Starting phenix.real_space_refine on Fri Aug 22 17:19:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yzj_39695/08_2025/8yzj_39695.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yzj_39695/08_2025/8yzj_39695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yzj_39695/08_2025/8yzj_39695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yzj_39695/08_2025/8yzj_39695.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yzj_39695/08_2025/8yzj_39695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yzj_39695/08_2025/8yzj_39695.map" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4089 2.51 5 N 1057 2.21 5 O 1206 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6389 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "B" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1532 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Time building chain proxies: 1.68, per 1000 atoms: 0.26 Number of scatterers: 6389 At special positions: 0 Unit cell: (74.8, 92.65, 124.1, 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 37 16.00 O 1206 8.00 N 1057 7.00 C 4089 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.97 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.82 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: 0.41 Conformation dependent library (CDL) restraints added in 238.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1484 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 7 sheets defined 56.5% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 20 through 52 removed outlier: 3.597A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.562A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 removed outlier: 4.118A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 148 through 154 Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.674A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 4.212A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.789A pdb=" N HIS A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.745A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.648A pdb=" N LEU A 278 " --> pdb=" O TRP A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 removed outlier: 3.533A pdb=" N GLN A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.667A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.642A pdb=" N PHE A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 370 " --> pdb=" O MET A 366 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.920A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.888A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.569A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 482 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.939A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 removed outlier: 4.587A pdb=" N GLU A 564 " --> pdb=" O GLY A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 4.271A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.838A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.148A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.769A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.632A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.489A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 5.942A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.863A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'B' and resid 473 through 474 305 hydrogen bonds defined for protein. 858 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: 1.00 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1538 1.33 - 1.45: 1566 1.45 - 1.58: 3407 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6569 Sorted by residual: bond pdb=" CA ARG A 192 " pdb=" C ARG A 192 " ideal model delta sigma weight residual 1.523 1.567 -0.044 1.35e-02 5.49e+03 1.04e+01 bond pdb=" N CYS B 391 " pdb=" CA CYS B 391 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.21e-02 6.83e+03 9.24e+00 bond pdb=" N LEU A 148 " pdb=" CA LEU A 148 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.07e+00 bond pdb=" N ASN A 53 " pdb=" CA ASN A 53 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.85e+00 bond pdb=" CA LEU B 390 " pdb=" C LEU B 390 " ideal model delta sigma weight residual 1.521 1.550 -0.029 1.24e-02 6.50e+03 5.62e+00 ... (remaining 6564 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 8698 2.34 - 4.68: 192 4.68 - 7.02: 26 7.02 - 9.36: 10 9.36 - 11.70: 5 Bond angle restraints: 8931 Sorted by residual: angle pdb=" N ARG A 192 " pdb=" CA ARG A 192 " pdb=" C ARG A 192 " ideal model delta sigma weight residual 111.33 123.03 -11.70 1.21e+00 6.83e-01 9.36e+01 angle pdb=" N ILE A 21 " pdb=" CA ILE A 21 " pdb=" C ILE A 21 " ideal model delta sigma weight residual 113.07 102.76 10.31 1.36e+00 5.41e-01 5.75e+01 angle pdb=" N GLU A 23 " pdb=" CA GLU A 23 " pdb=" C GLU A 23 " ideal model delta sigma weight residual 111.82 120.12 -8.30 1.16e+00 7.43e-01 5.12e+01 angle pdb=" N GLU A 145 " pdb=" CA GLU A 145 " pdb=" C GLU A 145 " ideal model delta sigma weight residual 113.16 121.86 -8.70 1.42e+00 4.96e-01 3.75e+01 angle pdb=" N ILE B 472 " pdb=" CA ILE B 472 " pdb=" CB ILE B 472 " ideal model delta sigma weight residual 110.53 116.93 -6.40 1.09e+00 8.42e-01 3.45e+01 ... (remaining 8926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 3435 16.00 - 32.01: 327 32.01 - 48.01: 67 48.01 - 64.02: 18 64.02 - 80.02: 11 Dihedral angle restraints: 3858 sinusoidal: 1544 harmonic: 2314 Sorted by residual: dihedral pdb=" CA CYS A 530 " pdb=" C CYS A 530 " pdb=" N GLN A 531 " pdb=" CA GLN A 531 " ideal model delta harmonic sigma weight residual 180.00 152.82 27.18 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 138.42 -45.42 1 1.00e+01 1.00e-02 2.86e+01 dihedral pdb=" CA CYS A 344 " pdb=" C CYS A 344 " pdb=" N HIS A 345 " pdb=" CA HIS A 345 " ideal model delta harmonic sigma weight residual 180.00 158.15 21.85 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 3855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 863 0.095 - 0.191: 64 0.191 - 0.286: 6 0.286 - 0.382: 0 0.382 - 0.477: 3 Chirality restraints: 936 Sorted by residual: chirality pdb=" CA GLU A 145 " pdb=" N GLU A 145 " pdb=" C GLU A 145 " pdb=" CB GLU A 145 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.70e+00 chirality pdb=" CA ASN A 432 " pdb=" N ASN A 432 " pdb=" C ASN A 432 " pdb=" CB ASN A 432 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" CA ARG A 192 " pdb=" N ARG A 192 " pdb=" C ARG A 192 " pdb=" CB ARG A 192 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.39 2.00e-01 2.50e+01 3.71e+00 ... (remaining 933 not shown) Planarity restraints: 1159 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 143 " -0.021 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C LEU A 143 " 0.071 2.00e-02 2.50e+03 pdb=" O LEU A 143 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU A 144 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 523 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.42e+00 pdb=" C THR B 523 " -0.053 2.00e-02 2.50e+03 pdb=" O THR B 523 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL B 524 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 22 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" C GLU A 22 " -0.036 2.00e-02 2.50e+03 pdb=" O GLU A 22 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU A 23 " 0.012 2.00e-02 2.50e+03 ... (remaining 1156 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1703 2.79 - 3.32: 5922 3.32 - 3.85: 10257 3.85 - 4.37: 11914 4.37 - 4.90: 20447 Nonbonded interactions: 50243 Sorted by model distance: nonbonded pdb=" OD1 ASN A 49 " pdb=" ND2 ASN A 58 " model vdw 2.265 3.120 nonbonded pdb=" OD1 ASP A 494 " pdb=" OG1 THR A 496 " model vdw 2.281 3.040 nonbonded pdb=" OE1 GLU A 110 " pdb=" NZ LYS A 114 " model vdw 2.293 3.120 nonbonded pdb=" NH2 ARG B 457 " pdb=" OD2 ASP B 467 " model vdw 2.310 3.120 nonbonded pdb=" OE2 GLU A 208 " pdb=" ND2 ASN A 210 " model vdw 2.342 3.120 ... (remaining 50238 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.440 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.020 Find NCS groups from input model: 0.030 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:9.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 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 : 0.017 0.938 6571 Z= 0.827 Angle : 0.991 27.501 8935 Z= 0.594 Chirality : 0.058 0.477 936 Planarity : 0.005 0.050 1159 Dihedral : 14.000 80.021 2368 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.97 % Favored : 94.78 % Rotamer: Outliers : 0.29 % Allowed : 3.31 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.29 (0.25), residues: 785 helix: -2.04 (0.21), residues: 391 sheet: 1.26 (0.73), residues: 51 loop : -2.88 (0.26), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 161 TYR 0.030 0.002 TYR B 453 PHE 0.019 0.002 PHE A 523 TRP 0.014 0.002 TRP A 48 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00701 ( 6569) covalent geometry : angle 0.90967 ( 8931) SS BOND : bond 0.86599 ( 2) SS BOND : angle 18.63490 ( 4) hydrogen bonds : bond 0.17323 ( 305) hydrogen bonds : angle 6.74542 ( 858) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 199 time to evaluate : 0.250 Fit side-chains REVERT: A 34 HIS cc_start: 0.7560 (m90) cc_final: 0.7156 (m-70) REVERT: A 49 ASN cc_start: 0.7400 (t0) cc_final: 0.7019 (t0) REVERT: A 77 SER cc_start: 0.7731 (t) cc_final: 0.7515 (m) REVERT: A 98 GLN cc_start: 0.7700 (tt0) cc_final: 0.7485 (mt0) REVERT: A 100 LEU cc_start: 0.8455 (tp) cc_final: 0.8132 (tt) REVERT: A 198 ASP cc_start: 0.6289 (p0) cc_final: 0.5604 (p0) REVERT: A 201 ASP cc_start: 0.7527 (t0) cc_final: 0.6950 (m-30) REVERT: A 226 VAL cc_start: 0.8035 (p) cc_final: 0.7794 (t) REVERT: A 279 TYR cc_start: 0.7928 (t80) cc_final: 0.7696 (t80) REVERT: A 355 ASP cc_start: 0.7906 (t0) cc_final: 0.7632 (t0) REVERT: A 421 ILE cc_start: 0.7735 (mt) cc_final: 0.7428 (pt) REVERT: A 441 LYS cc_start: 0.7664 (ttpt) cc_final: 0.7367 (ttmm) REVERT: A 462 MET cc_start: 0.7621 (mtt) cc_final: 0.7333 (mtm) REVERT: A 465 LYS cc_start: 0.7123 (ttmt) cc_final: 0.6863 (ttmm) REVERT: B 399 SER cc_start: 0.8505 (p) cc_final: 0.8273 (m) REVERT: B 448 ASN cc_start: 0.8237 (t0) cc_final: 0.7936 (t0) REVERT: B 470 THR cc_start: 0.8605 (p) cc_final: 0.8358 (t) outliers start: 2 outliers final: 1 residues processed: 201 average time/residue: 0.5076 time to fit residues: 107.1159 Evaluate side-chains 140 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 98 GLN A 340 GLN A 526 GLN A 578 ASN B 388 ASN B 460 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.122775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.110414 restraints weight = 9346.885| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.85 r_work: 0.3332 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6571 Z= 0.216 Angle : 0.670 9.183 8935 Z= 0.348 Chirality : 0.046 0.199 936 Planarity : 0.005 0.046 1159 Dihedral : 5.273 56.621 858 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.55 % Favored : 97.20 % Rotamer: Outliers : 3.75 % Allowed : 12.97 % Favored : 83.29 % 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 aren not related in a simple way. whole: -1.31 (0.28), residues: 785 helix: -0.33 (0.25), residues: 392 sheet: 1.60 (0.74), residues: 48 loop : -1.85 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 514 TYR 0.018 0.002 TYR A 385 PHE 0.021 0.002 PHE A 230 TRP 0.023 0.002 TRP B 353 HIS 0.009 0.002 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 6569) covalent geometry : angle 0.67018 ( 8931) SS BOND : bond 0.00555 ( 2) SS BOND : angle 0.69251 ( 4) hydrogen bonds : bond 0.06500 ( 305) hydrogen bonds : angle 4.85437 ( 858) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.250 Fit side-chains REVERT: A 21 ILE cc_start: 0.8410 (mt) cc_final: 0.8208 (mp) REVERT: A 34 HIS cc_start: 0.8040 (m90) cc_final: 0.7789 (m-70) REVERT: A 35 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7449 (tm-30) REVERT: A 49 ASN cc_start: 0.8180 (t0) cc_final: 0.7926 (t0) REVERT: A 77 SER cc_start: 0.8254 (t) cc_final: 0.7945 (m) REVERT: A 98 GLN cc_start: 0.8580 (tt0) cc_final: 0.8257 (tt0) REVERT: A 100 LEU cc_start: 0.8661 (tp) cc_final: 0.8246 (tt) REVERT: A 115 ARG cc_start: 0.7325 (tpt90) cc_final: 0.6982 (tpt90) REVERT: A 226 VAL cc_start: 0.8257 (p) cc_final: 0.8008 (m) REVERT: A 273 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8135 (ttt90) REVERT: A 435 GLU cc_start: 0.7512 (tt0) cc_final: 0.7293 (tt0) REVERT: A 564 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7437 (mt-10) REVERT: A 593 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8554 (t) REVERT: B 392 PHE cc_start: 0.7887 (m-80) cc_final: 0.7656 (m-80) outliers start: 26 outliers final: 9 residues processed: 171 average time/residue: 0.4860 time to fit residues: 87.4094 Evaluate side-chains 161 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 514 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 40 optimal weight: 0.0470 chunk 26 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 31 optimal weight: 0.0970 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 0.0570 chunk 20 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 522 GLN A 526 GLN A 578 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.123236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.110634 restraints weight = 9313.232| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.88 r_work: 0.3330 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6571 Z= 0.138 Angle : 0.582 7.689 8935 Z= 0.298 Chirality : 0.042 0.137 936 Planarity : 0.004 0.035 1159 Dihedral : 4.148 19.040 856 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.46 % Allowed : 18.30 % Favored : 78.24 % 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 aren not related in a simple way. whole: -0.58 (0.29), residues: 785 helix: 0.37 (0.27), residues: 388 sheet: 1.36 (0.75), residues: 49 loop : -1.52 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 514 TYR 0.017 0.001 TYR A 385 PHE 0.011 0.001 PHE A 230 TRP 0.013 0.001 TRP A 478 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 6569) covalent geometry : angle 0.58211 ( 8931) SS BOND : bond 0.00157 ( 2) SS BOND : angle 0.28951 ( 4) hydrogen bonds : bond 0.05440 ( 305) hydrogen bonds : angle 4.63746 ( 858) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 HIS cc_start: 0.7990 (m90) cc_final: 0.7763 (m-70) REVERT: A 35 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7440 (tm-30) REVERT: A 77 SER cc_start: 0.8197 (t) cc_final: 0.7923 (m) REVERT: A 81 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7655 (mm-40) REVERT: A 98 GLN cc_start: 0.8576 (tt0) cc_final: 0.8225 (tt0) REVERT: A 100 LEU cc_start: 0.8701 (tp) cc_final: 0.8248 (tt) REVERT: A 115 ARG cc_start: 0.7321 (tpt90) cc_final: 0.6943 (tpt90) REVERT: A 226 VAL cc_start: 0.8159 (p) cc_final: 0.7937 (m) REVERT: A 248 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8077 (mp) REVERT: A 273 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8143 (ttt90) REVERT: A 344 CYS cc_start: 0.8089 (p) cc_final: 0.7602 (m) REVERT: A 483 GLU cc_start: 0.7832 (mp0) cc_final: 0.7405 (mp0) REVERT: A 564 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7468 (mt-10) REVERT: A 582 ARG cc_start: 0.8290 (tpp80) cc_final: 0.7909 (mmm160) REVERT: A 604 VAL cc_start: 0.8106 (p) cc_final: 0.7796 (t) REVERT: B 343 ASN cc_start: 0.5449 (m-40) cc_final: 0.5223 (m110) REVERT: B 368 LEU cc_start: 0.8543 (mt) cc_final: 0.8341 (mp) REVERT: B 392 PHE cc_start: 0.7901 (m-80) cc_final: 0.7658 (m-80) REVERT: B 442 ASP cc_start: 0.8153 (m-30) cc_final: 0.7939 (m-30) outliers start: 24 outliers final: 13 residues processed: 169 average time/residue: 0.4899 time to fit residues: 87.1835 Evaluate side-chains 169 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 514 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 26 optimal weight: 0.0060 chunk 43 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 578 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.120354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.107934 restraints weight = 9294.677| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.92 r_work: 0.3288 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6571 Z= 0.173 Angle : 0.606 9.499 8935 Z= 0.309 Chirality : 0.043 0.141 936 Planarity : 0.004 0.032 1159 Dihedral : 4.082 18.578 856 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.03 % Allowed : 19.02 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.29), residues: 785 helix: 0.55 (0.27), residues: 400 sheet: 2.08 (0.85), residues: 39 loop : -1.50 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 582 TYR 0.018 0.002 TYR A 385 PHE 0.013 0.001 PHE A 308 TRP 0.014 0.001 TRP A 478 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 6569) covalent geometry : angle 0.60647 ( 8931) SS BOND : bond 0.00156 ( 2) SS BOND : angle 0.28443 ( 4) hydrogen bonds : bond 0.06090 ( 305) hydrogen bonds : angle 4.64522 ( 858) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7098 (mp0) cc_final: 0.6806 (mp0) REVERT: A 35 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7503 (tm-30) REVERT: A 58 ASN cc_start: 0.7096 (m-40) cc_final: 0.6803 (m-40) REVERT: A 77 SER cc_start: 0.8358 (t) cc_final: 0.8009 (m) REVERT: A 81 GLN cc_start: 0.7960 (mm-40) cc_final: 0.7703 (mm-40) REVERT: A 98 GLN cc_start: 0.8617 (tt0) cc_final: 0.8265 (tt0) REVERT: A 100 LEU cc_start: 0.8667 (tp) cc_final: 0.8232 (tt) REVERT: A 115 ARG cc_start: 0.7458 (tpt90) cc_final: 0.6993 (tpt90) REVERT: A 208 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7411 (tm-30) REVERT: A 226 VAL cc_start: 0.8228 (p) cc_final: 0.8010 (t) REVERT: A 488 VAL cc_start: 0.8492 (m) cc_final: 0.8245 (t) REVERT: A 604 VAL cc_start: 0.8127 (p) cc_final: 0.7864 (t) REVERT: B 343 ASN cc_start: 0.5561 (m-40) cc_final: 0.5329 (m110) REVERT: B 449 TYR cc_start: 0.8069 (m-80) cc_final: 0.7648 (m-80) REVERT: B 518 LEU cc_start: 0.5554 (OUTLIER) cc_final: 0.5297 (pp) outliers start: 28 outliers final: 14 residues processed: 179 average time/residue: 0.4328 time to fit residues: 81.9255 Evaluate side-chains 170 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 60 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 46 optimal weight: 0.2980 chunk 35 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 578 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.120078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.107844 restraints weight = 9365.060| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.90 r_work: 0.3284 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6571 Z= 0.174 Angle : 0.624 10.216 8935 Z= 0.312 Chirality : 0.044 0.140 936 Planarity : 0.004 0.034 1159 Dihedral : 4.057 22.235 856 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.31 % Allowed : 21.76 % Favored : 74.93 % 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 aren not related in a simple way. whole: -0.23 (0.29), residues: 785 helix: 0.67 (0.27), residues: 398 sheet: 1.86 (0.83), residues: 39 loop : -1.37 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 514 TYR 0.016 0.002 TYR A 385 PHE 0.012 0.001 PHE A 523 TRP 0.016 0.001 TRP A 478 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 6569) covalent geometry : angle 0.62415 ( 8931) SS BOND : bond 0.00109 ( 2) SS BOND : angle 0.23035 ( 4) hydrogen bonds : bond 0.05967 ( 305) hydrogen bonds : angle 4.58727 ( 858) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7095 (mp0) cc_final: 0.6754 (mp0) REVERT: A 35 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7572 (tm-30) REVERT: A 58 ASN cc_start: 0.7108 (m-40) cc_final: 0.6799 (m-40) REVERT: A 98 GLN cc_start: 0.8619 (tt0) cc_final: 0.8286 (tt0) REVERT: A 100 LEU cc_start: 0.8680 (tp) cc_final: 0.8158 (tt) REVERT: A 115 ARG cc_start: 0.7458 (tpt90) cc_final: 0.7003 (tpt90) REVERT: A 182 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6932 (pt0) REVERT: A 208 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7164 (tm-30) REVERT: A 273 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8224 (ttt90) REVERT: A 479 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: A 488 VAL cc_start: 0.8500 (m) cc_final: 0.8273 (t) REVERT: A 536 GLU cc_start: 0.7806 (pm20) cc_final: 0.7522 (pm20) REVERT: A 582 ARG cc_start: 0.8241 (tpp80) cc_final: 0.7914 (mmm160) REVERT: A 604 VAL cc_start: 0.8117 (p) cc_final: 0.7875 (t) REVERT: B 343 ASN cc_start: 0.5498 (m-40) cc_final: 0.5276 (m110) REVERT: B 449 TYR cc_start: 0.8132 (m-80) cc_final: 0.7599 (m-80) REVERT: B 518 LEU cc_start: 0.5539 (OUTLIER) cc_final: 0.5187 (pp) outliers start: 23 outliers final: 15 residues processed: 166 average time/residue: 0.4653 time to fit residues: 81.2211 Evaluate side-chains 167 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.0980 chunk 34 optimal weight: 0.0970 chunk 15 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 394 ASN A 578 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.121645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.109498 restraints weight = 9363.835| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.84 r_work: 0.3310 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6571 Z= 0.139 Angle : 0.590 10.138 8935 Z= 0.294 Chirality : 0.043 0.135 936 Planarity : 0.004 0.035 1159 Dihedral : 3.916 21.276 856 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.47 % Allowed : 22.19 % Favored : 73.34 % 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 aren not related in a simple way. whole: -0.04 (0.30), residues: 785 helix: 0.84 (0.27), residues: 396 sheet: 1.76 (0.83), residues: 39 loop : -1.26 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 273 TYR 0.015 0.001 TYR A 385 PHE 0.010 0.001 PHE A 523 TRP 0.013 0.001 TRP A 165 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6569) covalent geometry : angle 0.59040 ( 8931) SS BOND : bond 0.00073 ( 2) SS BOND : angle 0.15385 ( 4) hydrogen bonds : bond 0.05383 ( 305) hydrogen bonds : angle 4.50136 ( 858) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.6951 (mp0) cc_final: 0.6579 (mp0) REVERT: A 35 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7565 (tm-30) REVERT: A 81 GLN cc_start: 0.7909 (mm-40) cc_final: 0.7664 (mp10) REVERT: A 94 LYS cc_start: 0.7816 (mttt) cc_final: 0.7612 (mttt) REVERT: A 98 GLN cc_start: 0.8617 (tt0) cc_final: 0.8297 (tt0) REVERT: A 100 LEU cc_start: 0.8677 (tp) cc_final: 0.8369 (tt) REVERT: A 115 ARG cc_start: 0.7394 (tpt90) cc_final: 0.6961 (tpt90) REVERT: A 182 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6856 (pt0) REVERT: A 208 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7106 (tm-30) REVERT: A 216 ASP cc_start: 0.7743 (m-30) cc_final: 0.7491 (m-30) REVERT: A 273 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8191 (ttt90) REVERT: A 479 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.6643 (mp0) REVERT: A 483 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: A 488 VAL cc_start: 0.8428 (m) cc_final: 0.8212 (t) REVERT: A 536 GLU cc_start: 0.7720 (pm20) cc_final: 0.7433 (pm20) REVERT: A 582 ARG cc_start: 0.8226 (tpp80) cc_final: 0.7929 (mmm160) outliers start: 31 outliers final: 17 residues processed: 166 average time/residue: 0.4347 time to fit residues: 76.1139 Evaluate side-chains 168 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 0.3980 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 38 optimal weight: 0.0970 chunk 14 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 578 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.119378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.106796 restraints weight = 9270.619| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.96 r_work: 0.3269 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6571 Z= 0.183 Angle : 0.623 10.372 8935 Z= 0.312 Chirality : 0.044 0.145 936 Planarity : 0.004 0.036 1159 Dihedral : 4.072 21.692 856 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.60 % Allowed : 22.62 % Favored : 73.78 % 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 aren not related in a simple way. whole: -0.10 (0.29), residues: 785 helix: 0.77 (0.26), residues: 398 sheet: 1.70 (0.83), residues: 39 loop : -1.26 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 514 TYR 0.019 0.002 TYR B 489 PHE 0.014 0.001 PHE A 523 TRP 0.014 0.001 TRP A 165 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 6569) covalent geometry : angle 0.62292 ( 8931) SS BOND : bond 0.00088 ( 2) SS BOND : angle 0.21105 ( 4) hydrogen bonds : bond 0.06128 ( 305) hydrogen bonds : angle 4.59462 ( 858) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7088 (mp0) cc_final: 0.6654 (mp0) REVERT: A 35 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7584 (tm-30) REVERT: A 78 THR cc_start: 0.8532 (t) cc_final: 0.8328 (t) REVERT: A 81 GLN cc_start: 0.7954 (mm-40) cc_final: 0.7684 (mp10) REVERT: A 94 LYS cc_start: 0.7802 (mttt) cc_final: 0.7601 (mttt) REVERT: A 98 GLN cc_start: 0.8619 (tt0) cc_final: 0.8314 (tt0) REVERT: A 100 LEU cc_start: 0.8640 (tp) cc_final: 0.8338 (tt) REVERT: A 105 SER cc_start: 0.8359 (p) cc_final: 0.8110 (t) REVERT: A 166 GLU cc_start: 0.8050 (tp30) cc_final: 0.7661 (tp30) REVERT: A 208 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7226 (tm-30) REVERT: A 273 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8230 (ttt90) REVERT: A 331 SER cc_start: 0.8402 (p) cc_final: 0.8165 (p) REVERT: A 430 GLU cc_start: 0.7729 (pm20) cc_final: 0.7342 (pm20) REVERT: A 472 GLN cc_start: 0.7768 (mt0) cc_final: 0.7410 (mp10) REVERT: A 476 LYS cc_start: 0.8442 (tptp) cc_final: 0.8216 (tptm) REVERT: A 479 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: A 488 VAL cc_start: 0.8488 (m) cc_final: 0.8284 (t) REVERT: A 536 GLU cc_start: 0.7774 (pm20) cc_final: 0.7528 (pm20) outliers start: 25 outliers final: 18 residues processed: 177 average time/residue: 0.5171 time to fit residues: 96.0429 Evaluate side-chains 174 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 0.2980 chunk 21 optimal weight: 0.4980 chunk 16 optimal weight: 0.1980 chunk 19 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 58 ASN A 394 ASN A 578 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.121345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.109283 restraints weight = 9237.143| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.82 r_work: 0.3311 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6571 Z= 0.138 Angle : 0.601 10.337 8935 Z= 0.302 Chirality : 0.042 0.141 936 Planarity : 0.004 0.036 1159 Dihedral : 3.902 19.667 856 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.60 % Allowed : 24.35 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.30), residues: 785 helix: 0.97 (0.27), residues: 396 sheet: 1.61 (0.83), residues: 39 loop : -1.08 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 582 TYR 0.016 0.001 TYR A 385 PHE 0.008 0.001 PHE A 523 TRP 0.012 0.001 TRP A 165 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6569) covalent geometry : angle 0.60131 ( 8931) SS BOND : bond 0.00052 ( 2) SS BOND : angle 0.16213 ( 4) hydrogen bonds : bond 0.05243 ( 305) hydrogen bonds : angle 4.48267 ( 858) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7492 (tm-30) REVERT: A 81 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7641 (mm-40) REVERT: A 94 LYS cc_start: 0.7790 (mttt) cc_final: 0.7582 (mttt) REVERT: A 98 GLN cc_start: 0.8580 (tt0) cc_final: 0.8293 (tt0) REVERT: A 105 SER cc_start: 0.8286 (p) cc_final: 0.8037 (t) REVERT: A 166 GLU cc_start: 0.8014 (tp30) cc_final: 0.7782 (tp30) REVERT: A 208 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7268 (tm-30) REVERT: A 273 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8222 (ttt90) REVERT: A 331 SER cc_start: 0.8387 (p) cc_final: 0.8152 (p) REVERT: A 430 GLU cc_start: 0.7722 (pm20) cc_final: 0.7319 (pm20) REVERT: A 479 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.6670 (mp0) REVERT: A 483 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: A 488 VAL cc_start: 0.8418 (m) cc_final: 0.8218 (t) REVERT: A 536 GLU cc_start: 0.7721 (pm20) cc_final: 0.7475 (pm20) REVERT: A 582 ARG cc_start: 0.8203 (tpp80) cc_final: 0.7885 (mmm160) outliers start: 25 outliers final: 18 residues processed: 170 average time/residue: 0.4659 time to fit residues: 83.4634 Evaluate side-chains 170 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 59 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 73 optimal weight: 0.0570 chunk 17 optimal weight: 0.9980 chunk 44 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 578 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.120131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.108079 restraints weight = 9353.529| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.90 r_work: 0.3290 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6571 Z= 0.162 Angle : 0.630 10.823 8935 Z= 0.316 Chirality : 0.043 0.142 936 Planarity : 0.004 0.035 1159 Dihedral : 3.947 19.663 856 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.60 % Allowed : 25.07 % Favored : 71.33 % 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 aren not related in a simple way. whole: 0.14 (0.30), residues: 785 helix: 0.94 (0.27), residues: 399 sheet: 0.95 (0.71), residues: 49 loop : -1.06 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 582 TYR 0.017 0.002 TYR B 489 PHE 0.012 0.001 PHE A 523 TRP 0.012 0.001 TRP A 478 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 6569) covalent geometry : angle 0.63061 ( 8931) SS BOND : bond 0.00032 ( 2) SS BOND : angle 0.16604 ( 4) hydrogen bonds : bond 0.05709 ( 305) hydrogen bonds : angle 4.49423 ( 858) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.230 Fit side-chains REVERT: A 35 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7542 (tm-30) REVERT: A 81 GLN cc_start: 0.7937 (mm-40) cc_final: 0.7683 (mm-40) REVERT: A 94 LYS cc_start: 0.7826 (mttt) cc_final: 0.7623 (mttt) REVERT: A 98 GLN cc_start: 0.8605 (tt0) cc_final: 0.8307 (tt0) REVERT: A 166 GLU cc_start: 0.8054 (tp30) cc_final: 0.7821 (tp30) REVERT: A 208 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7239 (tm-30) REVERT: A 245 ARG cc_start: 0.8469 (ttm110) cc_final: 0.8200 (ttp-170) REVERT: A 273 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8231 (ttt90) REVERT: A 331 SER cc_start: 0.8397 (p) cc_final: 0.8135 (p) REVERT: A 430 GLU cc_start: 0.7775 (pm20) cc_final: 0.7369 (pm20) REVERT: A 472 GLN cc_start: 0.7804 (mt0) cc_final: 0.7423 (mp10) REVERT: A 479 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.6735 (mp0) REVERT: A 483 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: A 488 VAL cc_start: 0.8467 (m) cc_final: 0.8251 (t) REVERT: A 527 GLU cc_start: 0.8351 (tp30) cc_final: 0.8082 (tp30) REVERT: A 536 GLU cc_start: 0.7776 (pm20) cc_final: 0.7542 (pm20) REVERT: A 547 SER cc_start: 0.7990 (t) cc_final: 0.7721 (t) REVERT: B 343 ASN cc_start: 0.5612 (m-40) cc_final: 0.5408 (m110) outliers start: 25 outliers final: 21 residues processed: 166 average time/residue: 0.5260 time to fit residues: 91.7147 Evaluate side-chains 179 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 40 optimal weight: 0.0050 chunk 55 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 394 ASN A 578 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.119660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.107668 restraints weight = 9270.118| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.89 r_work: 0.3288 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6571 Z= 0.167 Angle : 0.651 11.281 8935 Z= 0.326 Chirality : 0.044 0.144 936 Planarity : 0.004 0.035 1159 Dihedral : 3.991 18.974 856 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.75 % Allowed : 24.78 % Favored : 71.47 % 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 aren not related in a simple way. whole: 0.16 (0.30), residues: 785 helix: 0.93 (0.27), residues: 399 sheet: 0.94 (0.72), residues: 49 loop : -1.00 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 582 TYR 0.017 0.002 TYR B 489 PHE 0.012 0.001 PHE A 523 TRP 0.013 0.001 TRP A 478 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 6569) covalent geometry : angle 0.65072 ( 8931) SS BOND : bond 0.00063 ( 2) SS BOND : angle 0.17891 ( 4) hydrogen bonds : bond 0.05761 ( 305) hydrogen bonds : angle 4.52847 ( 858) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7519 (tm-30) REVERT: A 81 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7687 (mm-40) REVERT: A 94 LYS cc_start: 0.7828 (mttt) cc_final: 0.7623 (mttt) REVERT: A 98 GLN cc_start: 0.8607 (tt0) cc_final: 0.8306 (tt0) REVERT: A 166 GLU cc_start: 0.8058 (tp30) cc_final: 0.7815 (tp30) REVERT: A 208 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7285 (tm-30) REVERT: A 245 ARG cc_start: 0.8441 (ttm110) cc_final: 0.8171 (ttp-170) REVERT: A 273 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8271 (ttt90) REVERT: A 331 SER cc_start: 0.8403 (p) cc_final: 0.8144 (p) REVERT: A 430 GLU cc_start: 0.7755 (pm20) cc_final: 0.7341 (pm20) REVERT: A 479 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.6747 (mp0) REVERT: A 483 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: A 527 GLU cc_start: 0.8371 (tp30) cc_final: 0.8162 (tp30) REVERT: A 536 GLU cc_start: 0.7794 (pm20) cc_final: 0.7561 (pm20) REVERT: A 547 SER cc_start: 0.7945 (t) cc_final: 0.7691 (t) REVERT: A 582 ARG cc_start: 0.8271 (tpp80) cc_final: 0.7928 (mmm160) REVERT: A 600 LYS cc_start: 0.8054 (ttmm) cc_final: 0.7842 (ttmm) outliers start: 26 outliers final: 19 residues processed: 164 average time/residue: 0.5080 time to fit residues: 87.3429 Evaluate side-chains 175 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 33 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 56 optimal weight: 0.1980 chunk 64 optimal weight: 0.0270 chunk 35 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 12 optimal weight: 0.2980 chunk 73 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 394 ASN A 578 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.120822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.108791 restraints weight = 9227.542| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.89 r_work: 0.3303 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6571 Z= 0.148 Angle : 0.635 10.919 8935 Z= 0.318 Chirality : 0.043 0.142 936 Planarity : 0.004 0.035 1159 Dihedral : 3.912 17.699 856 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.60 % Allowed : 25.36 % Favored : 71.04 % 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 aren not related in a simple way. whole: 0.30 (0.30), residues: 785 helix: 1.07 (0.27), residues: 393 sheet: 0.93 (0.72), residues: 49 loop : -0.92 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 582 TYR 0.016 0.001 TYR A 385 PHE 0.010 0.001 PHE A 523 TRP 0.012 0.001 TRP A 478 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 6569) covalent geometry : angle 0.63542 ( 8931) SS BOND : bond 0.00010 ( 2) SS BOND : angle 0.18980 ( 4) hydrogen bonds : bond 0.05382 ( 305) hydrogen bonds : angle 4.48109 ( 858) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2387.26 seconds wall clock time: 41 minutes 18.54 seconds (2478.54 seconds total)