Starting phenix.real_space_refine on Wed Sep 17 04:57:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f6o_50236/09_2025/9f6o_50236.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f6o_50236/09_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_50236/09_2025/9f6o_50236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f6o_50236/09_2025/9f6o_50236.map" model { file = "/net/cci-nas-00/data/ceres_data/9f6o_50236/09_2025/9f6o_50236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f6o_50236/09_2025/9f6o_50236.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.39, per 1000 atoms: 0.30 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: 0.41 Conformation dependent library (CDL) restraints added in 183.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.15 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: 0.76 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 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: 0.490 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.660 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.600 ------------------------------------------------------------------------------- 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 4683 Z= 0.214 Angle : 0.800 9.483 6372 Z= 0.441 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (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 ARG 0.007 0.001 ARG B 67 TYR 0.016 0.001 TYR B 95 PHE 0.015 0.001 PHE A 347 TRP 0.007 0.001 TRP B 36 HIS 0.004 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 4681) covalent geometry : angle 0.79840 ( 6368) SS BOND : bond 0.01014 ( 2) SS BOND : angle 2.07860 ( 4) hydrogen bonds : bond 0.13226 ( 316) hydrogen bonds : angle 6.15231 ( 933) *********************** 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 : 0.172 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: 0.0570 time to fit residues: 10.1485 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 : 0.175 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.133088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.110765 restraints weight = 9881.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.114258 restraints weight = 5035.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.116555 restraints weight = 3023.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.118014 restraints weight = 2072.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.119148 restraints weight = 1591.426| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4683 Z= 0.141 Angle : 0.638 9.452 6372 Z= 0.326 Chirality : 0.040 0.197 735 Planarity : 0.004 0.041 792 Dihedral : 6.635 56.929 653 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 7.99 % Allowed : 31.76 % Favored : 60.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.35), residues: 587 helix: 1.73 (0.26), residues: 388 sheet: -0.37 (0.69), residues: 57 loop : -1.82 (0.46), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 38 TYR 0.010 0.001 TYR B 103 PHE 0.015 0.001 PHE A 347 TRP 0.011 0.001 TRP A 179 HIS 0.002 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 4681) covalent geometry : angle 0.63777 ( 6368) SS BOND : bond 0.00151 ( 2) SS BOND : angle 1.32753 ( 4) hydrogen bonds : bond 0.04394 ( 316) hydrogen bonds : angle 4.90026 ( 933) *********************** 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 163 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 124 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ARG cc_start: 0.7406 (mtp180) cc_final: 0.6829 (mtp180) REVERT: A 283 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8648 (tm-30) REVERT: A 347 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8656 (t80) REVERT: A 435 TRP cc_start: 0.7566 (OUTLIER) cc_final: 0.7285 (m-10) REVERT: A 521 MET cc_start: 0.8484 (ppp) cc_final: 0.8115 (ppp) REVERT: A 537 TYR cc_start: 0.3925 (OUTLIER) cc_final: 0.2003 (t80) REVERT: B 20 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8509 (tm) REVERT: B 99 LYS cc_start: 0.8762 (mmmm) cc_final: 0.8461 (mmmm) outliers start: 39 outliers final: 24 residues processed: 150 average time/residue: 0.0552 time to fit residues: 11.3391 Evaluate side-chains 145 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 416 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 5 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.131311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.109031 restraints weight = 9872.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.112152 restraints weight = 5164.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.114328 restraints weight = 3211.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.115687 restraints weight = 2254.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.116806 restraints weight = 1764.349| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4683 Z= 0.150 Angle : 0.635 10.232 6372 Z= 0.322 Chirality : 0.040 0.218 735 Planarity : 0.004 0.043 792 Dihedral : 6.216 56.777 650 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 7.58 % Allowed : 31.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.35), residues: 587 helix: 1.75 (0.26), residues: 387 sheet: -0.36 (0.70), residues: 57 loop : -1.75 (0.47), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 440 TYR 0.011 0.001 TYR B 103 PHE 0.014 0.001 PHE A 347 TRP 0.011 0.001 TRP A 179 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 4681) covalent geometry : angle 0.63306 ( 6368) SS BOND : bond 0.00028 ( 2) SS BOND : angle 1.84817 ( 4) hydrogen bonds : bond 0.04185 ( 316) hydrogen bonds : angle 4.80156 ( 933) *********************** 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 168 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 ASP cc_start: 0.8469 (p0) cc_final: 0.8231 (p0) REVERT: A 153 ARG cc_start: 0.7569 (mtp180) cc_final: 0.7109 (mtp180) REVERT: A 225 PHE cc_start: 0.7901 (OUTLIER) cc_final: 0.7672 (t80) REVERT: A 283 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8577 (tm-30) REVERT: A 347 PHE cc_start: 0.9048 (OUTLIER) cc_final: 0.8786 (t80) REVERT: A 472 ASN cc_start: 0.9182 (t0) cc_final: 0.8919 (t0) REVERT: A 478 GLN cc_start: 0.9322 (pp30) cc_final: 0.9030 (pp30) REVERT: A 496 MET cc_start: 0.8897 (tpp) cc_final: 0.8506 (tpp) REVERT: A 521 MET cc_start: 0.8310 (ppp) cc_final: 0.7894 (ppp) REVERT: A 537 TYR cc_start: 0.4047 (OUTLIER) cc_final: 0.2063 (t80) REVERT: B 20 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8468 (tm) REVERT: B 80 TYR cc_start: 0.8004 (m-10) cc_final: 0.7513 (m-10) REVERT: B 99 LYS cc_start: 0.8832 (mmmm) cc_final: 0.8525 (mmmm) outliers start: 37 outliers final: 24 residues processed: 154 average time/residue: 0.0521 time to fit residues: 11.2156 Evaluate side-chains 149 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.194 ------------------------------------------------------------------------------- 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 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 245 THR 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 406 VAL 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 12 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN B 82 GLN B 116 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.132846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.110669 restraints weight = 9908.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.113879 restraints weight = 5146.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.116137 restraints weight = 3177.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.117470 restraints weight = 2203.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.118634 restraints weight = 1718.226| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4683 Z= 0.128 Angle : 0.624 13.383 6372 Z= 0.314 Chirality : 0.040 0.219 735 Planarity : 0.004 0.043 792 Dihedral : 5.734 56.965 647 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 6.97 % Allowed : 32.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.35), residues: 587 helix: 1.81 (0.26), residues: 387 sheet: -0.46 (0.70), residues: 57 loop : -1.69 (0.47), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 440 TYR 0.012 0.001 TYR B 103 PHE 0.017 0.001 PHE B 68 TRP 0.010 0.001 TRP A 179 HIS 0.003 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 4681) covalent geometry : angle 0.62283 ( 6368) SS BOND : bond 0.00188 ( 2) SS BOND : angle 1.47286 ( 4) hydrogen bonds : bond 0.03928 ( 316) hydrogen bonds : angle 4.66046 ( 933) *********************** 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 161 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.7648 (t80) REVERT: A 283 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8496 (tm-30) REVERT: A 431 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7419 (pp) REVERT: A 472 ASN cc_start: 0.9173 (t0) cc_final: 0.8969 (t0) REVERT: A 496 MET cc_start: 0.8879 (tpp) cc_final: 0.8457 (tpp) REVERT: A 521 MET cc_start: 0.8375 (ppp) cc_final: 0.7895 (ppp) REVERT: A 537 TYR cc_start: 0.4015 (OUTLIER) cc_final: 0.2029 (t80) REVERT: B 20 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8588 (tm) REVERT: B 80 TYR cc_start: 0.7938 (m-10) cc_final: 0.7450 (m-10) REVERT: B 99 LYS cc_start: 0.8795 (mmmm) cc_final: 0.8494 (mmmm) REVERT: B 115 THR cc_start: 0.7120 (OUTLIER) cc_final: 0.6843 (t) outliers start: 34 outliers final: 18 residues processed: 152 average time/residue: 0.0543 time to fit residues: 11.3096 Evaluate side-chains 142 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.179 ------------------------------------------------------------------------------- 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 224 VAL 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 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 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 14 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.131721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.109188 restraints weight = 9858.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.112353 restraints weight = 5194.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.114518 restraints weight = 3234.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.116036 restraints weight = 2274.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.116927 restraints weight = 1763.828| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4683 Z= 0.148 Angle : 0.661 14.166 6372 Z= 0.329 Chirality : 0.041 0.247 735 Planarity : 0.004 0.044 792 Dihedral : 5.802 57.711 647 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 7.79 % Allowed : 31.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.35), residues: 587 helix: 1.71 (0.26), residues: 387 sheet: -0.42 (0.69), residues: 57 loop : -1.59 (0.48), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 440 TYR 0.012 0.001 TYR B 103 PHE 0.018 0.001 PHE B 68 TRP 0.015 0.001 TRP A 179 HIS 0.003 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 4681) covalent geometry : angle 0.66021 ( 6368) SS BOND : bond 0.00183 ( 2) SS BOND : angle 1.37697 ( 4) hydrogen bonds : bond 0.03957 ( 316) hydrogen bonds : angle 4.69645 ( 933) *********************** 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 160 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 GLN cc_start: 0.8588 (pt0) cc_final: 0.7868 (mt0) REVERT: A 225 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.7669 (t80) REVERT: A 283 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8539 (tm-30) REVERT: A 431 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7564 (pp) REVERT: A 472 ASN cc_start: 0.9170 (t0) cc_final: 0.8931 (t0) REVERT: A 496 MET cc_start: 0.8948 (tpp) cc_final: 0.8408 (tpp) REVERT: A 537 TYR cc_start: 0.3930 (OUTLIER) cc_final: 0.2024 (t80) REVERT: B 11 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8179 (mp) REVERT: B 20 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8594 (tm) REVERT: B 59 TYR cc_start: 0.5215 (OUTLIER) cc_final: 0.3945 (p90) REVERT: B 80 TYR cc_start: 0.8022 (m-10) cc_final: 0.7527 (m-10) REVERT: B 99 LYS cc_start: 0.8819 (mmmm) cc_final: 0.8477 (mmmm) REVERT: B 115 THR cc_start: 0.7224 (OUTLIER) cc_final: 0.6987 (t) outliers start: 38 outliers final: 24 residues processed: 146 average time/residue: 0.0531 time to fit residues: 10.7787 Evaluate side-chains 144 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 216 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 224 VAL 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 344 VAL Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 391 VAL 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 59 TYR Chi-restraints excluded: chain B residue 115 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 0.0870 chunk 6 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.133644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.111297 restraints weight = 9898.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.114522 restraints weight = 5102.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.116756 restraints weight = 3142.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.118083 restraints weight = 2188.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.119269 restraints weight = 1708.681| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4683 Z= 0.131 Angle : 0.653 14.596 6372 Z= 0.324 Chirality : 0.041 0.186 735 Planarity : 0.004 0.043 792 Dihedral : 5.768 57.446 647 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 6.56 % Allowed : 32.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.35), residues: 587 helix: 1.79 (0.26), residues: 389 sheet: -0.46 (0.69), residues: 57 loop : -1.54 (0.50), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 440 TYR 0.012 0.001 TYR B 103 PHE 0.018 0.001 PHE B 68 TRP 0.016 0.001 TRP A 179 HIS 0.004 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 4681) covalent geometry : angle 0.65216 ( 6368) SS BOND : bond 0.00235 ( 2) SS BOND : angle 1.22536 ( 4) hydrogen bonds : bond 0.03838 ( 316) hydrogen bonds : angle 4.63281 ( 933) *********************** 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 151 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8754 (m-80) cc_final: 0.8495 (m-80) REVERT: A 225 PHE cc_start: 0.7791 (OUTLIER) cc_final: 0.7564 (t80) REVERT: A 283 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8523 (tm-30) REVERT: A 472 ASN cc_start: 0.9197 (t0) cc_final: 0.8989 (t0) REVERT: A 496 MET cc_start: 0.8954 (tpp) cc_final: 0.8397 (tpp) REVERT: A 537 TYR cc_start: 0.3898 (OUTLIER) cc_final: 0.1985 (t80) REVERT: B 11 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8140 (mp) REVERT: B 20 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8664 (tm) REVERT: B 46 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8141 (pp20) REVERT: B 59 TYR cc_start: 0.5053 (OUTLIER) cc_final: 0.3837 (p90) REVERT: B 80 TYR cc_start: 0.8016 (m-10) cc_final: 0.7561 (m-10) REVERT: B 99 LYS cc_start: 0.8812 (mmmm) cc_final: 0.8518 (mmmm) REVERT: B 115 THR cc_start: 0.7060 (OUTLIER) cc_final: 0.6853 (t) outliers start: 32 outliers final: 20 residues processed: 141 average time/residue: 0.0537 time to fit residues: 10.5133 Evaluate side-chains 140 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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 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 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 46 GLU Chi-restraints excluded: chain B residue 54 TRP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 115 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 52 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 14 optimal weight: 0.0030 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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 ** 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 = 0.3787 r_free = 0.3787 target = 0.134253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.111960 restraints weight = 9814.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.115200 restraints weight = 5106.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.117431 restraints weight = 3155.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.118830 restraints weight = 2198.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.119944 restraints weight = 1703.545| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4683 Z= 0.131 Angle : 0.680 14.382 6372 Z= 0.339 Chirality : 0.041 0.269 735 Planarity : 0.004 0.044 792 Dihedral : 5.822 55.774 647 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 5.74 % Allowed : 32.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.35), residues: 587 helix: 1.86 (0.27), residues: 389 sheet: -0.02 (0.70), residues: 51 loop : -1.50 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 440 TYR 0.011 0.001 TYR B 103 PHE 0.022 0.001 PHE B 68 TRP 0.015 0.001 TRP A 179 HIS 0.003 0.000 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 4681) covalent geometry : angle 0.67895 ( 6368) SS BOND : bond 0.00048 ( 2) SS BOND : angle 1.87902 ( 4) hydrogen bonds : bond 0.03809 ( 316) hydrogen bonds : angle 4.68164 ( 933) *********************** 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 155 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8712 (m-80) cc_final: 0.8500 (m-80) REVERT: A 192 GLN cc_start: 0.8567 (pt0) cc_final: 0.7843 (mt0) REVERT: A 283 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8506 (tm-30) REVERT: A 472 ASN cc_start: 0.9150 (t0) cc_final: 0.8919 (t0) REVERT: A 496 MET cc_start: 0.8933 (tpp) cc_final: 0.8372 (tpp) REVERT: A 537 TYR cc_start: 0.3883 (OUTLIER) cc_final: 0.1973 (t80) REVERT: B 20 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8604 (tm) REVERT: B 46 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8129 (pp20) REVERT: B 95 TYR cc_start: 0.8521 (m-80) cc_final: 0.8290 (m-10) REVERT: B 115 THR cc_start: 0.6873 (OUTLIER) cc_final: 0.6596 (t) outliers start: 28 outliers final: 20 residues processed: 146 average time/residue: 0.0534 time to fit residues: 10.8130 Evaluate side-chains 142 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.102 ------------------------------------------------------------------------------- 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 258 VAL Chi-restraints excluded: chain A residue 286 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 20 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 115 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 52 ASN ** 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 = 0.3777 r_free = 0.3777 target = 0.133240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.110680 restraints weight = 9875.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.113939 restraints weight = 5180.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.116196 restraints weight = 3219.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.117564 restraints weight = 2258.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.118673 restraints weight = 1767.006| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 4683 Z= 0.141 Angle : 0.703 15.290 6372 Z= 0.346 Chirality : 0.042 0.238 735 Planarity : 0.004 0.043 792 Dihedral : 5.806 59.082 647 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 5.74 % Allowed : 34.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.35), residues: 587 helix: 1.85 (0.27), residues: 390 sheet: 0.22 (0.75), residues: 44 loop : -1.47 (0.48), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 440 TYR 0.012 0.001 TYR B 103 PHE 0.012 0.001 PHE A 347 TRP 0.016 0.001 TRP A 179 HIS 0.004 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 4681) covalent geometry : angle 0.70238 ( 6368) SS BOND : bond 0.00110 ( 2) SS BOND : angle 1.55424 ( 4) hydrogen bonds : bond 0.03842 ( 316) hydrogen bonds : angle 4.68934 ( 933) *********************** 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 148 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 TYR cc_start: 0.8752 (m-80) cc_final: 0.8433 (m-80) REVERT: A 192 GLN cc_start: 0.8521 (pt0) cc_final: 0.7869 (mt0) REVERT: A 283 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8535 (tm-30) REVERT: A 496 MET cc_start: 0.8929 (tpp) cc_final: 0.8389 (tpp) REVERT: A 537 TYR cc_start: 0.3885 (OUTLIER) cc_final: 0.1990 (t80) REVERT: B 20 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8774 (tm) REVERT: B 95 TYR cc_start: 0.8516 (m-80) cc_final: 0.7951 (m-10) REVERT: B 99 LYS cc_start: 0.8472 (mmmm) cc_final: 0.8245 (mmmm) outliers start: 28 outliers final: 24 residues processed: 139 average time/residue: 0.0565 time to fit residues: 10.6974 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 : 0.186 ------------------------------------------------------------------------------- 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 181 MET 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 258 VAL 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 20 LEU Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 54 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 56 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 51 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3792 r_free = 0.3792 target = 0.134389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.111210 restraints weight = 9891.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.114589 restraints weight = 5141.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.116979 restraints weight = 3186.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.118438 restraints weight = 2232.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.119550 restraints weight = 1741.547| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4683 Z= 0.138 Angle : 0.719 15.380 6372 Z= 0.350 Chirality : 0.042 0.259 735 Planarity : 0.004 0.044 792 Dihedral : 5.738 57.673 647 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 5.53 % Allowed : 34.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.35), residues: 587 helix: 1.83 (0.27), residues: 390 sheet: -0.01 (0.70), residues: 44 loop : -1.47 (0.48), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 38 TYR 0.012 0.001 TYR B 103 PHE 0.013 0.001 PHE A 347 TRP 0.015 0.001 TRP A 179 HIS 0.004 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 4681) covalent geometry : angle 0.71862 ( 6368) SS BOND : bond 0.00121 ( 2) SS BOND : angle 1.44937 ( 4) hydrogen bonds : bond 0.03803 ( 316) hydrogen bonds : angle 4.63950 ( 933) *********************** 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: 27 poor density : 118 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 GLN cc_start: 0.8548 (pt0) cc_final: 0.7882 (mt0) REVERT: A 283 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8563 (tm-30) REVERT: A 496 MET cc_start: 0.8926 (tpp) cc_final: 0.8412 (tpp) REVERT: A 537 TYR cc_start: 0.3840 (OUTLIER) cc_final: 0.2001 (t80) REVERT: B 20 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8649 (tm) REVERT: B 95 TYR cc_start: 0.8552 (m-80) cc_final: 0.8092 (m-10) REVERT: B 99 LYS cc_start: 0.8543 (mmmm) cc_final: 0.8288 (mmmm) outliers start: 27 outliers final: 20 residues processed: 136 average time/residue: 0.0505 time to fit residues: 9.6220 Evaluate side-chains 139 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.184 ------------------------------------------------------------------------------- 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 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 20 LEU Chi-restraints excluded: chain B residue 36 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 50 optimal weight: 0.0270 chunk 11 optimal weight: 0.0670 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 0.0270 chunk 48 optimal weight: 0.1980 chunk 58 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.2434 ------------------------------------------------------------------------------- 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 = 0.3816 r_free = 0.3816 target = 0.136378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.113531 restraints weight = 9934.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.116860 restraints weight = 5214.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.119170 restraints weight = 3236.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.120664 restraints weight = 2264.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.121746 restraints weight = 1757.554| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4683 Z= 0.130 Angle : 0.734 15.336 6372 Z= 0.355 Chirality : 0.043 0.225 735 Planarity : 0.004 0.043 792 Dihedral : 5.367 56.458 645 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.48 % Allowed : 36.27 % Favored : 60.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.35), residues: 587 helix: 1.86 (0.27), residues: 391 sheet: -0.08 (0.68), residues: 44 loop : -1.38 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 38 TYR 0.012 0.001 TYR B 103 PHE 0.013 0.001 PHE A 347 TRP 0.015 0.001 TRP A 179 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 4681) covalent geometry : angle 0.73279 ( 6368) SS BOND : bond 0.00212 ( 2) SS BOND : angle 1.48463 ( 4) hydrogen bonds : bond 0.03675 ( 316) hydrogen bonds : angle 4.57416 ( 933) ********************** 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 140 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 GLN cc_start: 0.8525 (pt0) cc_final: 0.7839 (mt0) REVERT: A 283 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8464 (tm-30) REVERT: A 431 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7376 (pt) REVERT: A 496 MET cc_start: 0.8919 (tpp) cc_final: 0.8640 (tpp) REVERT: A 537 TYR cc_start: 0.3911 (OUTLIER) cc_final: 0.2006 (t80) REVERT: B 95 TYR cc_start: 0.8402 (m-80) cc_final: 0.7976 (m-10) REVERT: B 99 LYS cc_start: 0.8571 (mmmm) cc_final: 0.8332 (mmmm) outliers start: 17 outliers final: 12 residues processed: 133 average time/residue: 0.0504 time to fit residues: 9.2815 Evaluate side-chains 131 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.160 ------------------------------------------------------------------------------- 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 286 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 537 TYR Chi-restraints excluded: chain B residue 7 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 43 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 2 optimal weight: 0.3980 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.134947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.112296 restraints weight = 9942.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.115592 restraints weight = 5194.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.117836 restraints weight = 3210.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.119197 restraints weight = 2241.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.120339 restraints weight = 1760.639| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4683 Z= 0.145 Angle : 0.760 16.648 6372 Z= 0.371 Chirality : 0.044 0.259 735 Planarity : 0.004 0.043 792 Dihedral : 4.894 50.158 643 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.48 % Allowed : 36.89 % Favored : 59.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.35), residues: 587 helix: 1.79 (0.27), residues: 391 sheet: 0.16 (0.69), residues: 44 loop : -1.40 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 38 TYR 0.011 0.001 TYR B 103 PHE 0.016 0.001 PHE A 550 TRP 0.020 0.001 TRP B 36 HIS 0.004 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 4681) covalent geometry : angle 0.75923 ( 6368) SS BOND : bond 0.00328 ( 2) SS BOND : angle 1.58066 ( 4) hydrogen bonds : bond 0.03650 ( 316) hydrogen bonds : angle 4.61761 ( 933) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 946.78 seconds wall clock time: 17 minutes 4.26 seconds (1024.26 seconds total)