Starting phenix.real_space_refine on Tue Jan 14 00:05:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f6o_50236/01_2025/9f6o_50236.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f6o_50236/01_2025/9f6o_50236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f6o_50236/01_2025/9f6o_50236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f6o_50236/01_2025/9f6o_50236.map" model { file = "/net/cci-nas-00/data/ceres_data/9f6o_50236/01_2025/9f6o_50236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f6o_50236/01_2025/9f6o_50236.cif" } resolution = 3.9 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= 0.025 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 25 5.16 5 C 2995 2.51 5 N 747 2.21 5 O 804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 4571 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3651 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 16, 'TRANS': 454} Chain: "B" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 920 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Time building chain proxies: 3.16, per 1000 atoms: 0.69 Number of scatterers: 4571 At special positions: 0 Unit cell: (100.254, 72.912, 88.536, 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 25 16.00 O 804 8.00 N 747 7.00 C 2995 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 363 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.02 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: 1.21 Conformation dependent library (CDL) restraints added in 542.8 milliseconds 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1074 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 3 sheets defined 70.1% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 95 through 102 Processing helix chain 'A' and resid 104 through 112 removed outlier: 3.823A pdb=" N LEU A 108 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 111 " --> pdb=" O PHE A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 128 removed outlier: 3.623A pdb=" N SER A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 158 removed outlier: 3.577A pdb=" N LEU A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 168 Processing helix chain 'A' and resid 171 through 205 removed outlier: 3.578A pdb=" N ALA A 185 " --> pdb=" O MET A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 removed outlier: 3.866A pdb=" N THR A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 232 removed outlier: 3.728A pdb=" N THR A 222 " --> pdb=" O THR A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 259 Processing helix chain 'A' and resid 261 through 271 Processing helix chain 'A' and resid 278 through 293 Processing helix chain 'A' and resid 296 through 308 removed outlier: 3.660A pdb=" N ARG A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 350 removed outlier: 4.011A pdb=" N VAL A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU A 320 " --> pdb=" O GLN A 316 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 367 removed outlier: 3.603A pdb=" N VAL A 359 " --> pdb=" O THR A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 430 Proline residue: A 398 - end of helix removed outlier: 3.739A pdb=" N LEU A 401 " --> pdb=" O GLY A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 459 removed outlier: 3.692A pdb=" N ILE A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix removed outlier: 3.688A pdb=" N LEU A 454 " --> pdb=" O ILE A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 478 removed outlier: 3.867A pdb=" N ASN A 468 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP A 469 " --> pdb=" O THR A 465 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 482 Processing helix chain 'A' and resid 483 through 490 removed outlier: 3.640A pdb=" N LEU A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 497 Processing helix chain 'A' and resid 502 through 532 removed outlier: 3.645A pdb=" N VAL A 525 " --> pdb=" O MET A 521 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 526 " --> pdb=" O TYR A 522 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 531 " --> pdb=" O TYR A 527 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 532 " --> pdb=" O VAL A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 562 Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.628A pdb=" N THR B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.857A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER B 25 " --> pdb=" O GLN B 3 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL B 79 " --> pdb=" O CYS B 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.462A pdb=" N GLY B 10 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N SER B 120 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL B 12 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS B 99 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLY B 33 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ARG B 38 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLY B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.462A pdb=" N GLY B 10 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N SER B 120 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL B 12 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 98 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR B 110 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP B 100 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR B 108 " --> pdb=" O ASP B 100 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 933 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: 1.29 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1421 1.34 - 1.46: 1181 1.46 - 1.58: 2040 1.58 - 1.70: 0 1.70 - 1.82: 39 Bond restraints: 4681 Sorted by residual: bond pdb=" N GLY B 16 " pdb=" CA GLY B 16 " ideal model delta sigma weight residual 1.444 1.474 -0.030 9.60e-03 1.09e+04 9.47e+00 bond pdb=" N ARG B 19 " pdb=" CA ARG B 19 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 7.17e+00 bond pdb=" CA SER A 414 " pdb=" CB SER A 414 " ideal model delta sigma weight residual 1.530 1.489 0.041 1.57e-02 4.06e+03 6.70e+00 bond pdb=" N LEU B 20 " pdb=" CA LEU B 20 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.31e-02 5.83e+03 6.67e+00 bond pdb=" CA SER A 476 " pdb=" CB SER A 476 " ideal model delta sigma weight residual 1.528 1.488 0.040 1.66e-02 3.63e+03 5.93e+00 ... (remaining 4676 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 6172 1.90 - 3.79: 138 3.79 - 5.69: 44 5.69 - 7.59: 7 7.59 - 9.48: 7 Bond angle restraints: 6368 Sorted by residual: angle pdb=" N ILE B 51 " pdb=" CA ILE B 51 " pdb=" C ILE B 51 " ideal model delta sigma weight residual 111.88 104.09 7.79 1.06e+00 8.90e-01 5.41e+01 angle pdb=" N GLY B 10 " pdb=" CA GLY B 10 " pdb=" C GLY B 10 " ideal model delta sigma weight residual 110.46 117.17 -6.71 1.43e+00 4.89e-01 2.20e+01 angle pdb=" CA THR A 103 " pdb=" CB THR A 103 " pdb=" OG1 THR A 103 " ideal model delta sigma weight residual 109.60 103.33 6.27 1.50e+00 4.44e-01 1.74e+01 angle pdb=" N SER A 476 " pdb=" CA SER A 476 " pdb=" C SER A 476 " ideal model delta sigma weight residual 111.82 107.22 4.60 1.16e+00 7.43e-01 1.57e+01 angle pdb=" N GLN A 478 " pdb=" CA GLN A 478 " pdb=" C GLN A 478 " ideal model delta sigma weight residual 113.15 108.97 4.18 1.19e+00 7.06e-01 1.23e+01 ... (remaining 6363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 2202 15.07 - 30.14: 327 30.14 - 45.21: 131 45.21 - 60.27: 42 60.27 - 75.34: 2 Dihedral angle restraints: 2704 sinusoidal: 1015 harmonic: 1689 Sorted by residual: dihedral pdb=" CA ASN B 52 " pdb=" C ASN B 52 " pdb=" N SER B 53 " pdb=" CA SER B 53 " ideal model delta harmonic sigma weight residual -180.00 -162.30 -17.70 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA TYR B 80 " pdb=" C TYR B 80 " pdb=" N LEU B 81 " pdb=" CA LEU B 81 " ideal model delta harmonic sigma weight residual 180.00 163.68 16.32 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" N TYR A 231 " pdb=" CA TYR A 231 " pdb=" CB TYR A 231 " pdb=" CG TYR A 231 " ideal model delta sinusoidal sigma weight residual -180.00 -120.14 -59.86 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 2701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 525 0.040 - 0.079: 152 0.079 - 0.119: 45 0.119 - 0.159: 8 0.159 - 0.199: 5 Chirality restraints: 735 Sorted by residual: chirality pdb=" CA ILE B 51 " pdb=" N ILE B 51 " pdb=" C ILE B 51 " pdb=" CB ILE B 51 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.86e-01 chirality pdb=" CB ILE B 51 " pdb=" CA ILE B 51 " pdb=" CG1 ILE B 51 " pdb=" CG2 ILE B 51 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.20 2.00e-01 2.50e+01 9.51e-01 chirality pdb=" CA CYS B 22 " pdb=" N CYS B 22 " pdb=" C CYS B 22 " pdb=" CB CYS B 22 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.01e-01 ... (remaining 732 not shown) Planarity restraints: 792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 475 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C GLN A 475 " -0.062 2.00e-02 2.50e+03 pdb=" O GLN A 475 " 0.023 2.00e-02 2.50e+03 pdb=" N SER A 476 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 301 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C HIS A 301 " 0.030 2.00e-02 2.50e+03 pdb=" O HIS A 301 " -0.011 2.00e-02 2.50e+03 pdb=" N SER A 302 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 104 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.62e+00 pdb=" N PRO A 105 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 105 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 105 " -0.023 5.00e-02 4.00e+02 ... (remaining 789 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1226 2.79 - 3.32: 4704 3.32 - 3.85: 7890 3.85 - 4.37: 8410 4.37 - 4.90: 14273 Nonbonded interactions: 36503 Sorted by model distance: nonbonded pdb=" OD2 ASP A 377 " pdb=" OG SER A 379 " model vdw 2.268 3.040 nonbonded pdb=" O SER B 85 " pdb=" OG SER B 85 " model vdw 2.270 3.040 nonbonded pdb=" O GLY A 353 " pdb=" ND2 ASN B 74 " model vdw 2.287 3.120 nonbonded pdb=" O LEU A 487 " pdb=" OG SER A 491 " model vdw 2.290 3.040 nonbonded pdb=" N GLN B 13 " pdb=" OE1 GLN B 13 " model vdw 2.324 3.120 ... (remaining 36498 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.600 Find NCS groups from input model: 0.040 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 4681 Z= 0.255 Angle : 0.798 9.483 6368 Z= 0.440 Chirality : 0.043 0.199 735 Planarity : 0.004 0.040 792 Dihedral : 17.495 75.343 1624 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.07 % Allowed : 40.78 % Favored : 56.15 % 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: 0.92 (0.35), residues: 587 helix: 1.62 (0.27), residues: 379 sheet: -0.29 (0.59), residues: 65 loop : -1.68 (0.49), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 36 HIS 0.004 0.001 HIS A 301 PHE 0.015 0.001 PHE A 347 TYR 0.016 0.001 TYR B 95 ARG 0.007 0.001 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8587 (tm-30) REVERT: A 347 PHE cc_start: 0.8947 (m-80) cc_final: 0.8452 (t80) REVERT: A 478 GLN cc_start: 0.9334 (pp30) cc_final: 0.8968 (pp30) REVERT: A 521 MET cc_start: 0.8459 (ppp) cc_final: 0.8166 (ppp) REVERT: A 537 TYR cc_start: 0.3868 (OUTLIER) cc_final: 0.1977 (t80) REVERT: B 21 SER cc_start: 0.8393 (OUTLIER) cc_final: 0.8155 (p) REVERT: B 80 TYR cc_start: 0.8030 (m-10) cc_final: 0.7644 (m-10) REVERT: B 99 LYS cc_start: 0.8723 (mmmm) cc_final: 0.7959 (mmtm) outliers start: 15 outliers final: 6 residues processed: 129 average time/residue: 0.1307 time to fit residues: 22.5664 Evaluate side-chains 123 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 54 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.131101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.108995 restraints weight = 9681.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.112234 restraints weight = 5027.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.114423 restraints weight = 3086.182| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4681 Z= 0.255 Angle : 0.650 8.882 6368 Z= 0.336 Chirality : 0.041 0.201 735 Planarity : 0.004 0.044 792 Dihedral : 6.763 57.039 653 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 8.81 % Allowed : 31.35 % Favored : 59.84 % 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: 0.91 (0.34), residues: 587 helix: 1.61 (0.26), residues: 388 sheet: -0.40 (0.69), residues: 57 loop : -1.78 (0.46), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 179 HIS 0.002 0.001 HIS A 301 PHE 0.017 0.001 PHE A 347 TYR 0.010 0.001 TYR B 103 ARG 0.005 0.001 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 121 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ASP cc_start: 0.8494 (p0) cc_final: 0.7965 (p0) REVERT: A 153 ARG cc_start: 0.7582 (mtp180) cc_final: 0.7099 (mtp180) REVERT: A 269 MET cc_start: 0.7758 (ttm) cc_final: 0.7532 (ttp) REVERT: A 283 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8649 (tm-30) REVERT: A 347 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.8766 (t80) REVERT: A 395 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.8475 (m-10) REVERT: A 435 TRP cc_start: 0.7711 (OUTLIER) cc_final: 0.7319 (m-10) REVERT: A 537 TYR cc_start: 0.4009 (OUTLIER) cc_final: 0.2013 (t80) REVERT: B 20 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8592 (tm) REVERT: B 99 LYS cc_start: 0.8786 (mmmm) cc_final: 0.8488 (mmmm) outliers start: 43 outliers final: 28 residues processed: 152 average time/residue: 0.1224 time to fit residues: 24.8746 Evaluate side-chains 144 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 395 TYR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 435 TRP Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 54 TRP Chi-restraints excluded: chain B residue 118 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 40 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.131134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.108947 restraints weight = 9855.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.112149 restraints weight = 5113.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.114320 restraints weight = 3153.740| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4681 Z= 0.203 Angle : 0.627 9.935 6368 Z= 0.316 Chirality : 0.040 0.223 735 Planarity : 0.004 0.043 792 Dihedral : 6.291 56.475 650 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 7.17 % Allowed : 30.53 % Favored : 62.30 % 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: 1.00 (0.35), residues: 587 helix: 1.70 (0.26), residues: 387 sheet: -0.53 (0.68), residues: 57 loop : -1.72 (0.47), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 179 HIS 0.005 0.001 HIS A 301 PHE 0.015 0.001 PHE A 347 TYR 0.012 0.001 TYR B 103 ARG 0.004 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ARG cc_start: 0.7629 (mtp180) cc_final: 0.7149 (mtp180) REVERT: A 225 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7655 (t80) REVERT: A 283 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8613 (tm-30) REVERT: A 347 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.8757 (t80) REVERT: A 472 ASN cc_start: 0.9232 (t0) cc_final: 0.8949 (t0) REVERT: A 496 MET cc_start: 0.8785 (tpp) cc_final: 0.8465 (tpp) REVERT: A 537 TYR cc_start: 0.3874 (OUTLIER) cc_final: 0.2030 (t80) REVERT: B 20 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8438 (tm) REVERT: B 80 TYR cc_start: 0.8004 (m-10) cc_final: 0.7528 (m-10) REVERT: B 99 LYS cc_start: 0.8819 (mmmm) cc_final: 0.8490 (mmmm) outliers start: 35 outliers final: 22 residues processed: 146 average time/residue: 0.1238 time to fit residues: 24.2523 Evaluate side-chains 142 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 54 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 50 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 0.0370 chunk 57 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.132392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.109871 restraints weight = 9968.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.113214 restraints weight = 5160.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.115534 restraints weight = 3156.815| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4681 Z= 0.197 Angle : 0.626 13.723 6368 Z= 0.314 Chirality : 0.040 0.225 735 Planarity : 0.004 0.043 792 Dihedral : 5.792 58.400 647 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 7.79 % Allowed : 30.12 % Favored : 62.09 % 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: 1.11 (0.35), residues: 587 helix: 1.77 (0.26), residues: 387 sheet: -0.48 (0.67), residues: 57 loop : -1.65 (0.48), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 179 HIS 0.003 0.001 HIS A 301 PHE 0.017 0.001 PHE B 68 TYR 0.012 0.001 TYR B 103 ARG 0.004 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ARG cc_start: 0.7678 (mtp180) cc_final: 0.7202 (mtp180) REVERT: A 183 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8589 (mp0) REVERT: A 192 GLN cc_start: 0.8547 (pt0) cc_final: 0.7854 (mt0) REVERT: A 225 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.7670 (t80) REVERT: A 283 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8612 (tm-30) REVERT: A 431 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7380 (pp) REVERT: A 472 ASN cc_start: 0.9220 (t0) cc_final: 0.8985 (t0) REVERT: A 496 MET cc_start: 0.8884 (tpp) cc_final: 0.8523 (tpp) REVERT: A 521 MET cc_start: 0.8412 (ppp) cc_final: 0.7933 (ppp) REVERT: A 537 TYR cc_start: 0.3841 (OUTLIER) cc_final: 0.2030 (t80) REVERT: B 20 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8640 (tm) REVERT: B 80 TYR cc_start: 0.8038 (m-10) cc_final: 0.7540 (m-10) REVERT: B 99 LYS cc_start: 0.8836 (mmmm) cc_final: 0.8490 (mmmm) REVERT: B 115 THR cc_start: 0.7382 (OUTLIER) cc_final: 0.7169 (t) outliers start: 38 outliers final: 19 residues processed: 149 average time/residue: 0.1249 time to fit residues: 25.2528 Evaluate side-chains 144 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 54 TRP Chi-restraints excluded: chain B residue 115 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.132042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.109158 restraints weight = 10218.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.112437 restraints weight = 5260.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.114707 restraints weight = 3224.132| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4681 Z= 0.197 Angle : 0.637 13.733 6368 Z= 0.316 Chirality : 0.040 0.180 735 Planarity : 0.004 0.042 792 Dihedral : 5.848 59.871 647 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 6.15 % Allowed : 31.56 % Favored : 62.30 % 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: 1.06 (0.35), residues: 587 helix: 1.73 (0.26), residues: 387 sheet: -0.59 (0.66), residues: 57 loop : -1.60 (0.48), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 179 HIS 0.005 0.001 HIS A 301 PHE 0.018 0.001 PHE B 68 TYR 0.012 0.001 TYR B 103 ARG 0.004 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ARG cc_start: 0.7720 (mtp180) cc_final: 0.7317 (mtp180) REVERT: A 192 GLN cc_start: 0.8552 (pt0) cc_final: 0.7879 (mt0) REVERT: A 225 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7650 (t80) REVERT: A 283 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8564 (tm-30) REVERT: A 472 ASN cc_start: 0.9157 (t0) cc_final: 0.8918 (t0) REVERT: A 488 THR cc_start: 0.8766 (m) cc_final: 0.8523 (p) REVERT: A 496 MET cc_start: 0.8864 (tpp) cc_final: 0.8530 (tpp) REVERT: A 537 TYR cc_start: 0.3897 (OUTLIER) cc_final: 0.1999 (t80) REVERT: B 11 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8204 (mp) REVERT: B 20 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8683 (tm) REVERT: B 80 TYR cc_start: 0.7995 (m-10) cc_final: 0.7514 (m-10) REVERT: B 99 LYS cc_start: 0.8862 (mmmm) cc_final: 0.8553 (mmmm) outliers start: 30 outliers final: 19 residues processed: 144 average time/residue: 0.1285 time to fit residues: 24.6441 Evaluate side-chains 139 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 54 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 22 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.132961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.110113 restraints weight = 9944.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.113446 restraints weight = 5130.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.115735 restraints weight = 3149.144| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4681 Z= 0.185 Angle : 0.654 14.754 6368 Z= 0.322 Chirality : 0.041 0.250 735 Planarity : 0.004 0.043 792 Dihedral : 5.812 58.421 647 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.94 % Allowed : 32.79 % Favored : 61.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.20 (0.35), residues: 587 helix: 1.80 (0.26), residues: 389 sheet: -0.27 (0.69), residues: 52 loop : -1.56 (0.49), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 179 HIS 0.003 0.001 HIS A 301 PHE 0.017 0.001 PHE B 68 TYR 0.012 0.001 TYR B 103 ARG 0.003 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8752 (m-80) cc_final: 0.8455 (m-80) REVERT: A 153 ARG cc_start: 0.7711 (mtp180) cc_final: 0.7509 (mtp180) REVERT: A 192 GLN cc_start: 0.8548 (pt0) cc_final: 0.7894 (mt0) REVERT: A 225 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.7585 (t80) REVERT: A 283 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8543 (tm-30) REVERT: A 472 ASN cc_start: 0.9149 (t0) cc_final: 0.8910 (t0) REVERT: A 488 THR cc_start: 0.8764 (m) cc_final: 0.8518 (p) REVERT: A 496 MET cc_start: 0.8833 (tpp) cc_final: 0.8523 (tpp) REVERT: A 537 TYR cc_start: 0.3853 (OUTLIER) cc_final: 0.1991 (t80) REVERT: B 11 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8237 (mp) REVERT: B 20 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8726 (tm) REVERT: B 59 TYR cc_start: 0.4648 (OUTLIER) cc_final: 0.3941 (p90) REVERT: B 80 TYR cc_start: 0.7941 (m-10) cc_final: 0.7478 (m-10) REVERT: B 99 LYS cc_start: 0.8801 (mmmm) cc_final: 0.8572 (mmmm) outliers start: 29 outliers final: 20 residues processed: 139 average time/residue: 0.1415 time to fit residues: 26.0741 Evaluate side-chains 134 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 54 TRP Chi-restraints excluded: chain B residue 59 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 1 optimal weight: 0.0870 chunk 35 optimal weight: 0.0970 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.133679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.111195 restraints weight = 9833.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.114498 restraints weight = 4996.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.116780 restraints weight = 3042.522| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 4681 Z= 0.196 Angle : 0.673 14.220 6368 Z= 0.333 Chirality : 0.041 0.222 735 Planarity : 0.004 0.043 792 Dihedral : 5.758 57.343 647 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 5.94 % Allowed : 32.38 % Favored : 61.68 % 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: 1.24 (0.35), residues: 587 helix: 1.83 (0.27), residues: 390 sheet: -0.41 (0.66), residues: 52 loop : -1.52 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 179 HIS 0.003 0.001 HIS A 301 PHE 0.021 0.001 PHE B 68 TYR 0.012 0.001 TYR B 103 ARG 0.010 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8766 (m-80) cc_final: 0.8530 (m-80) REVERT: A 153 ARG cc_start: 0.7747 (mtp180) cc_final: 0.7309 (mtp180) REVERT: A 192 GLN cc_start: 0.8513 (pt0) cc_final: 0.7878 (mt0) REVERT: A 283 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8597 (tm-30) REVERT: A 472 ASN cc_start: 0.9187 (t0) cc_final: 0.8950 (t0) REVERT: A 488 THR cc_start: 0.8734 (m) cc_final: 0.8508 (p) REVERT: A 496 MET cc_start: 0.8854 (tpp) cc_final: 0.8540 (tpp) REVERT: A 537 TYR cc_start: 0.3807 (OUTLIER) cc_final: 0.1989 (t80) REVERT: B 11 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8159 (mp) REVERT: B 46 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8184 (pp20) REVERT: B 80 TYR cc_start: 0.7939 (m-10) cc_final: 0.7438 (m-10) REVERT: B 99 LYS cc_start: 0.8808 (mmmm) cc_final: 0.8466 (mmmm) outliers start: 29 outliers final: 21 residues processed: 145 average time/residue: 0.1323 time to fit residues: 25.5762 Evaluate side-chains 140 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 54 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 54 optimal weight: 0.2980 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.133318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.110315 restraints weight = 9889.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.113620 restraints weight = 5177.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.115865 restraints weight = 3212.135| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4681 Z= 0.215 Angle : 0.710 16.620 6368 Z= 0.352 Chirality : 0.043 0.276 735 Planarity : 0.004 0.043 792 Dihedral : 5.819 59.960 647 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 5.94 % Allowed : 32.99 % Favored : 61.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.23 (0.35), residues: 587 helix: 1.83 (0.27), residues: 390 sheet: -0.52 (0.65), residues: 52 loop : -1.48 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 179 HIS 0.003 0.001 HIS A 301 PHE 0.014 0.001 PHE A 347 TYR 0.020 0.001 TYR B 95 ARG 0.007 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8769 (m-80) cc_final: 0.8446 (m-80) REVERT: A 153 ARG cc_start: 0.7765 (mtp180) cc_final: 0.7339 (mtp180) REVERT: A 192 GLN cc_start: 0.8540 (pt0) cc_final: 0.7877 (mt0) REVERT: A 283 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8555 (tm-30) REVERT: A 472 ASN cc_start: 0.9141 (t0) cc_final: 0.8902 (t0) REVERT: A 496 MET cc_start: 0.8863 (tpp) cc_final: 0.8559 (tpp) REVERT: A 537 TYR cc_start: 0.3846 (OUTLIER) cc_final: 0.1997 (t80) REVERT: B 11 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8109 (mp) REVERT: B 46 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8168 (pp20) outliers start: 29 outliers final: 23 residues processed: 136 average time/residue: 0.1285 time to fit residues: 23.6691 Evaluate side-chains 140 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 54 TRP Chi-restraints excluded: chain B residue 65 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 0.0070 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.133853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.110822 restraints weight = 9857.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.114158 restraints weight = 5173.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.116274 restraints weight = 3214.868| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 4681 Z= 0.210 Angle : 0.720 15.832 6368 Z= 0.355 Chirality : 0.043 0.248 735 Planarity : 0.004 0.043 792 Dihedral : 5.751 59.773 647 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.33 % Allowed : 33.20 % Favored : 61.48 % 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: 1.22 (0.35), residues: 587 helix: 1.80 (0.26), residues: 391 sheet: -0.35 (0.66), residues: 52 loop : -1.51 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 179 HIS 0.003 0.000 HIS A 301 PHE 0.014 0.001 PHE A 347 TYR 0.012 0.001 TYR B 103 ARG 0.007 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8735 (m-80) cc_final: 0.8439 (m-80) REVERT: A 153 ARG cc_start: 0.7789 (mtp180) cc_final: 0.7381 (mtp180) REVERT: A 192 GLN cc_start: 0.8538 (pt0) cc_final: 0.7874 (mt0) REVERT: A 283 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8565 (tm-30) REVERT: A 496 MET cc_start: 0.8856 (tpp) cc_final: 0.8545 (tpp) REVERT: A 537 TYR cc_start: 0.3812 (OUTLIER) cc_final: 0.1993 (t80) REVERT: B 46 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8174 (pp20) REVERT: B 80 TYR cc_start: 0.7834 (m-10) cc_final: 0.7498 (m-10) REVERT: B 99 LYS cc_start: 0.8593 (mmmm) cc_final: 0.7712 (mmtm) outliers start: 26 outliers final: 23 residues processed: 135 average time/residue: 0.1418 time to fit residues: 25.5779 Evaluate side-chains 141 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 65 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 40 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.133512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.110682 restraints weight = 9800.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.113893 restraints weight = 5153.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.116176 restraints weight = 3221.058| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 4681 Z= 0.219 Angle : 0.731 16.153 6368 Z= 0.360 Chirality : 0.043 0.239 735 Planarity : 0.004 0.043 792 Dihedral : 5.517 59.629 645 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.71 % Allowed : 34.63 % Favored : 60.66 % 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: 1.22 (0.35), residues: 587 helix: 1.78 (0.27), residues: 391 sheet: -0.34 (0.66), residues: 52 loop : -1.47 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 179 HIS 0.003 0.000 HIS A 301 PHE 0.014 0.001 PHE A 347 TYR 0.012 0.001 TYR B 103 ARG 0.007 0.001 ARG B 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1174 Ramachandran restraints generated. 587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8739 (m-80) cc_final: 0.8420 (m-80) REVERT: A 153 ARG cc_start: 0.7819 (mtp180) cc_final: 0.7598 (mtp180) REVERT: A 192 GLN cc_start: 0.8596 (pt0) cc_final: 0.7921 (mt0) REVERT: A 283 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8451 (tm-30) REVERT: A 294 MET cc_start: 0.7966 (mtm) cc_final: 0.7364 (mtp) REVERT: A 496 MET cc_start: 0.8867 (tpp) cc_final: 0.8526 (tpp) REVERT: A 537 TYR cc_start: 0.3853 (OUTLIER) cc_final: 0.1985 (t80) REVERT: B 46 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8141 (pp20) REVERT: B 80 TYR cc_start: 0.7852 (m-10) cc_final: 0.7492 (m-10) outliers start: 23 outliers final: 20 residues processed: 131 average time/residue: 0.1427 time to fit residues: 24.5906 Evaluate side-chains 132 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 45 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 0.0010 chunk 40 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.133812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.110538 restraints weight = 10052.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.113865 restraints weight = 5272.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.116212 restraints weight = 3276.461| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 4681 Z= 0.217 Angle : 0.745 15.968 6368 Z= 0.368 Chirality : 0.042 0.234 735 Planarity : 0.004 0.043 792 Dihedral : 5.433 58.899 645 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.51 % Allowed : 35.04 % Favored : 60.45 % 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: 1.24 (0.35), residues: 587 helix: 1.79 (0.27), residues: 390 sheet: -0.40 (0.65), residues: 52 loop : -1.39 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 179 HIS 0.003 0.000 HIS A 301 PHE 0.014 0.001 PHE A 550 TYR 0.019 0.001 TYR B 95 ARG 0.008 0.001 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1573.96 seconds wall clock time: 28 minutes 59.69 seconds (1739.69 seconds total)