Starting phenix.real_space_refine on Sun Apr 27 18:32:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yzj_39695/04_2025/8yzj_39695.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yzj_39695/04_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_39695/04_2025/8yzj_39695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yzj_39695/04_2025/8yzj_39695.map" model { file = "/net/cci-nas-00/data/ceres_data/8yzj_39695/04_2025/8yzj_39695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yzj_39695/04_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-5669/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: 4.98, per 1000 atoms: 0.78 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: 1.62 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.66 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: 2.14 Time building geometry restraints manager: 1.93 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: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.070 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:13.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.190 ------------------------------------------------------------------------------- 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 : 0.728 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: 1.2275 time to fit residues: 259.6511 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 : 0.898 ------------------------------------------------------------------------------- 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 = 0.113059 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: 0.7794 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 : 1.039 Fit side-chains REVERT: A 34 HIS cc_start: 0.8029 (m90) cc_final: 0.7670 (m-70) REVERT: A 35 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7475 (tm-30) REVERT: A 49 ASN cc_start: 0.8131 (t0) cc_final: 0.7847 (t0) REVERT: A 77 SER cc_start: 0.8059 (t) cc_final: 0.7820 (m) REVERT: A 81 GLN cc_start: 0.7869 (mm-40) cc_final: 0.7537 (mm110) REVERT: A 98 GLN cc_start: 0.8451 (tt0) cc_final: 0.8100 (tt0) REVERT: A 115 ARG cc_start: 0.7135 (tpt90) cc_final: 0.6843 (tpt90) REVERT: A 226 VAL cc_start: 0.8097 (p) cc_final: 0.7889 (m) REVERT: A 273 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8133 (ttt90) REVERT: A 274 PHE cc_start: 0.8415 (m-80) cc_final: 0.8209 (m-80) REVERT: A 287 GLN cc_start: 0.7565 (pm20) cc_final: 0.7182 (pm20) REVERT: A 360 MET cc_start: 0.7653 (ttt) cc_final: 0.7394 (ttp) REVERT: A 435 GLU cc_start: 0.7402 (tt0) cc_final: 0.7188 (tt0) REVERT: A 483 GLU cc_start: 0.7785 (mp0) cc_final: 0.7482 (mp0) REVERT: A 507 SER cc_start: 0.8249 (p) cc_final: 0.8031 (t) REVERT: B 354 ASN cc_start: 0.8031 (t0) cc_final: 0.7831 (t0) outliers start: 24 outliers final: 11 residues processed: 171 average time/residue: 1.0738 time to fit residues: 193.7035 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 : 0.682 ------------------------------------------------------------------------------- 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: 0.7980 chunk 45 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 71 optimal weight: 0.0570 chunk 42 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.122468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.109985 restraints weight = 9298.913| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.92 r_work: 0.3323 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3733 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= 0.157 Angle : 0.598 9.114 8935 Z= 0.306 Chirality : 0.043 0.142 936 Planarity : 0.004 0.035 1159 Dihedral : 4.185 21.159 856 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.75 % Allowed : 17.44 % 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: -0.56 (0.29), residues: 785 helix: 0.40 (0.27), residues: 391 sheet: 1.29 (0.75), residues: 49 loop : -1.53 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 353 HIS 0.008 0.001 HIS A 241 PHE 0.014 0.001 PHE A 230 TYR 0.018 0.002 TYR A 385 ARG 0.004 0.001 ARG A 582 Details of bonding type rmsd hydrogen bonds : bond 0.05794 ( 305) hydrogen bonds : angle 4.63112 ( 858) SS BOND : bond 0.00158 ( 2) SS BOND : angle 0.38661 ( 4) covalent geometry : bond 0.00354 ( 6569) covalent geometry : angle 0.59786 ( 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 185 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 HIS cc_start: 0.8010 (m90) cc_final: 0.7784 (m-70) REVERT: A 35 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7496 (tm-30) REVERT: A 77 SER cc_start: 0.8224 (t) cc_final: 0.7939 (m) REVERT: A 81 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7567 (mm110) REVERT: A 91 LEU cc_start: 0.8196 (tp) cc_final: 0.7976 (mp) REVERT: A 98 GLN cc_start: 0.8578 (tt0) cc_final: 0.8229 (tt0) REVERT: A 115 ARG cc_start: 0.7318 (tpt90) cc_final: 0.6929 (tpt90) REVERT: A 226 VAL cc_start: 0.8166 (p) cc_final: 0.7927 (t) REVERT: A 248 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8111 (mp) REVERT: A 273 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8147 (ttt90) REVERT: A 344 CYS cc_start: 0.8095 (p) cc_final: 0.7578 (m) REVERT: A 435 GLU cc_start: 0.7554 (tt0) cc_final: 0.7289 (mt-10) REVERT: A 479 GLU cc_start: 0.7522 (tp30) cc_final: 0.6998 (mm-30) REVERT: A 483 GLU cc_start: 0.7857 (mp0) cc_final: 0.7488 (mp0) REVERT: A 564 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7490 (mt-10) REVERT: A 604 VAL cc_start: 0.8073 (OUTLIER) cc_final: 0.7815 (t) REVERT: B 368 LEU cc_start: 0.8534 (mt) cc_final: 0.8283 (mp) REVERT: B 392 PHE cc_start: 0.7873 (m-10) cc_final: 0.7453 (m-80) REVERT: B 442 ASP cc_start: 0.8143 (m-30) cc_final: 0.7936 (m-30) REVERT: B 448 ASN cc_start: 0.8330 (t0) cc_final: 0.7907 (t0) outliers start: 26 outliers final: 13 residues processed: 169 average time/residue: 1.0018 time to fit residues: 178.9147 Evaluate side-chains 171 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 A residue 604 VAL Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 393 THR 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: 0.6980 chunk 49 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 B 343 ASN B 487 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.118992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.106804 restraints weight = 9358.690| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.90 r_work: 0.3273 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6571 Z= 0.218 Angle : 0.655 11.450 8935 Z= 0.333 Chirality : 0.046 0.151 936 Planarity : 0.004 0.032 1159 Dihedral : 4.326 20.786 856 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.18 % Allowed : 19.88 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.35 (0.29), residues: 785 helix: 0.51 (0.27), residues: 392 sheet: 1.95 (0.85), residues: 39 loop : -1.34 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 353 HIS 0.008 0.001 HIS A 241 PHE 0.016 0.002 PHE A 285 TYR 0.019 0.002 TYR A 385 ARG 0.003 0.001 ARG A 582 Details of bonding type rmsd hydrogen bonds : bond 0.06706 ( 305) hydrogen bonds : angle 4.82566 ( 858) SS BOND : bond 0.00139 ( 2) SS BOND : angle 0.34439 ( 4) covalent geometry : bond 0.00513 ( 6569) covalent geometry : angle 0.65471 ( 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 196 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7493 (tm-30) REVERT: A 49 ASN cc_start: 0.8150 (t0) cc_final: 0.7917 (t0) REVERT: A 58 ASN cc_start: 0.7205 (m-40) cc_final: 0.6836 (m-40) REVERT: A 77 SER cc_start: 0.8414 (t) cc_final: 0.8059 (m) REVERT: A 91 LEU cc_start: 0.8276 (tp) cc_final: 0.8061 (mp) REVERT: A 98 GLN cc_start: 0.8614 (tt0) cc_final: 0.8282 (tt0) REVERT: A 115 ARG cc_start: 0.7456 (tpt90) cc_final: 0.7009 (tpt90) REVERT: A 208 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7343 (tm-30) REVERT: A 273 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8226 (ttt90) REVERT: A 488 VAL cc_start: 0.8477 (m) cc_final: 0.8243 (t) REVERT: A 582 ARG cc_start: 0.8280 (tpp80) cc_final: 0.7950 (mmm160) REVERT: A 604 VAL cc_start: 0.8157 (p) cc_final: 0.7913 (t) REVERT: B 368 LEU cc_start: 0.8532 (mt) cc_final: 0.8275 (mp) REVERT: B 392 PHE cc_start: 0.7998 (m-80) cc_final: 0.7628 (m-80) REVERT: B 518 LEU cc_start: 0.5577 (OUTLIER) cc_final: 0.5301 (pp) outliers start: 29 outliers final: 15 residues processed: 181 average time/residue: 1.0587 time to fit residues: 202.4345 Evaluate side-chains 173 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 491 VAL Chi-restraints excluded: chain A residue 547 SER 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: 0.7980 chunk 6 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.120231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.107857 restraints weight = 9181.600| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.91 r_work: 0.3281 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6571 Z= 0.178 Angle : 0.616 10.538 8935 Z= 0.311 Chirality : 0.044 0.142 936 Planarity : 0.004 0.035 1159 Dihedral : 4.178 22.675 856 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.75 % Allowed : 22.48 % 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 (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: -0.29 (0.29), residues: 785 helix: 0.64 (0.27), residues: 400 sheet: 1.86 (0.84), residues: 39 loop : -1.45 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 478 HIS 0.008 0.001 HIS A 374 PHE 0.013 0.001 PHE A 523 TYR 0.015 0.002 TYR A 385 ARG 0.002 0.000 ARG A 582 Details of bonding type rmsd hydrogen bonds : bond 0.06055 ( 305) hydrogen bonds : angle 4.73568 ( 858) SS BOND : bond 0.00121 ( 2) SS BOND : angle 0.24796 ( 4) covalent geometry : bond 0.00415 ( 6569) covalent geometry : angle 0.61653 ( 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 185 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.8321 (mp) cc_final: 0.8037 (mm) REVERT: A 35 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7549 (tm-30) REVERT: A 58 ASN cc_start: 0.7117 (m-40) cc_final: 0.6818 (m-40) REVERT: A 81 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7733 (mm-40) REVERT: A 91 LEU cc_start: 0.8208 (tp) cc_final: 0.8006 (mp) REVERT: A 98 GLN cc_start: 0.8589 (tt0) cc_final: 0.8260 (tt0) REVERT: A 105 SER cc_start: 0.8350 (p) cc_final: 0.8118 (t) REVERT: A 115 ARG cc_start: 0.7433 (tpt90) cc_final: 0.6956 (tpt90) REVERT: A 182 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6958 (pt0) REVERT: A 208 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7131 (tm-30) REVERT: A 273 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8221 (ttt90) REVERT: A 479 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: A 483 GLU cc_start: 0.7900 (mp0) cc_final: 0.7694 (mp0) REVERT: A 488 VAL cc_start: 0.8483 (m) cc_final: 0.8261 (t) REVERT: A 604 VAL cc_start: 0.8137 (p) cc_final: 0.7919 (t) REVERT: B 354 ASN cc_start: 0.8033 (t0) cc_final: 0.7810 (t0) REVERT: B 368 LEU cc_start: 0.8529 (mt) cc_final: 0.8278 (mp) REVERT: B 392 PHE cc_start: 0.8035 (m-80) cc_final: 0.7709 (m-80) outliers start: 26 outliers final: 15 residues processed: 172 average time/residue: 1.0818 time to fit residues: 196.3469 Evaluate side-chains 174 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 257 SER 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 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: 0.5980 chunk 48 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 54 optimal weight: 0.0370 chunk 72 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 = 0.3571 r_free = 0.3571 target = 0.120524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.108474 restraints weight = 9137.497| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.80 r_work: 0.3295 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6571 Z= 0.163 Angle : 0.603 10.132 8935 Z= 0.303 Chirality : 0.043 0.139 936 Planarity : 0.004 0.036 1159 Dihedral : 4.042 22.047 856 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % 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: -0.23 (0.29), residues: 785 helix: 0.71 (0.27), residues: 398 sheet: 1.81 (0.85), residues: 39 loop : -1.42 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 478 HIS 0.006 0.001 HIS A 374 PHE 0.012 0.001 PHE A 523 TYR 0.016 0.002 TYR A 385 ARG 0.002 0.000 ARG A 582 Details of bonding type rmsd hydrogen bonds : bond 0.05790 ( 305) hydrogen bonds : angle 4.67770 ( 858) SS BOND : bond 0.00087 ( 2) SS BOND : angle 0.22259 ( 4) covalent geometry : bond 0.00378 ( 6569) covalent geometry : angle 0.60339 ( 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 184 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 0.747 Fit side-chains REVERT: A 35 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7536 (tm-30) REVERT: A 91 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.8005 (mp) REVERT: A 98 GLN cc_start: 0.8604 (tt0) cc_final: 0.8269 (tt0) REVERT: A 105 SER cc_start: 0.8321 (p) cc_final: 0.8094 (t) REVERT: A 208 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7095 (tm-30) REVERT: A 472 GLN cc_start: 0.7682 (mt0) cc_final: 0.7402 (mp10) REVERT: A 479 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: A 488 VAL cc_start: 0.8447 (m) cc_final: 0.8245 (t) REVERT: A 582 ARG cc_start: 0.8222 (tpp80) cc_final: 0.7910 (mmm160) REVERT: A 604 VAL cc_start: 0.8163 (p) cc_final: 0.7941 (t) REVERT: B 392 PHE cc_start: 0.7995 (m-80) cc_final: 0.7781 (m-80) REVERT: B 424 LYS cc_start: 0.8757 (tppp) cc_final: 0.8418 (tppt) outliers start: 29 outliers final: 18 residues processed: 169 average time/residue: 1.0520 time to fit residues: 187.6815 Evaluate side-chains 173 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 91 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 257 SER 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 479 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 57 optimal weight: 0.4980 chunk 41 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 40 optimal weight: 0.0980 chunk 67 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 42 GLN A 58 ASN A 394 ASN A 578 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.119054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.107021 restraints weight = 9246.045| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.88 r_work: 0.3278 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6571 Z= 0.184 Angle : 0.622 9.877 8935 Z= 0.313 Chirality : 0.044 0.142 936 Planarity : 0.004 0.035 1159 Dihedral : 4.080 21.751 856 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.89 % Allowed : 24.64 % 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 (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: -0.19 (0.29), residues: 785 helix: 0.74 (0.26), residues: 398 sheet: 1.77 (0.86), residues: 39 loop : -1.38 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 165 HIS 0.007 0.001 HIS A 374 PHE 0.013 0.001 PHE A 523 TYR 0.018 0.002 TYR A 183 ARG 0.004 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.06102 ( 305) hydrogen bonds : angle 4.69454 ( 858) SS BOND : bond 0.00051 ( 2) SS BOND : angle 0.22617 ( 4) covalent geometry : bond 0.00431 ( 6569) covalent geometry : angle 0.62242 ( 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 178 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7563 (tm-30) REVERT: A 81 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7783 (mp10) REVERT: A 91 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.8012 (mp) REVERT: A 98 GLN cc_start: 0.8612 (tt0) cc_final: 0.8289 (tt0) REVERT: A 105 SER cc_start: 0.8372 (p) cc_final: 0.8163 (t) REVERT: A 208 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7104 (tm-30) REVERT: A 273 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8216 (ttt90) REVERT: A 331 SER cc_start: 0.8423 (p) cc_final: 0.8218 (p) REVERT: A 479 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: A 488 VAL cc_start: 0.8480 (m) cc_final: 0.8266 (t) REVERT: A 582 ARG cc_start: 0.8274 (tpp80) cc_final: 0.7945 (mmm160) REVERT: A 604 VAL cc_start: 0.8148 (p) cc_final: 0.7940 (t) REVERT: B 392 PHE cc_start: 0.7990 (m-80) cc_final: 0.7751 (m-80) outliers start: 27 outliers final: 20 residues processed: 163 average time/residue: 1.4513 time to fit residues: 249.7389 Evaluate side-chains 177 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 1.505 ------------------------------------------------------------------------------- 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 91 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 210 ASN 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 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 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 500 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: 0.4980 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 0.2980 chunk 7 optimal weight: 0.0980 chunk 53 optimal weight: 0.9980 chunk 44 optimal weight: 0.0770 chunk 30 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 overall best weight: 0.3338 ------------------------------------------------------------------------------- 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 = 0.121326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.109316 restraints weight = 9229.372| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.88 r_work: 0.3311 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4907 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= 0.133 Angle : 0.590 10.746 8935 Z= 0.295 Chirality : 0.042 0.137 936 Planarity : 0.004 0.037 1159 Dihedral : 3.887 19.761 856 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.03 % Allowed : 25.50 % 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 (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: 0.11 (0.30), residues: 785 helix: 0.98 (0.27), residues: 396 sheet: 0.99 (0.74), residues: 49 loop : -1.14 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 165 HIS 0.005 0.001 HIS A 241 PHE 0.009 0.001 PHE A 523 TYR 0.015 0.001 TYR A 385 ARG 0.004 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.05105 ( 305) hydrogen bonds : angle 4.55523 ( 858) SS BOND : bond 0.00057 ( 2) SS BOND : angle 0.17984 ( 4) covalent geometry : bond 0.00299 ( 6569) covalent geometry : angle 0.58963 ( 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 179 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7551 (tm-30) REVERT: A 98 GLN cc_start: 0.8585 (tt0) cc_final: 0.8288 (tt0) REVERT: A 105 SER cc_start: 0.8293 (p) cc_final: 0.8072 (t) REVERT: A 208 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7046 (tm-30) REVERT: A 331 SER cc_start: 0.8385 (p) cc_final: 0.8138 (p) REVERT: A 479 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7262 (mp0) REVERT: A 488 VAL cc_start: 0.8420 (m) cc_final: 0.8207 (t) REVERT: A 547 SER cc_start: 0.7960 (t) cc_final: 0.7710 (t) REVERT: B 392 PHE cc_start: 0.7960 (m-80) cc_final: 0.7720 (m-80) REVERT: B 424 LYS cc_start: 0.8748 (tppp) cc_final: 0.8489 (tppt) outliers start: 21 outliers final: 17 residues processed: 167 average time/residue: 1.5226 time to fit residues: 268.5883 Evaluate side-chains 172 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 132 VAL 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 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 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 500 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: 0.6980 chunk 4 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 60 optimal weight: 0.0770 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 81 GLN 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 = 0.3577 r_free = 0.3577 target = 0.120125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.108129 restraints weight = 9352.369| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.89 r_work: 0.3289 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: 0.7892 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6571 Z= 0.164 Angle : 0.629 10.780 8935 Z= 0.317 Chirality : 0.043 0.143 936 Planarity : 0.004 0.035 1159 Dihedral : 3.936 19.633 856 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.46 % Allowed : 25.50 % 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: 0.07 (0.29), residues: 785 helix: 0.92 (0.27), residues: 398 sheet: 0.96 (0.73), residues: 49 loop : -1.15 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 0.003 0.000 ARG A 582 Details of bonding type rmsd hydrogen bonds : bond 0.05668 ( 305) hydrogen bonds : angle 4.59672 ( 858) SS BOND : bond 0.00063 ( 2) SS BOND : angle 0.17514 ( 4) covalent geometry : bond 0.00382 ( 6569) covalent geometry : angle 0.62939 ( 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 175 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.708 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.6921 (mp0) cc_final: 0.6693 (mp0) REVERT: A 35 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7525 (tm-30) REVERT: A 81 GLN cc_start: 0.7962 (mm110) cc_final: 0.7737 (mp10) REVERT: A 98 GLN cc_start: 0.8603 (tt0) cc_final: 0.8306 (tt0) REVERT: A 105 SER cc_start: 0.8328 (p) cc_final: 0.8121 (t) REVERT: A 208 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7062 (tm-30) REVERT: A 273 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8219 (ttt90) REVERT: A 331 SER cc_start: 0.8386 (p) cc_final: 0.8183 (p) REVERT: A 408 MET cc_start: 0.8236 (mpp) cc_final: 0.8010 (mmt) REVERT: A 479 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: A 488 VAL cc_start: 0.8469 (m) cc_final: 0.8266 (t) REVERT: A 547 SER cc_start: 0.7995 (t) cc_final: 0.7743 (t) REVERT: A 582 ARG cc_start: 0.8240 (tpp80) cc_final: 0.7914 (mmm160) REVERT: B 392 PHE cc_start: 0.7957 (m-80) cc_final: 0.7718 (m-80) REVERT: B 424 LYS cc_start: 0.8734 (tppp) cc_final: 0.8462 (tppt) outliers start: 24 outliers final: 16 residues processed: 161 average time/residue: 1.4851 time to fit residues: 252.3870 Evaluate side-chains 168 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 132 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 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 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: 0.6980 chunk 64 optimal weight: 0.0050 chunk 56 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 16 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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 = 0.120480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.108489 restraints weight = 9324.401| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.82 r_work: 0.3297 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6571 Z= 0.160 Angle : 0.624 11.245 8935 Z= 0.314 Chirality : 0.043 0.145 936 Planarity : 0.004 0.036 1159 Dihedral : 3.939 19.193 856 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.17 % Allowed : 25.65 % 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: 0.12 (0.29), residues: 785 helix: 0.99 (0.27), residues: 392 sheet: 0.97 (0.72), residues: 49 loop : -1.12 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 478 HIS 0.006 0.001 HIS A 374 PHE 0.011 0.001 PHE A 523 TYR 0.017 0.001 TYR B 489 ARG 0.003 0.000 ARG A 582 Details of bonding type rmsd hydrogen bonds : bond 0.05617 ( 305) hydrogen bonds : angle 4.59603 ( 858) SS BOND : bond 0.00045 ( 2) SS BOND : angle 0.17784 ( 4) covalent geometry : bond 0.00370 ( 6569) covalent geometry : angle 0.62449 ( 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 171 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7507 (tm-30) REVERT: A 98 GLN cc_start: 0.8608 (tt0) cc_final: 0.8328 (tt0) REVERT: A 105 SER cc_start: 0.8297 (p) cc_final: 0.8088 (t) REVERT: A 208 GLU cc_start: 0.7548 (tm-30) cc_final: 0.6993 (tm-30) REVERT: A 331 SER cc_start: 0.8393 (p) cc_final: 0.8156 (p) REVERT: A 479 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: A 547 SER cc_start: 0.7977 (t) cc_final: 0.7735 (t) REVERT: A 582 ARG cc_start: 0.8227 (tpp80) cc_final: 0.7917 (mmm160) REVERT: A 600 LYS cc_start: 0.8054 (ttmm) cc_final: 0.7841 (ttmm) REVERT: B 392 PHE cc_start: 0.7959 (m-80) cc_final: 0.7716 (m-80) REVERT: B 424 LYS cc_start: 0.8719 (tppp) cc_final: 0.8451 (tppt) outliers start: 22 outliers final: 19 residues processed: 157 average time/residue: 1.0934 time to fit residues: 181.3405 Evaluate side-chains 169 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU 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 210 ASN Chi-restraints excluded: chain A residue 259 ILE 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 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 500 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: 0.3980 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 62 optimal weight: 0.1980 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 60 optimal weight: 0.0980 chunk 13 optimal weight: 0.7980 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 81 GLN 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 = 0.3576 r_free = 0.3576 target = 0.120721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.108676 restraints weight = 9507.785| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.86 r_work: 0.3301 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.5034 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= 0.153 Angle : 0.624 11.190 8935 Z= 0.313 Chirality : 0.043 0.142 936 Planarity : 0.004 0.036 1159 Dihedral : 3.908 18.358 856 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.46 % Allowed : 25.94 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.33 (0.30), residues: 785 helix: 1.16 (0.27), residues: 383 sheet: 0.99 (0.72), residues: 49 loop : -0.94 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 478 HIS 0.006 0.001 HIS A 374 PHE 0.010 0.001 PHE A 523 TYR 0.016 0.001 TYR B 489 ARG 0.003 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.05466 ( 305) hydrogen bonds : angle 4.58612 ( 858) SS BOND : bond 0.00040 ( 2) SS BOND : angle 0.16479 ( 4) covalent geometry : bond 0.00352 ( 6569) covalent geometry : angle 0.62462 ( 8931) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5747.85 seconds wall clock time: 102 minutes 11.90 seconds (6131.90 seconds total)