051 (tpt170) cc_final: 0.6780 (tpp80) REVERT: A 233 MET cc_start: 0.8738 (mtm) cc_final: 0.8314 (mtt) REVERT: A 347 VAL cc_start: 0.8921 (OUTLIER) cc_final: 0.8648 (m) REVERT: A 349 SER cc_start: 0.9059 (m) cc_final: 0.8750 (p) REVERT: A 373 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8313 (tt) REVERT: B 88 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8554 (pttm) outliers start: 28 outliers final: 19 residues processed: 121 average time/residue: 0.0661 time to fit residues: 10.6111 Evaluate side-chains 115 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 88 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 28 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 35 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.128475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.108133 restraints weight = 10105.482| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.76 r_work: 0.3576 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5431 Z= 0.137 Angle : 0.647 9.119 7422 Z= 0.322 Chirality : 0.042 0.251 884 Planarity : 0.004 0.050 902 Dihedral : 5.325 56.976 811 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 5.91 % Allowed : 21.81 % Favored : 72.27 % 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: 0.09 (0.34), residues: 692 helix: 1.38 (0.27), residues: 406 sheet: -0.54 (0.74), residues: 48 loop : -2.21 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 47 TYR 0.015 0.001 TYR A 229 PHE 0.025 0.002 PHE B 69 TRP 0.009 0.001 TRP A 68 HIS 0.007 0.001 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 5426) covalent geometry : angle 0.64705 ( 7412) SS BOND : bond 0.00404 ( 5) SS BOND : angle 0.92292 ( 10) hydrogen bonds : bond 0.03481 ( 309) hydrogen bonds : angle 4.51612 ( 912) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: A 65 MET cc_start: 0.8151 (mmm) cc_final: 0.7760 (mtt) REVERT: A 133 ARG cc_start: 0.7159 (tpt170) cc_final: 0.6827 (tpp80) REVERT: A 328 MET cc_start: 0.8562 (tpp) cc_final: 0.8242 (ttm) REVERT: A 347 VAL cc_start: 0.8941 (OUTLIER) cc_final: 0.8689 (m) REVERT: A 349 SER cc_start: 0.9157 (m) cc_final: 0.8824 (p) REVERT: A 373 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8356 (tt) REVERT: B 88 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8603 (pttm) REVERT: B 90 GLU cc_start: 0.7501 (pm20) cc_final: 0.7272 (pm20) outliers start: 32 outliers final: 21 residues processed: 115 average time/residue: 0.0583 time to fit residues: 9.2399 Evaluate side-chains 112 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 61 TYR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 88 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 2 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.131268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.111591 restraints weight = 9109.794| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.41 r_work: 0.3555 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5431 Z= 0.132 Angle : 0.678 11.159 7422 Z= 0.335 Chirality : 0.042 0.236 884 Planarity : 0.004 0.050 902 Dihedral : 5.328 56.059 811 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 5.73 % Allowed : 22.37 % Favored : 71.90 % 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 (0.34), residues: 692 helix: 1.48 (0.27), residues: 407 sheet: -0.36 (0.75), residues: 48 loop : -2.16 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 47 TYR 0.013 0.001 TYR A 229 PHE 0.019 0.001 PHE A 339 TRP 0.009 0.001 TRP A 660 HIS 0.004 0.001 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 5426) covalent geometry : angle 0.67726 ( 7412) SS BOND : bond 0.00375 ( 5) SS BOND : angle 1.17271 ( 10) hydrogen bonds : bond 0.03445 ( 309) hydrogen bonds : angle 4.54320 ( 912) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: A 65 MET cc_start: 0.8106 (mmm) cc_final: 0.7715 (mtt) REVERT: A 133 ARG cc_start: 0.7122 (tpt170) cc_final: 0.6662 (tpt170) REVERT: A 328 MET cc_start: 0.8462 (tpp) cc_final: 0.8179 (ttm) REVERT: A 347 VAL cc_start: 0.8957 (OUTLIER) cc_final: 0.8726 (m) REVERT: A 349 SER cc_start: 0.9136 (m) cc_final: 0.8806 (p) REVERT: A 373 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8301 (tt) REVERT: B 88 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8564 (pttm) outliers start: 31 outliers final: 24 residues processed: 112 average time/residue: 0.0595 time to fit residues: 9.1521 Evaluate side-chains 113 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 88 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 24 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS A 666 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.129357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.108845 restraints weight = 9995.925| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.75 r_work: 0.3580 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5431 Z= 0.133 Angle : 0.674 13.272 7422 Z= 0.333 Chirality : 0.042 0.232 884 Planarity : 0.004 0.046 902 Dihedral : 5.311 55.968 811 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 5.91 % Allowed : 22.92 % Favored : 71.16 % 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: 0.31 (0.34), residues: 692 helix: 1.56 (0.27), residues: 408 sheet: -0.66 (0.72), residues: 49 loop : -2.10 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 47 TYR 0.011 0.001 TYR A 229 PHE 0.016 0.001 PHE A 339 TRP 0.009 0.001 TRP A 660 HIS 0.005 0.001 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 5426) covalent geometry : angle 0.67297 ( 7412) SS BOND : bond 0.00403 ( 5) SS BOND : angle 1.19279 ( 10) hydrogen bonds : bond 0.03411 ( 309) hydrogen bonds : angle 4.53110 ( 912) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8143 (mmm) cc_final: 0.7759 (mtt) REVERT: A 347 VAL cc_start: 0.8982 (OUTLIER) cc_final: 0.8755 (m) REVERT: A 349 SER cc_start: 0.9171 (m) cc_final: 0.8815 (p) REVERT: A 373 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8370 (tt) REVERT: A 557 TYR cc_start: 0.7753 (m-80) cc_final: 0.7525 (m-80) REVERT: B 60 ASN cc_start: 0.8010 (t0) cc_final: 0.7786 (t0) REVERT: B 68 ARG cc_start: 0.6449 (mtm110) cc_final: 0.5284 (ttp-170) outliers start: 32 outliers final: 25 residues processed: 114 average time/residue: 0.0663 time to fit residues: 10.2573 Evaluate side-chains 119 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 80 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.130831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.110737 restraints weight = 9149.440| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.55 r_work: 0.3548 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5431 Z= 0.132 Angle : 0.685 14.365 7422 Z= 0.336 Chirality : 0.042 0.250 884 Planarity : 0.004 0.044 902 Dihedral : 5.329 55.742 811 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 5.36 % Allowed : 24.03 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.38 (0.34), residues: 692 helix: 1.59 (0.27), residues: 408 sheet: -0.50 (0.71), residues: 48 loop : -2.04 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 47 TYR 0.011 0.001 TYR A 229 PHE 0.016 0.001 PHE A 339 TRP 0.009 0.001 TRP A 660 HIS 0.010 0.002 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 5426) covalent geometry : angle 0.68377 ( 7412) SS BOND : bond 0.00382 ( 5) SS BOND : angle 1.10722 ( 10) hydrogen bonds : bond 0.03386 ( 309) hydrogen bonds : angle 4.54551 ( 912) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8114 (mmm) cc_final: 0.7733 (mtt) REVERT: A 347 VAL cc_start: 0.8975 (OUTLIER) cc_final: 0.8753 (m) REVERT: A 349 SER cc_start: 0.9138 (m) cc_final: 0.8793 (p) REVERT: A 373 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8279 (tt) REVERT: B 60 ASN cc_start: 0.8069 (t0) cc_final: 0.7860 (t0) REVERT: B 68 ARG cc_start: 0.6326 (mtm110) cc_final: 0.5146 (ttp-170) outliers start: 29 outliers final: 24 residues processed: 115 average time/residue: 0.0648 time to fit residues: 9.9579 Evaluate side-chains 116 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 80 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 1 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 41 optimal weight: 0.0870 chunk 66 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.131786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.110765 restraints weight = 10057.680| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.81 r_work: 0.3597 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5431 Z= 0.127 Angle : 0.688 14.519 7422 Z= 0.336 Chirality : 0.043 0.253 884 Planarity : 0.004 0.044 902 Dihedral : 5.293 55.406 811 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.81 % Allowed : 25.14 % Favored : 70.06 % 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: 0.40 (0.34), residues: 692 helix: 1.63 (0.27), residues: 407 sheet: -0.47 (0.70), residues: 49 loop : -2.10 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 47 TYR 0.012 0.001 TYR B 61 PHE 0.016 0.001 PHE A 339 TRP 0.009 0.001 TRP A 68 HIS 0.012 0.002 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 5426) covalent geometry : angle 0.68778 ( 7412) SS BOND : bond 0.00346 ( 5) SS BOND : angle 1.01688 ( 10) hydrogen bonds : bond 0.03362 ( 309) hydrogen bonds : angle 4.52797 ( 912) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1205.20 seconds wall clock time: 21 minutes 18.34 seconds (1278.34 seconds total)