Starting phenix.real_space_refine on Sat May 10 13:45:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yzj_39695/05_2025/8yzj_39695.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yzj_39695/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8yzj_39695/05_2025/8yzj_39695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yzj_39695/05_2025/8yzj_39695.map" model { file = "/net/cci-nas-00/data/ceres_data/8yzj_39695/05_2025/8yzj_39695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yzj_39695/05_2025/8yzj_39695.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.41, per 1000 atoms: 0.69 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: 1.40 Conformation dependent library (CDL) restraints added in 862.4 milliseconds 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 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: 1.30 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: 1.92 Time building geometry restraints manager: 1.67 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: 2.150 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.630 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:11.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.930 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.002 TRP A 48 HIS 0.006 0.001 HIS A 374 PHE 0.019 0.002 PHE A 523 TYR 0.030 0.002 TYR B 453 ARG 0.002 0.000 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.17323 ( 305) hydrogen bonds : angle 6.74542 ( 858) SS BOND : bond 0.86599 ( 2) SS BOND : angle 18.63490 ( 4) covalent geometry : bond 0.00701 ( 6569) covalent geometry : angle 0.90967 ( 8931) *********************** 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 : 0.705 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: 0.7633 (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: 1.0509 time to fit residues: 222.5759 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 : 0.642 ------------------------------------------------------------------------------- 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 65 optimal weight: 0.8980 chunk 59 optimal weight: 0.0670 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 70 optimal weight: 0.0030 overall best weight: 0.4728 ------------------------------------------------------------------------------- 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 394 ASN A 526 GLN A 578 ASN B 388 ASN B 460 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.125673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.113060 restraints weight = 9197.175| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.91 r_work: 0.3371 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6571 Z= 0.167 Angle : 0.624 8.329 8935 Z= 0.323 Chirality : 0.044 0.183 936 Planarity : 0.004 0.045 1159 Dihedral : 5.100 56.183 858 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.68 % Favored : 97.07 % Rotamer: Outliers : 3.46 % Allowed : 12.54 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.28), residues: 785 helix: -0.35 (0.25), residues: 391 sheet: 1.48 (0.73), residues: 48 loop : -1.89 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 353 HIS 0.007 0.001 HIS A 241 PHE 0.020 0.002 PHE A 230 TYR 0.017 0.002 TYR A 385 ARG 0.004 0.001 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.05857 ( 305) hydrogen bonds : angle 4.77872 ( 858) SS BOND : bond 0.00835 ( 2) SS BOND : angle 0.78949 ( 4) covalent geometry : bond 0.00374 ( 6569) covalent geometry : angle 0.62393 ( 8931) *********************** 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 185 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.638 Fit side-chains REVERT: A 34 HIS cc_start: 0.8031 (m90) cc_final: 0.7670 (m-70) REVERT: A 35 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7475 (tm-30) REVERT: A 49 ASN cc_start: 0.8129 (t0) cc_final: 0.7843 (t0) REVERT: A 77 SER cc_start: 0.8058 (t) cc_final: 0.7819 (m) REVERT: A 81 GLN cc_start: 0.7866 (mm-40) cc_final: 0.7531 (mm110) REVERT: A 98 GLN cc_start: 0.8448 (tt0) cc_final: 0.8096 (tt0) REVERT: A 115 ARG cc_start: 0.7132 (tpt90) cc_final: 0.6840 (tpt90) REVERT: A 226 VAL cc_start: 0.8099 (p) cc_final: 0.7891 (m) REVERT: A 273 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8130 (ttt90) REVERT: A 274 PHE cc_start: 0.8413 (m-80) cc_final: 0.8207 (m-80) REVERT: A 287 GLN cc_start: 0.7567 (pm20) cc_final: 0.7184 (pm20) REVERT: A 360 MET cc_start: 0.7652 (ttt) cc_final: 0.7393 (ttp) REVERT: A 435 GLU cc_start: 0.7402 (tt0) cc_final: 0.7188 (tt0) REVERT: A 483 GLU cc_start: 0.7790 (mp0) cc_final: 0.7484 (mp0) REVERT: A 507 SER cc_start: 0.8248 (p) cc_final: 0.8031 (t) REVERT: B 354 ASN cc_start: 0.8033 (t0) cc_final: 0.7832 (t0) outliers start: 24 outliers final: 11 residues processed: 171 average time/residue: 0.9862 time to fit residues: 178.0582 Evaluate side-chains 163 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 68 optimal weight: 0.4980 chunk 48 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 71 optimal weight: 0.0570 chunk 42 optimal weight: 0.9990 chunk 13 optimal weight: 0.0070 overall best weight: 0.4516 ------------------------------------------------------------------------------- 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 556 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.122704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.110123 restraints weight = 9296.912| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.93 r_work: 0.3327 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6571 Z= 0.154 Angle : 0.595 8.776 8935 Z= 0.304 Chirality : 0.043 0.143 936 Planarity : 0.004 0.034 1159 Dihedral : 4.181 21.206 856 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.31 % Allowed : 17.87 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.29), residues: 785 helix: 0.41 (0.27), residues: 390 sheet: 1.27 (0.75), residues: 49 loop : -1.55 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 478 HIS 0.008 0.001 HIS A 241 PHE 0.013 0.001 PHE A 230 TYR 0.018 0.002 TYR A 385 ARG 0.004 0.000 ARG A 582 Details of bonding type rmsd hydrogen bonds : bond 0.05720 ( 305) hydrogen bonds : angle 4.62871 ( 858) SS BOND : bond 0.00142 ( 2) SS BOND : angle 0.34054 ( 4) covalent geometry : bond 0.00346 ( 6569) covalent geometry : angle 0.59533 ( 8931) *********************** 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 184 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 HIS cc_start: 0.8006 (m90) cc_final: 0.7737 (m-70) REVERT: A 35 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7519 (tm-30) REVERT: A 77 SER cc_start: 0.8204 (t) cc_final: 0.7916 (m) REVERT: A 81 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7555 (mm110) REVERT: A 91 LEU cc_start: 0.8191 (tp) cc_final: 0.7986 (mp) REVERT: A 98 GLN cc_start: 0.8565 (tt0) cc_final: 0.8199 (tt0) REVERT: A 115 ARG cc_start: 0.7303 (tpt90) cc_final: 0.6927 (tpt90) REVERT: A 226 VAL cc_start: 0.8152 (p) cc_final: 0.7927 (m) REVERT: A 248 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8077 (mp) REVERT: A 273 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8140 (ttt90) REVERT: A 344 CYS cc_start: 0.8111 (p) cc_final: 0.7492 (m) REVERT: A 483 GLU cc_start: 0.7859 (mp0) cc_final: 0.7477 (mp0) REVERT: A 564 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7490 (mt-10) REVERT: A 604 VAL cc_start: 0.8096 (p) cc_final: 0.7830 (t) REVERT: B 368 LEU cc_start: 0.8556 (mt) cc_final: 0.8308 (mp) REVERT: B 378 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8301 (mtpp) REVERT: B 442 ASP cc_start: 0.8154 (m-30) cc_final: 0.7894 (m-30) REVERT: B 448 ASN cc_start: 0.8329 (t0) cc_final: 0.7919 (t0) outliers start: 23 outliers final: 11 residues processed: 171 average time/residue: 1.0044 time to fit residues: 181.2698 Evaluate side-chains 166 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 259 ILE Chi-restraints excluded: chain A residue 273 ARG 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 50 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 12 optimal weight: 0.0470 chunk 16 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS A 578 ASN B 343 ASN B 487 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.120966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.108620 restraints weight = 9332.628| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.93 r_work: 0.3300 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6571 Z= 0.171 Angle : 0.611 9.597 8935 Z= 0.309 Chirality : 0.043 0.142 936 Planarity : 0.004 0.032 1159 Dihedral : 4.055 19.033 856 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.03 % Allowed : 20.32 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.29), residues: 785 helix: 0.66 (0.27), residues: 392 sheet: 1.87 (0.84), residues: 39 loop : -1.48 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 478 HIS 0.007 0.001 HIS A 241 PHE 0.014 0.002 PHE A 285 TYR 0.018 0.002 TYR A 385 ARG 0.003 0.000 ARG A 582 Details of bonding type rmsd hydrogen bonds : bond 0.05875 ( 305) hydrogen bonds : angle 4.61790 ( 858) SS BOND : bond 0.00128 ( 2) SS BOND : angle 0.27663 ( 4) covalent geometry : bond 0.00394 ( 6569) covalent geometry : angle 0.61117 ( 8931) *********************** 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 193 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7527 (tm-30) REVERT: A 58 ASN cc_start: 0.7094 (m-40) cc_final: 0.6821 (m-40) REVERT: A 77 SER cc_start: 0.8323 (t) cc_final: 0.8003 (m) REVERT: A 91 LEU cc_start: 0.8312 (tp) cc_final: 0.8106 (mp) REVERT: A 98 GLN cc_start: 0.8598 (tt0) cc_final: 0.8256 (tt0) REVERT: A 115 ARG cc_start: 0.7409 (tpt90) cc_final: 0.7041 (tpt90) REVERT: A 226 VAL cc_start: 0.8164 (p) cc_final: 0.7962 (t) REVERT: A 476 LYS cc_start: 0.8067 (tppp) cc_final: 0.7865 (tptp) REVERT: A 488 VAL cc_start: 0.8471 (m) cc_final: 0.8225 (t) REVERT: A 582 ARG cc_start: 0.8266 (tpp80) cc_final: 0.7921 (mmm160) REVERT: A 604 VAL cc_start: 0.8147 (p) cc_final: 0.7885 (t) REVERT: B 354 ASN cc_start: 0.8020 (OUTLIER) cc_final: 0.7818 (t0) REVERT: B 368 LEU cc_start: 0.8501 (mt) cc_final: 0.8271 (mp) REVERT: B 449 TYR cc_start: 0.8184 (m-80) cc_final: 0.7716 (m-80) REVERT: B 518 LEU cc_start: 0.5509 (OUTLIER) cc_final: 0.5296 (pp) outliers start: 28 outliers final: 14 residues processed: 176 average time/residue: 0.9864 time to fit residues: 183.8257 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 : 0.648 ------------------------------------------------------------------------------- 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 410 LEU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain B residue 354 ASN 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 36 optimal weight: 0.8980 chunk 6 optimal weight: 0.2980 chunk 29 optimal weight: 0.6980 chunk 17 optimal weight: 0.0270 chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 34 optimal weight: 0.0770 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.121464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.109284 restraints weight = 9181.483| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.89 r_work: 0.3309 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6571 Z= 0.141 Angle : 0.591 9.829 8935 Z= 0.297 Chirality : 0.043 0.137 936 Planarity : 0.004 0.034 1159 Dihedral : 3.933 21.698 856 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.17 % Allowed : 21.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.30), residues: 785 helix: 0.77 (0.27), residues: 398 sheet: 1.72 (0.83), residues: 39 loop : -1.32 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 477 HIS 0.005 0.001 HIS A 241 PHE 0.010 0.001 PHE A 308 TYR 0.015 0.001 TYR A 385 ARG 0.003 0.000 ARG A 582 Details of bonding type rmsd hydrogen bonds : bond 0.05315 ( 305) hydrogen bonds : angle 4.49910 ( 858) SS BOND : bond 0.00115 ( 2) SS BOND : angle 0.19596 ( 4) covalent geometry : bond 0.00317 ( 6569) covalent geometry : angle 0.59161 ( 8931) *********************** 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 184 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.8282 (mp) cc_final: 0.7976 (mm) REVERT: A 35 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7584 (tm-30) REVERT: A 58 ASN cc_start: 0.6994 (m-40) cc_final: 0.6689 (m-40) REVERT: A 91 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8050 (mp) REVERT: A 98 GLN cc_start: 0.8585 (tt0) cc_final: 0.8241 (tt0) REVERT: A 105 SER cc_start: 0.8311 (p) cc_final: 0.8048 (t) REVERT: A 115 ARG cc_start: 0.7265 (tpt90) cc_final: 0.6863 (tpt90) REVERT: A 166 GLU cc_start: 0.8019 (tp30) cc_final: 0.7754 (tp30) REVERT: A 216 ASP cc_start: 0.7775 (m-30) cc_final: 0.7510 (m-30) REVERT: A 226 VAL cc_start: 0.8112 (p) cc_final: 0.7901 (t) REVERT: A 273 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8177 (ttt90) REVERT: A 476 LYS cc_start: 0.8090 (tppp) cc_final: 0.7868 (tptp) REVERT: A 488 VAL cc_start: 0.8475 (m) cc_final: 0.8239 (t) REVERT: A 541 LYS cc_start: 0.8206 (mtpp) cc_final: 0.8005 (mttm) REVERT: A 604 VAL cc_start: 0.8116 (p) cc_final: 0.7886 (t) REVERT: B 368 LEU cc_start: 0.8494 (mt) cc_final: 0.8254 (mp) REVERT: B 518 LEU cc_start: 0.5406 (OUTLIER) cc_final: 0.5062 (pp) outliers start: 22 outliers final: 14 residues processed: 169 average time/residue: 1.0537 time to fit residues: 188.8496 Evaluate side-chains 174 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU 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 273 ARG 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 485 VAL 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 21 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 54 optimal weight: 0.0050 chunk 72 optimal weight: 0.3980 chunk 34 optimal weight: 0.0570 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 overall best weight: 0.3312 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.122134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.109975 restraints weight = 9167.631| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.89 r_work: 0.3321 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6571 Z= 0.130 Angle : 0.593 11.198 8935 Z= 0.294 Chirality : 0.042 0.134 936 Planarity : 0.004 0.034 1159 Dihedral : 3.793 20.395 856 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.60 % Allowed : 23.34 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.29), residues: 785 helix: 0.81 (0.27), residues: 398 sheet: 1.76 (0.84), residues: 39 loop : -1.29 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 478 HIS 0.005 0.001 HIS A 374 PHE 0.009 0.001 PHE A 308 TYR 0.016 0.001 TYR B 489 ARG 0.002 0.000 ARG A 582 Details of bonding type rmsd hydrogen bonds : bond 0.05043 ( 305) hydrogen bonds : angle 4.42925 ( 858) SS BOND : bond 0.00074 ( 2) SS BOND : angle 0.18380 ( 4) covalent geometry : bond 0.00292 ( 6569) covalent geometry : angle 0.59319 ( 8931) *********************** 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 183 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.8137 (mp) cc_final: 0.7881 (mm) REVERT: A 35 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7521 (tm-30) REVERT: A 98 GLN cc_start: 0.8625 (tt0) cc_final: 0.8265 (tt0) REVERT: A 105 SER cc_start: 0.8313 (p) cc_final: 0.8051 (t) REVERT: A 185 VAL cc_start: 0.7742 (p) cc_final: 0.7480 (m) REVERT: A 216 ASP cc_start: 0.7801 (m-30) cc_final: 0.7519 (m-30) REVERT: A 479 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: A 488 VAL cc_start: 0.8501 (m) cc_final: 0.8256 (t) REVERT: A 582 ARG cc_start: 0.8221 (tpp80) cc_final: 0.7912 (mmm160) REVERT: A 604 VAL cc_start: 0.8126 (p) cc_final: 0.7901 (t) REVERT: B 368 LEU cc_start: 0.8473 (mt) cc_final: 0.8235 (mp) REVERT: B 392 PHE cc_start: 0.7981 (m-10) cc_final: 0.7565 (m-80) outliers start: 25 outliers final: 20 residues processed: 168 average time/residue: 1.0448 time to fit residues: 185.3483 Evaluate side-chains 176 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 132 VAL 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 362 THR 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 485 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 542 CYS 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 53 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 63 optimal weight: 0.0470 chunk 40 optimal weight: 0.2980 chunk 67 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.120563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.108557 restraints weight = 9192.978| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.88 r_work: 0.3296 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6571 Z= 0.162 Angle : 0.623 10.124 8935 Z= 0.311 Chirality : 0.043 0.143 936 Planarity : 0.004 0.035 1159 Dihedral : 3.878 20.591 856 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.18 % Allowed : 23.63 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.29), residues: 785 helix: 0.82 (0.26), residues: 399 sheet: 1.70 (0.84), residues: 39 loop : -1.32 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.006 0.001 HIS A 374 PHE 0.012 0.001 PHE A 523 TYR 0.018 0.002 TYR B 489 ARG 0.002 0.000 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.05686 ( 305) hydrogen bonds : angle 4.47835 ( 858) SS BOND : bond 0.00061 ( 2) SS BOND : angle 0.20378 ( 4) covalent geometry : bond 0.00375 ( 6569) covalent geometry : angle 0.62361 ( 8931) *********************** 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 179 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7584 (tm-30) REVERT: A 58 ASN cc_start: 0.7064 (m-40) cc_final: 0.6758 (m-40) REVERT: A 94 LYS cc_start: 0.7800 (mttt) cc_final: 0.7570 (mttt) REVERT: A 98 GLN cc_start: 0.8617 (tt0) cc_final: 0.8264 (tt0) REVERT: A 105 SER cc_start: 0.8339 (p) cc_final: 0.8095 (t) REVERT: A 185 VAL cc_start: 0.7873 (p) cc_final: 0.7634 (m) REVERT: A 273 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8196 (ttt90) REVERT: A 408 MET cc_start: 0.8414 (mpp) cc_final: 0.8187 (mmt) REVERT: A 479 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: A 488 VAL cc_start: 0.8500 (m) cc_final: 0.8279 (t) REVERT: A 509 ASP cc_start: 0.7057 (OUTLIER) cc_final: 0.6776 (t0) REVERT: A 604 VAL cc_start: 0.8131 (p) cc_final: 0.7905 (t) REVERT: B 392 PHE cc_start: 0.7986 (m-10) cc_final: 0.7590 (m-80) outliers start: 29 outliers final: 18 residues processed: 161 average time/residue: 1.0304 time to fit residues: 175.0140 Evaluate side-chains 169 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 132 VAL 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 273 ARG Chi-restraints excluded: chain A residue 362 THR 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 491 VAL Chi-restraints excluded: chain A residue 509 ASP 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 13 optimal weight: 0.7980 chunk 39 optimal weight: 0.0870 chunk 24 optimal weight: 0.1980 chunk 21 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 53 optimal weight: 0.0070 chunk 44 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 64 optimal weight: 0.0040 overall best weight: 0.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 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 = 0.3652 r_free = 0.3652 target = 0.125478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.113469 restraints weight = 9240.650| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.90 r_work: 0.3375 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6571 Z= 0.109 Angle : 0.567 10.374 8935 Z= 0.281 Chirality : 0.040 0.129 936 Planarity : 0.004 0.035 1159 Dihedral : 3.564 17.171 856 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.88 % Allowed : 25.50 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.30), residues: 785 helix: 1.24 (0.27), residues: 390 sheet: 0.63 (0.72), residues: 51 loop : -0.92 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 165 HIS 0.003 0.001 HIS A 241 PHE 0.010 0.001 PHE B 377 TYR 0.014 0.001 TYR A 385 ARG 0.002 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.03955 ( 305) hydrogen bonds : angle 4.26202 ( 858) SS BOND : bond 0.00095 ( 2) SS BOND : angle 0.12997 ( 4) covalent geometry : bond 0.00232 ( 6569) covalent geometry : angle 0.56760 ( 8931) *********************** 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 175 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.7938 (mp) cc_final: 0.7665 (mm) REVERT: A 35 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7530 (tm-30) REVERT: A 94 LYS cc_start: 0.7804 (mttt) cc_final: 0.7557 (mttt) REVERT: A 98 GLN cc_start: 0.8524 (tt0) cc_final: 0.8232 (tt0) REVERT: A 105 SER cc_start: 0.8241 (p) cc_final: 0.7980 (t) REVERT: A 185 VAL cc_start: 0.7503 (p) cc_final: 0.7192 (m) REVERT: A 216 ASP cc_start: 0.7660 (m-30) cc_final: 0.7393 (m-30) REVERT: A 479 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: A 488 VAL cc_start: 0.8402 (m) cc_final: 0.8148 (t) REVERT: A 582 ARG cc_start: 0.8167 (tpp80) cc_final: 0.7851 (mmm160) REVERT: A 604 VAL cc_start: 0.8101 (p) cc_final: 0.7887 (t) REVERT: B 392 PHE cc_start: 0.7985 (m-10) cc_final: 0.7606 (m-80) outliers start: 20 outliers final: 13 residues processed: 161 average time/residue: 0.9764 time to fit residues: 166.4435 Evaluate side-chains 164 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 45 LEU 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 293 VAL Chi-restraints excluded: chain A residue 364 VAL 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 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 37 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 60 optimal weight: 0.0970 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.119317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.107430 restraints weight = 9347.305| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.89 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: 0.7895 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 6571 Z= 0.193 Angle : 0.654 10.992 8935 Z= 0.326 Chirality : 0.044 0.146 936 Planarity : 0.004 0.033 1159 Dihedral : 3.904 19.556 856 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.88 % Allowed : 25.94 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.29), residues: 785 helix: 0.95 (0.27), residues: 399 sheet: 1.66 (0.84), residues: 39 loop : -1.24 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 353 HIS 0.007 0.001 HIS A 241 PHE 0.013 0.001 PHE A 523 TYR 0.022 0.002 TYR B 489 ARG 0.002 0.000 ARG A 582 Details of bonding type rmsd hydrogen bonds : bond 0.06131 ( 305) hydrogen bonds : angle 4.49437 ( 858) SS BOND : bond 0.00066 ( 2) SS BOND : angle 0.22980 ( 4) covalent geometry : bond 0.00455 ( 6569) covalent geometry : angle 0.65458 ( 8931) *********************** 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 165 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7560 (tm-30) REVERT: A 58 ASN cc_start: 0.7081 (m-40) cc_final: 0.6765 (m-40) REVERT: A 94 LYS cc_start: 0.7797 (mttt) cc_final: 0.7558 (mttt) REVERT: A 98 GLN cc_start: 0.8611 (tt0) cc_final: 0.8298 (tt0) REVERT: A 105 SER cc_start: 0.8341 (p) cc_final: 0.8132 (t) REVERT: A 131 LYS cc_start: 0.7563 (mppt) cc_final: 0.7026 (mppt) REVERT: A 156 LEU cc_start: 0.8712 (mp) cc_final: 0.8471 (mp) REVERT: A 216 ASP cc_start: 0.7819 (m-30) cc_final: 0.7556 (m-30) REVERT: A 410 LEU cc_start: 0.8689 (tt) cc_final: 0.8465 (tp) REVERT: A 479 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: A 488 VAL cc_start: 0.8536 (m) cc_final: 0.8308 (t) REVERT: A 547 SER cc_start: 0.8067 (t) cc_final: 0.7782 (t) REVERT: A 604 VAL cc_start: 0.8100 (p) cc_final: 0.7882 (t) outliers start: 20 outliers final: 13 residues processed: 153 average time/residue: 1.1055 time to fit residues: 178.1021 Evaluate side-chains 158 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 189 GLU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 364 VAL 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 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 13 optimal weight: 0.7980 chunk 64 optimal weight: 0.0470 chunk 56 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 61 optimal weight: 0.2980 chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 578 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.121019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.109125 restraints weight = 9337.841| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.89 r_work: 0.3314 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6571 Z= 0.139 Angle : 0.622 11.417 8935 Z= 0.309 Chirality : 0.042 0.136 936 Planarity : 0.004 0.035 1159 Dihedral : 3.813 18.100 856 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.74 % Allowed : 26.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.30), residues: 785 helix: 1.06 (0.27), residues: 397 sheet: 0.90 (0.72), residues: 49 loop : -1.06 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 478 HIS 0.005 0.001 HIS A 241 PHE 0.009 0.001 PHE A 523 TYR 0.017 0.001 TYR B 489 ARG 0.006 0.000 ARG A 582 Details of bonding type rmsd hydrogen bonds : bond 0.05194 ( 305) hydrogen bonds : angle 4.40937 ( 858) SS BOND : bond 0.00053 ( 2) SS BOND : angle 0.14846 ( 4) covalent geometry : bond 0.00316 ( 6569) covalent geometry : angle 0.62164 ( 8931) ********************** 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 166 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.8067 (mp) cc_final: 0.7807 (mm) REVERT: A 35 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7542 (tm-30) REVERT: A 94 LYS cc_start: 0.7790 (mttt) cc_final: 0.7545 (mttt) REVERT: A 98 GLN cc_start: 0.8600 (tt0) cc_final: 0.8335 (tt0) REVERT: A 105 SER cc_start: 0.8271 (p) cc_final: 0.8055 (t) REVERT: A 131 LYS cc_start: 0.7514 (mppt) cc_final: 0.6998 (mppt) REVERT: A 185 VAL cc_start: 0.7820 (p) cc_final: 0.7561 (m) REVERT: A 197 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7081 (tm-30) REVERT: A 216 ASP cc_start: 0.7802 (m-30) cc_final: 0.7525 (m-30) REVERT: A 273 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8190 (ttt90) REVERT: A 410 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8486 (tp) REVERT: A 479 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: A 485 VAL cc_start: 0.8440 (t) cc_final: 0.8101 (p) REVERT: A 488 VAL cc_start: 0.8458 (m) cc_final: 0.8234 (t) REVERT: A 547 SER cc_start: 0.7939 (t) cc_final: 0.7666 (t) REVERT: A 582 ARG cc_start: 0.8253 (tpp80) cc_final: 0.7908 (mmm160) outliers start: 19 outliers final: 12 residues processed: 156 average time/residue: 1.0324 time to fit residues: 169.8377 Evaluate side-chains 159 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 47 SER 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 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 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 17 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 62 optimal weight: 0.0980 chunk 11 optimal weight: 0.0980 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 578 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.120446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.108529 restraints weight = 9529.306| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.91 r_work: 0.3305 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4996 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= 0.151 Angle : 0.632 11.444 8935 Z= 0.316 Chirality : 0.043 0.138 936 Planarity : 0.004 0.034 1159 Dihedral : 3.862 17.688 856 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.74 % Allowed : 26.37 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.30), residues: 785 helix: 0.99 (0.27), residues: 399 sheet: 0.87 (0.72), residues: 49 loop : -1.09 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 478 HIS 0.005 0.001 HIS A 241 PHE 0.009 0.001 PHE A 523 TYR 0.018 0.002 TYR B 489 ARG 0.005 0.000 ARG A 582 Details of bonding type rmsd hydrogen bonds : bond 0.05438 ( 305) hydrogen bonds : angle 4.43146 ( 858) SS BOND : bond 0.00041 ( 2) SS BOND : angle 0.16814 ( 4) covalent geometry : bond 0.00344 ( 6569) covalent geometry : angle 0.63187 ( 8931) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5173.09 seconds wall clock time: 89 minutes 44.73 seconds (5384.73 seconds total)