Starting phenix.real_space_refine on Fri May 23 14:33:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jm9_36410/05_2025/8jm9_36410_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jm9_36410/05_2025/8jm9_36410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jm9_36410/05_2025/8jm9_36410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jm9_36410/05_2025/8jm9_36410.map" model { file = "/net/cci-nas-00/data/ceres_data/8jm9_36410/05_2025/8jm9_36410_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jm9_36410/05_2025/8jm9_36410_neut.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians S 72 5.16 5 C 7824 2.51 5 N 2056 2.21 5 O 2096 1.98 5 H 12472 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24520 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 6130 Classifications: {'peptide': 381} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 374} Chain breaks: 1 Restraints were copied for chains: C, B, D Time building chain proxies: 14.88, per 1000 atoms: 0.61 Number of scatterers: 24520 At special positions: 0 Unit cell: (110.67, 110.67, 104.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 O 2096 8.00 N 2056 7.00 C 7824 6.00 H 12472 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 6.64 Conformation dependent library (CDL) restraints added in 1.9 seconds 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2904 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 8 sheets defined 85.0% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 7 through 17 removed outlier: 3.503A pdb=" N PHE A 11 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 65 Processing helix chain 'A' and resid 73 through 100 Processing helix chain 'A' and resid 101 through 119 Processing helix chain 'A' and resid 120 through 123 Processing helix chain 'A' and resid 124 through 161 Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.765A pdb=" N VAL A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 215 Processing helix chain 'A' and resid 263 through 321 removed outlier: 6.206A pdb=" N ILE A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ALA A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 369 Proline residue: A 347 - end of helix removed outlier: 3.753A pdb=" N THR A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN A 360 " --> pdb=" O ARG A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 387 removed outlier: 4.012A pdb=" N VAL A 387 " --> pdb=" O GLN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 425 removed outlier: 3.553A pdb=" N THR A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 17 removed outlier: 3.503A pdb=" N PHE B 11 " --> pdb=" O SER B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 65 Processing helix chain 'B' and resid 73 through 100 Processing helix chain 'B' and resid 101 through 119 Processing helix chain 'B' and resid 120 through 123 Processing helix chain 'B' and resid 124 through 161 Processing helix chain 'B' and resid 168 through 174 removed outlier: 3.765A pdb=" N VAL B 172 " --> pdb=" O THR B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 215 Processing helix chain 'B' and resid 263 through 321 removed outlier: 6.206A pdb=" N ILE B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ALA B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 369 Proline residue: B 347 - end of helix removed outlier: 3.753A pdb=" N THR B 358 " --> pdb=" O GLU B 354 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN B 360 " --> pdb=" O ARG B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 387 removed outlier: 4.012A pdb=" N VAL B 387 " --> pdb=" O GLN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 425 removed outlier: 3.553A pdb=" N THR B 406 " --> pdb=" O ARG B 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 17 removed outlier: 3.503A pdb=" N PHE C 11 " --> pdb=" O SER C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 65 Processing helix chain 'C' and resid 73 through 100 Processing helix chain 'C' and resid 101 through 119 Processing helix chain 'C' and resid 120 through 123 Processing helix chain 'C' and resid 124 through 161 Processing helix chain 'C' and resid 168 through 174 removed outlier: 3.765A pdb=" N VAL C 172 " --> pdb=" O THR C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 215 Processing helix chain 'C' and resid 263 through 321 removed outlier: 6.206A pdb=" N ILE C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ALA C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 369 Proline residue: C 347 - end of helix removed outlier: 3.753A pdb=" N THR C 358 " --> pdb=" O GLU C 354 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN C 360 " --> pdb=" O ARG C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 387 removed outlier: 4.012A pdb=" N VAL C 387 " --> pdb=" O GLN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 425 removed outlier: 3.553A pdb=" N THR C 406 " --> pdb=" O ARG C 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 17 removed outlier: 3.503A pdb=" N PHE D 11 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 65 Processing helix chain 'D' and resid 73 through 100 Processing helix chain 'D' and resid 101 through 119 Processing helix chain 'D' and resid 120 through 123 Processing helix chain 'D' and resid 124 through 161 Processing helix chain 'D' and resid 168 through 174 removed outlier: 3.765A pdb=" N VAL D 172 " --> pdb=" O THR D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 215 Processing helix chain 'D' and resid 263 through 321 removed outlier: 6.206A pdb=" N ILE D 294 " --> pdb=" O ASN D 290 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ALA D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 369 Proline residue: D 347 - end of helix removed outlier: 3.753A pdb=" N THR D 358 " --> pdb=" O GLU D 354 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE D 359 " --> pdb=" O SER D 355 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN D 360 " --> pdb=" O ARG D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 387 removed outlier: 4.012A pdb=" N VAL D 387 " --> pdb=" O GLN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 425 removed outlier: 3.553A pdb=" N THR D 406 " --> pdb=" O ARG D 402 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 392 through 393 removed outlier: 4.578A pdb=" N PHE A 392 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 22 through 26 Processing sheet with id=AA4, first strand: chain 'B' and resid 392 through 393 removed outlier: 4.578A pdb=" N PHE B 392 " --> pdb=" O VAL B 400 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 26 Processing sheet with id=AA6, first strand: chain 'C' and resid 392 through 393 removed outlier: 4.578A pdb=" N PHE C 392 " --> pdb=" O VAL C 400 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 22 through 26 Processing sheet with id=AA8, first strand: chain 'D' and resid 392 through 393 removed outlier: 4.578A pdb=" N PHE D 392 " --> pdb=" O VAL D 400 " (cutoff:3.500A) 1080 hydrogen bonds defined for protein. 3228 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: 9.21 Time building geometry restraints manager: 7.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12440 1.03 - 1.22: 32 1.22 - 1.42: 5112 1.42 - 1.61: 7056 1.61 - 1.81: 112 Bond restraints: 24752 Sorted by residual: bond pdb=" CB LYS C 379 " pdb=" CG LYS C 379 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.51e-01 bond pdb=" CB LYS D 379 " pdb=" CG LYS D 379 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.51e-01 bond pdb=" CB LYS B 379 " pdb=" CG LYS B 379 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.51e-01 bond pdb=" CB LYS A 379 " pdb=" CG LYS A 379 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.51e-01 bond pdb=" C LYS B 357 " pdb=" O LYS B 357 " ideal model delta sigma weight residual 1.236 1.246 -0.010 1.31e-02 5.83e+03 6.00e-01 ... (remaining 24747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 41844 1.04 - 2.08: 2708 2.08 - 3.12: 116 3.12 - 4.16: 40 4.16 - 5.21: 12 Bond angle restraints: 44720 Sorted by residual: angle pdb=" N VAL D 69 " pdb=" CA VAL D 69 " pdb=" C VAL D 69 " ideal model delta sigma weight residual 111.81 109.28 2.53 8.60e-01 1.35e+00 8.67e+00 angle pdb=" N VAL B 69 " pdb=" CA VAL B 69 " pdb=" C VAL B 69 " ideal model delta sigma weight residual 111.81 109.28 2.53 8.60e-01 1.35e+00 8.67e+00 angle pdb=" N VAL A 69 " pdb=" CA VAL A 69 " pdb=" C VAL A 69 " ideal model delta sigma weight residual 111.81 109.28 2.53 8.60e-01 1.35e+00 8.67e+00 angle pdb=" N VAL C 69 " pdb=" CA VAL C 69 " pdb=" C VAL C 69 " ideal model delta sigma weight residual 111.81 109.28 2.53 8.60e-01 1.35e+00 8.67e+00 angle pdb=" CA LYS A 379 " pdb=" CB LYS A 379 " pdb=" CG LYS A 379 " ideal model delta sigma weight residual 114.10 118.99 -4.89 2.00e+00 2.50e-01 5.97e+00 ... (remaining 44715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.72: 9532 11.72 - 23.45: 1192 23.45 - 35.17: 400 35.17 - 46.89: 220 46.89 - 58.62: 164 Dihedral angle restraints: 11508 sinusoidal: 6176 harmonic: 5332 Sorted by residual: dihedral pdb=" N GLN C 5 " pdb=" CA GLN C 5 " pdb=" CB GLN C 5 " pdb=" CG GLN C 5 " ideal model delta sinusoidal sigma weight residual -60.00 -116.83 56.83 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" N GLN B 5 " pdb=" CA GLN B 5 " pdb=" CB GLN B 5 " pdb=" CG GLN B 5 " ideal model delta sinusoidal sigma weight residual -60.00 -116.83 56.83 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" N GLN D 5 " pdb=" CA GLN D 5 " pdb=" CB GLN D 5 " pdb=" CG GLN D 5 " ideal model delta sinusoidal sigma weight residual -60.00 -116.83 56.83 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 11505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1516 0.036 - 0.071: 384 0.071 - 0.107: 80 0.107 - 0.142: 12 0.142 - 0.178: 4 Chirality restraints: 1996 Sorted by residual: chirality pdb=" CB THR B 46 " pdb=" CA THR B 46 " pdb=" OG1 THR B 46 " pdb=" CG2 THR B 46 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CB THR C 46 " pdb=" CA THR C 46 " pdb=" OG1 THR C 46 " pdb=" CG2 THR C 46 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CB THR A 46 " pdb=" CA THR A 46 " pdb=" OG1 THR A 46 " pdb=" CG2 THR A 46 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.88e-01 ... (remaining 1993 not shown) Planarity restraints: 3532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP C 83 " 0.005 2.00e-02 2.50e+03 1.01e-02 1.02e+00 pdb=" CG ASP C 83 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASP C 83 " 0.006 2.00e-02 2.50e+03 pdb=" OD2 ASP C 83 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 83 " 0.005 2.00e-02 2.50e+03 1.01e-02 1.02e+00 pdb=" CG ASP D 83 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASP D 83 " 0.006 2.00e-02 2.50e+03 pdb=" OD2 ASP D 83 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 83 " -0.005 2.00e-02 2.50e+03 1.01e-02 1.02e+00 pdb=" CG ASP B 83 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASP B 83 " -0.006 2.00e-02 2.50e+03 pdb=" OD2 ASP B 83 " -0.006 2.00e-02 2.50e+03 ... (remaining 3529 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1060 2.18 - 2.78: 49068 2.78 - 3.39: 73844 3.39 - 3.99: 91204 3.99 - 4.60: 146036 Nonbonded interactions: 361212 Sorted by model distance: nonbonded pdb=" OD1 ASN C 207 " pdb=" HG1 THR C 358 " model vdw 1.569 2.450 nonbonded pdb=" OD1 ASN D 207 " pdb=" HG1 THR D 358 " model vdw 1.569 2.450 nonbonded pdb=" OD1 ASN A 207 " pdb=" HG1 THR A 358 " model vdw 1.569 2.450 nonbonded pdb=" OD1 ASN B 207 " pdb=" HG1 THR B 358 " model vdw 1.569 2.450 nonbonded pdb=" OE2 GLU C 346 " pdb=" HE ARG C 402 " model vdw 1.622 2.450 ... (remaining 361207 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 0.400 Extract box with map and model: 0.870 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 53.620 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:12.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 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 : 0.003 0.026 12280 Z= 0.145 Angle : 0.466 5.206 16656 Z= 0.263 Chirality : 0.034 0.178 1996 Planarity : 0.002 0.017 2040 Dihedral : 15.463 58.615 4376 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.61 % Allowed : 19.76 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.59 (0.21), residues: 1508 helix: 2.97 (0.14), residues: 1256 sheet: 0.61 (0.68), residues: 48 loop : -1.37 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 38 HIS 0.001 0.000 HIS B 306 PHE 0.013 0.001 PHE C 125 TYR 0.008 0.001 TYR D 56 ARG 0.003 0.000 ARG D 129 Details of bonding type rmsd hydrogen bonds : bond 0.08186 ( 1080) hydrogen bonds : angle 4.11403 ( 3228) covalent geometry : bond 0.00292 (12280) covalent geometry : angle 0.46639 (16656) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 188 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.6196 (tpt170) cc_final: 0.5099 (tpp-160) REVERT: A 78 VAL cc_start: 0.7240 (t) cc_final: 0.6845 (p) REVERT: A 328 TRP cc_start: 0.5594 (m100) cc_final: 0.5281 (m-90) REVERT: A 399 ARG cc_start: 0.7231 (mtm-85) cc_final: 0.6965 (ttp80) REVERT: A 403 THR cc_start: 0.7874 (m) cc_final: 0.7644 (p) REVERT: B 57 ARG cc_start: 0.6197 (tpt170) cc_final: 0.5100 (tpp-160) REVERT: B 78 VAL cc_start: 0.7241 (t) cc_final: 0.6846 (p) REVERT: B 328 TRP cc_start: 0.5592 (m100) cc_final: 0.5280 (m-90) REVERT: B 399 ARG cc_start: 0.7231 (mtm-85) cc_final: 0.6964 (ttp80) REVERT: B 403 THR cc_start: 0.7873 (m) cc_final: 0.7642 (p) REVERT: C 57 ARG cc_start: 0.6196 (tpt170) cc_final: 0.5098 (tpp-160) REVERT: C 78 VAL cc_start: 0.7240 (t) cc_final: 0.6846 (p) REVERT: C 328 TRP cc_start: 0.5593 (m100) cc_final: 0.5280 (m-90) REVERT: C 399 ARG cc_start: 0.7230 (mtm-85) cc_final: 0.6964 (ttp80) REVERT: C 403 THR cc_start: 0.7874 (m) cc_final: 0.7643 (p) REVERT: D 57 ARG cc_start: 0.6197 (tpt170) cc_final: 0.5098 (tpp-160) REVERT: D 78 VAL cc_start: 0.7240 (t) cc_final: 0.6846 (p) REVERT: D 328 TRP cc_start: 0.5592 (m100) cc_final: 0.5280 (m-90) REVERT: D 399 ARG cc_start: 0.7229 (mtm-85) cc_final: 0.6963 (ttp80) REVERT: D 403 THR cc_start: 0.7875 (m) cc_final: 0.7645 (p) outliers start: 8 outliers final: 8 residues processed: 196 average time/residue: 2.7431 time to fit residues: 583.1334 Evaluate side-chains 180 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 1.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 345 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 1.9990 chunk 115 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 77 optimal weight: 0.2980 chunk 61 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.141733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.101532 restraints weight = 37736.922| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.90 r_work: 0.3001 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.0735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12280 Z= 0.122 Angle : 0.438 4.726 16656 Z= 0.242 Chirality : 0.033 0.128 1996 Planarity : 0.002 0.020 2040 Dihedral : 4.381 50.685 1676 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.91 % Allowed : 17.33 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.69 (0.21), residues: 1508 helix: 3.04 (0.14), residues: 1260 sheet: 0.46 (0.71), residues: 48 loop : -1.38 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 38 HIS 0.002 0.001 HIS A 306 PHE 0.009 0.001 PHE A 125 TYR 0.007 0.001 TYR A 175 ARG 0.002 0.000 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.04324 ( 1080) hydrogen bonds : angle 3.84749 ( 3228) covalent geometry : bond 0.00239 (12280) covalent geometry : angle 0.43820 (16656) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.7339 (tpt170) cc_final: 0.6083 (tpp-160) REVERT: A 67 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7650 (tt) REVERT: A 78 VAL cc_start: 0.8293 (t) cc_final: 0.7843 (p) REVERT: A 110 ASP cc_start: 0.7838 (t0) cc_final: 0.7625 (m-30) REVERT: A 120 ASN cc_start: 0.7605 (p0) cc_final: 0.6781 (t160) REVERT: A 159 GLN cc_start: 0.6230 (OUTLIER) cc_final: 0.5787 (mt0) REVERT: A 169 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6653 (mp0) REVERT: A 328 TRP cc_start: 0.6433 (m100) cc_final: 0.6100 (m-90) REVERT: A 399 ARG cc_start: 0.7978 (mtm-85) cc_final: 0.7564 (mtt90) REVERT: A 403 THR cc_start: 0.8974 (m) cc_final: 0.8697 (p) REVERT: B 57 ARG cc_start: 0.7351 (tpt170) cc_final: 0.6089 (tpp-160) REVERT: B 67 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7644 (tt) REVERT: B 78 VAL cc_start: 0.8285 (t) cc_final: 0.7833 (p) REVERT: B 110 ASP cc_start: 0.7831 (t0) cc_final: 0.7622 (m-30) REVERT: B 120 ASN cc_start: 0.7631 (p0) cc_final: 0.6806 (t160) REVERT: B 159 GLN cc_start: 0.6234 (OUTLIER) cc_final: 0.5790 (mt0) REVERT: B 169 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6664 (mp0) REVERT: B 328 TRP cc_start: 0.6460 (m100) cc_final: 0.6125 (m-90) REVERT: B 399 ARG cc_start: 0.7989 (mtm-85) cc_final: 0.7582 (mtt90) REVERT: B 403 THR cc_start: 0.8970 (m) cc_final: 0.8695 (p) REVERT: C 57 ARG cc_start: 0.7348 (tpt170) cc_final: 0.6093 (tpp-160) REVERT: C 67 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7647 (tt) REVERT: C 78 VAL cc_start: 0.8288 (t) cc_final: 0.7836 (p) REVERT: C 110 ASP cc_start: 0.7826 (t0) cc_final: 0.7618 (m-30) REVERT: C 120 ASN cc_start: 0.7602 (p0) cc_final: 0.6774 (t160) REVERT: C 159 GLN cc_start: 0.6239 (OUTLIER) cc_final: 0.5795 (mt0) REVERT: C 169 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6642 (mp0) REVERT: C 328 TRP cc_start: 0.6454 (m100) cc_final: 0.6121 (m-90) REVERT: C 399 ARG cc_start: 0.7980 (mtm-85) cc_final: 0.7577 (mtt90) REVERT: C 403 THR cc_start: 0.8969 (m) cc_final: 0.8698 (p) REVERT: D 57 ARG cc_start: 0.7347 (tpt170) cc_final: 0.6090 (tpp-160) REVERT: D 67 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7649 (tt) REVERT: D 78 VAL cc_start: 0.8281 (t) cc_final: 0.7838 (p) REVERT: D 110 ASP cc_start: 0.7832 (t0) cc_final: 0.7620 (m-30) REVERT: D 120 ASN cc_start: 0.7620 (p0) cc_final: 0.6799 (t160) REVERT: D 159 GLN cc_start: 0.6231 (OUTLIER) cc_final: 0.5788 (mt0) REVERT: D 169 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6651 (mp0) REVERT: D 328 TRP cc_start: 0.6450 (m100) cc_final: 0.6116 (m-90) REVERT: D 399 ARG cc_start: 0.7974 (mtm-85) cc_final: 0.7563 (mtt90) REVERT: D 403 THR cc_start: 0.8966 (m) cc_final: 0.8700 (p) outliers start: 12 outliers final: 0 residues processed: 204 average time/residue: 2.5781 time to fit residues: 573.1507 Evaluate side-chains 192 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 180 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 159 GLN Chi-restraints excluded: chain D residue 169 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 65 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.138790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.097773 restraints weight = 37748.879| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.91 r_work: 0.2920 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12280 Z= 0.193 Angle : 0.473 4.780 16656 Z= 0.263 Chirality : 0.035 0.134 1996 Planarity : 0.003 0.022 2040 Dihedral : 3.322 11.237 1660 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.52 % Allowed : 15.20 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.20 (0.21), residues: 1508 helix: 2.70 (0.13), residues: 1260 sheet: 0.20 (0.69), residues: 48 loop : -1.52 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 154 HIS 0.003 0.001 HIS A 278 PHE 0.026 0.002 PHE C 422 TYR 0.011 0.001 TYR C 56 ARG 0.003 0.000 ARG C 111 Details of bonding type rmsd hydrogen bonds : bond 0.04856 ( 1080) hydrogen bonds : angle 3.98331 ( 3228) covalent geometry : bond 0.00427 (12280) covalent geometry : angle 0.47258 (16656) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 2.024 Fit side-chains REVERT: A 57 ARG cc_start: 0.7453 (tpt170) cc_final: 0.6162 (tpp-160) REVERT: A 78 VAL cc_start: 0.8279 (t) cc_final: 0.7847 (p) REVERT: A 110 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7728 (m-30) REVERT: A 120 ASN cc_start: 0.7583 (p0) cc_final: 0.6703 (t0) REVERT: A 159 GLN cc_start: 0.6152 (OUTLIER) cc_final: 0.5736 (mt0) REVERT: A 276 ASP cc_start: 0.8175 (t0) cc_final: 0.7972 (m-30) REVERT: A 328 TRP cc_start: 0.6502 (m100) cc_final: 0.6190 (m-90) REVERT: A 399 ARG cc_start: 0.8226 (mtm-85) cc_final: 0.7824 (mtt90) REVERT: B 57 ARG cc_start: 0.7458 (tpt170) cc_final: 0.6169 (tpp-160) REVERT: B 78 VAL cc_start: 0.8275 (t) cc_final: 0.7839 (p) REVERT: B 110 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7712 (m-30) REVERT: B 120 ASN cc_start: 0.7596 (p0) cc_final: 0.6713 (t0) REVERT: B 159 GLN cc_start: 0.6150 (OUTLIER) cc_final: 0.5734 (mt0) REVERT: B 276 ASP cc_start: 0.8186 (t0) cc_final: 0.7978 (m-30) REVERT: B 328 TRP cc_start: 0.6492 (m100) cc_final: 0.6180 (m-90) REVERT: B 399 ARG cc_start: 0.8220 (mtm-85) cc_final: 0.7817 (mtt90) REVERT: C 57 ARG cc_start: 0.7461 (tpt170) cc_final: 0.6175 (tpp-160) REVERT: C 78 VAL cc_start: 0.8276 (t) cc_final: 0.7844 (p) REVERT: C 110 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7722 (m-30) REVERT: C 120 ASN cc_start: 0.7576 (p0) cc_final: 0.6684 (t0) REVERT: C 159 GLN cc_start: 0.6152 (OUTLIER) cc_final: 0.5732 (mt0) REVERT: C 328 TRP cc_start: 0.6482 (m100) cc_final: 0.6172 (m-90) REVERT: C 399 ARG cc_start: 0.8210 (mtm-85) cc_final: 0.7816 (mtt90) REVERT: D 57 ARG cc_start: 0.7467 (tpt170) cc_final: 0.6181 (tpp-160) REVERT: D 78 VAL cc_start: 0.8272 (t) cc_final: 0.7840 (p) REVERT: D 110 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7718 (m-30) REVERT: D 120 ASN cc_start: 0.7592 (p0) cc_final: 0.6709 (t0) REVERT: D 159 GLN cc_start: 0.6156 (OUTLIER) cc_final: 0.5739 (mt0) REVERT: D 276 ASP cc_start: 0.8188 (t0) cc_final: 0.7982 (m-30) REVERT: D 328 TRP cc_start: 0.6501 (m100) cc_final: 0.6190 (m-90) REVERT: D 399 ARG cc_start: 0.8223 (mtm-85) cc_final: 0.7820 (mtt90) outliers start: 20 outliers final: 0 residues processed: 188 average time/residue: 2.9849 time to fit residues: 611.1741 Evaluate side-chains 183 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 175 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 159 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 66 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 80 optimal weight: 0.1980 chunk 110 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 83 optimal weight: 0.0370 chunk 58 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.8464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.139532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.098465 restraints weight = 37761.071| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.92 r_work: 0.2932 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12280 Z= 0.159 Angle : 0.454 5.201 16656 Z= 0.251 Chirality : 0.034 0.131 1996 Planarity : 0.003 0.049 2040 Dihedral : 3.327 11.493 1660 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.22 % Allowed : 15.43 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.21), residues: 1508 helix: 2.71 (0.13), residues: 1260 sheet: 0.26 (0.71), residues: 48 loop : -1.48 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 154 HIS 0.002 0.001 HIS C 278 PHE 0.023 0.002 PHE C 422 TYR 0.008 0.001 TYR B 56 ARG 0.007 0.000 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.04567 ( 1080) hydrogen bonds : angle 3.90387 ( 3228) covalent geometry : bond 0.00334 (12280) covalent geometry : angle 0.45428 (16656) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 2.053 Fit side-chains REVERT: A 57 ARG cc_start: 0.7461 (tpt170) cc_final: 0.6117 (tpp-160) REVERT: A 78 VAL cc_start: 0.8257 (t) cc_final: 0.7828 (p) REVERT: A 110 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7700 (m-30) REVERT: A 120 ASN cc_start: 0.7579 (p0) cc_final: 0.6695 (t0) REVERT: A 159 GLN cc_start: 0.6131 (OUTLIER) cc_final: 0.5795 (mt0) REVERT: A 328 TRP cc_start: 0.6491 (m100) cc_final: 0.6152 (m-90) REVERT: A 399 ARG cc_start: 0.8206 (mtm-85) cc_final: 0.7816 (mtt90) REVERT: B 57 ARG cc_start: 0.7481 (tpt170) cc_final: 0.6137 (tpp-160) REVERT: B 78 VAL cc_start: 0.8256 (t) cc_final: 0.7827 (p) REVERT: B 110 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7692 (m-30) REVERT: B 120 ASN cc_start: 0.7591 (p0) cc_final: 0.6707 (t0) REVERT: B 159 GLN cc_start: 0.6132 (OUTLIER) cc_final: 0.5788 (mt0) REVERT: B 328 TRP cc_start: 0.6471 (m100) cc_final: 0.6136 (m-90) REVERT: B 399 ARG cc_start: 0.8218 (mtm-85) cc_final: 0.7824 (mtt90) REVERT: C 57 ARG cc_start: 0.7470 (tpt170) cc_final: 0.6127 (tpp-160) REVERT: C 78 VAL cc_start: 0.8265 (t) cc_final: 0.7835 (p) REVERT: C 110 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7702 (m-30) REVERT: C 120 ASN cc_start: 0.7575 (p0) cc_final: 0.6683 (t0) REVERT: C 159 GLN cc_start: 0.6138 (OUTLIER) cc_final: 0.5792 (mt0) REVERT: C 328 TRP cc_start: 0.6470 (m100) cc_final: 0.6135 (m-90) REVERT: C 399 ARG cc_start: 0.8203 (mtm-85) cc_final: 0.7821 (mtt90) REVERT: D 57 ARG cc_start: 0.7467 (tpt170) cc_final: 0.6125 (tpp-160) REVERT: D 78 VAL cc_start: 0.8256 (t) cc_final: 0.7826 (p) REVERT: D 110 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7687 (m-30) REVERT: D 120 ASN cc_start: 0.7586 (p0) cc_final: 0.6704 (t0) REVERT: D 159 GLN cc_start: 0.6143 (OUTLIER) cc_final: 0.5799 (mt0) REVERT: D 328 TRP cc_start: 0.6486 (m100) cc_final: 0.6151 (m-90) REVERT: D 399 ARG cc_start: 0.8216 (mtm-85) cc_final: 0.7821 (mtt90) outliers start: 16 outliers final: 4 residues processed: 195 average time/residue: 2.7267 time to fit residues: 577.8882 Evaluate side-chains 192 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 180 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 159 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 121 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.138688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.097453 restraints weight = 37871.175| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.92 r_work: 0.2916 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12280 Z= 0.181 Angle : 0.461 4.502 16656 Z= 0.256 Chirality : 0.034 0.130 1996 Planarity : 0.004 0.045 2040 Dihedral : 3.405 11.613 1660 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.82 % Allowed : 15.12 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.21), residues: 1508 helix: 2.60 (0.13), residues: 1260 sheet: 0.22 (0.71), residues: 48 loop : -1.50 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 154 HIS 0.003 0.001 HIS C 278 PHE 0.030 0.002 PHE A 422 TYR 0.009 0.001 TYR B 56 ARG 0.009 0.000 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.04722 ( 1080) hydrogen bonds : angle 3.94796 ( 3228) covalent geometry : bond 0.00395 (12280) covalent geometry : angle 0.46122 (16656) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 1.751 Fit side-chains REVERT: A 57 ARG cc_start: 0.7459 (tpt170) cc_final: 0.6086 (tpp-160) REVERT: A 78 VAL cc_start: 0.8240 (t) cc_final: 0.7809 (p) REVERT: A 110 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7708 (m-30) REVERT: A 120 ASN cc_start: 0.7554 (p0) cc_final: 0.6620 (t0) REVERT: A 129 ARG cc_start: 0.7869 (ttm-80) cc_final: 0.7621 (ttm110) REVERT: A 159 GLN cc_start: 0.6145 (OUTLIER) cc_final: 0.5821 (mt0) REVERT: A 328 TRP cc_start: 0.6484 (m100) cc_final: 0.5729 (m-10) REVERT: A 399 ARG cc_start: 0.8240 (mtm-85) cc_final: 0.7848 (mtt90) REVERT: B 57 ARG cc_start: 0.7478 (tpt170) cc_final: 0.6102 (tpp-160) REVERT: B 78 VAL cc_start: 0.8234 (t) cc_final: 0.7804 (p) REVERT: B 110 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7682 (m-30) REVERT: B 120 ASN cc_start: 0.7566 (p0) cc_final: 0.6631 (t0) REVERT: B 129 ARG cc_start: 0.7871 (ttm-80) cc_final: 0.7622 (ttm110) REVERT: B 159 GLN cc_start: 0.6181 (OUTLIER) cc_final: 0.5818 (mt0) REVERT: B 328 TRP cc_start: 0.6476 (m100) cc_final: 0.5726 (m-10) REVERT: B 399 ARG cc_start: 0.8240 (mtm-85) cc_final: 0.7853 (mtt90) REVERT: C 57 ARG cc_start: 0.7457 (tpt170) cc_final: 0.6085 (tpp-160) REVERT: C 78 VAL cc_start: 0.8252 (t) cc_final: 0.7821 (p) REVERT: C 110 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7707 (m-30) REVERT: C 120 ASN cc_start: 0.7540 (p0) cc_final: 0.6596 (t0) REVERT: C 129 ARG cc_start: 0.7878 (ttm-80) cc_final: 0.7629 (ttm110) REVERT: C 159 GLN cc_start: 0.6181 (OUTLIER) cc_final: 0.5819 (mt0) REVERT: C 328 TRP cc_start: 0.6473 (m100) cc_final: 0.5724 (m-10) REVERT: C 399 ARG cc_start: 0.8217 (mtm-85) cc_final: 0.7839 (mtt90) REVERT: D 57 ARG cc_start: 0.7473 (tpt170) cc_final: 0.6102 (tpp-160) REVERT: D 78 VAL cc_start: 0.8234 (t) cc_final: 0.7803 (p) REVERT: D 110 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7703 (m-30) REVERT: D 120 ASN cc_start: 0.7556 (p0) cc_final: 0.6622 (t0) REVERT: D 129 ARG cc_start: 0.7875 (ttm-80) cc_final: 0.7629 (ttm110) REVERT: D 159 GLN cc_start: 0.6185 (OUTLIER) cc_final: 0.5824 (mt0) REVERT: D 328 TRP cc_start: 0.6484 (m100) cc_final: 0.5731 (m-10) REVERT: D 399 ARG cc_start: 0.8238 (mtm-85) cc_final: 0.7847 (mtt90) outliers start: 24 outliers final: 8 residues processed: 198 average time/residue: 2.8539 time to fit residues: 611.5542 Evaluate side-chains 200 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 159 GLN Chi-restraints excluded: chain D residue 345 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 149 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 7 optimal weight: 0.0060 chunk 58 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.138697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.097479 restraints weight = 37684.238| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.92 r_work: 0.2917 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12280 Z= 0.179 Angle : 0.467 5.735 16656 Z= 0.258 Chirality : 0.034 0.129 1996 Planarity : 0.003 0.033 2040 Dihedral : 3.419 11.765 1660 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.52 % Allowed : 15.50 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.10 (0.21), residues: 1508 helix: 2.62 (0.13), residues: 1260 sheet: 0.21 (0.71), residues: 48 loop : -1.45 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 154 HIS 0.003 0.001 HIS C 278 PHE 0.033 0.002 PHE B 422 TYR 0.007 0.001 TYR D 56 ARG 0.005 0.000 ARG D 129 Details of bonding type rmsd hydrogen bonds : bond 0.04687 ( 1080) hydrogen bonds : angle 3.93812 ( 3228) covalent geometry : bond 0.00388 (12280) covalent geometry : angle 0.46661 (16656) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 1.826 Fit side-chains REVERT: A 57 ARG cc_start: 0.7461 (tpt170) cc_final: 0.6084 (tpp-160) REVERT: A 78 VAL cc_start: 0.8238 (t) cc_final: 0.7808 (p) REVERT: A 110 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7707 (m-30) REVERT: A 120 ASN cc_start: 0.7564 (p0) cc_final: 0.6625 (t0) REVERT: A 159 GLN cc_start: 0.6140 (OUTLIER) cc_final: 0.5816 (mt0) REVERT: A 328 TRP cc_start: 0.6492 (m100) cc_final: 0.5730 (m-10) REVERT: A 399 ARG cc_start: 0.8249 (mtm-85) cc_final: 0.7861 (mtt180) REVERT: B 57 ARG cc_start: 0.7465 (tpt170) cc_final: 0.6088 (tpp-160) REVERT: B 78 VAL cc_start: 0.8229 (t) cc_final: 0.7800 (p) REVERT: B 110 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7697 (m-30) REVERT: B 120 ASN cc_start: 0.7570 (p0) cc_final: 0.6632 (t0) REVERT: B 159 GLN cc_start: 0.6150 (OUTLIER) cc_final: 0.5820 (mt0) REVERT: B 328 TRP cc_start: 0.6480 (m100) cc_final: 0.5725 (m-10) REVERT: B 399 ARG cc_start: 0.8256 (mtm-85) cc_final: 0.7864 (mtt180) REVERT: C 57 ARG cc_start: 0.7457 (tpt170) cc_final: 0.6082 (tpp-160) REVERT: C 78 VAL cc_start: 0.8245 (t) cc_final: 0.7812 (p) REVERT: C 110 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7711 (m-30) REVERT: C 120 ASN cc_start: 0.7545 (p0) cc_final: 0.6601 (t0) REVERT: C 159 GLN cc_start: 0.6150 (OUTLIER) cc_final: 0.5820 (mt0) REVERT: C 328 TRP cc_start: 0.6478 (m100) cc_final: 0.5724 (m-10) REVERT: C 399 ARG cc_start: 0.8239 (mtm-85) cc_final: 0.7852 (mtt180) REVERT: D 57 ARG cc_start: 0.7471 (tpt170) cc_final: 0.6096 (tpp-160) REVERT: D 78 VAL cc_start: 0.8232 (t) cc_final: 0.7802 (p) REVERT: D 110 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7703 (m-30) REVERT: D 120 ASN cc_start: 0.7568 (p0) cc_final: 0.6627 (t0) REVERT: D 159 GLN cc_start: 0.6149 (OUTLIER) cc_final: 0.5822 (mt0) REVERT: D 328 TRP cc_start: 0.6489 (m100) cc_final: 0.5729 (m-10) REVERT: D 399 ARG cc_start: 0.8251 (mtm-85) cc_final: 0.7861 (mtt180) outliers start: 20 outliers final: 8 residues processed: 196 average time/residue: 2.6909 time to fit residues: 573.9608 Evaluate side-chains 194 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 159 GLN Chi-restraints excluded: chain D residue 345 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 111 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.138641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.097379 restraints weight = 37874.540| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.92 r_work: 0.2916 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12280 Z= 0.180 Angle : 0.465 4.928 16656 Z= 0.257 Chirality : 0.034 0.130 1996 Planarity : 0.004 0.063 2040 Dihedral : 3.460 11.240 1660 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.81 % Allowed : 13.91 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.10 (0.21), residues: 1508 helix: 2.61 (0.13), residues: 1260 sheet: 0.20 (0.71), residues: 48 loop : -1.38 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 154 HIS 0.003 0.001 HIS B 278 PHE 0.035 0.002 PHE C 422 TYR 0.008 0.001 TYR C 56 ARG 0.010 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.04710 ( 1080) hydrogen bonds : angle 3.94610 ( 3228) covalent geometry : bond 0.00392 (12280) covalent geometry : angle 0.46465 (16656) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 177 time to evaluate : 1.745 Fit side-chains REVERT: A 26 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.7167 (ttm170) REVERT: A 57 ARG cc_start: 0.7481 (tpt170) cc_final: 0.6075 (tpp-160) REVERT: A 59 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7202 (mp) REVERT: A 78 VAL cc_start: 0.8218 (t) cc_final: 0.7789 (p) REVERT: A 110 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7713 (m-30) REVERT: A 120 ASN cc_start: 0.7489 (p0) cc_final: 0.6545 (t0) REVERT: A 159 GLN cc_start: 0.6191 (OUTLIER) cc_final: 0.5829 (mt0) REVERT: A 328 TRP cc_start: 0.6465 (m100) cc_final: 0.5713 (m-10) REVERT: B 26 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.7169 (ttm170) REVERT: B 57 ARG cc_start: 0.7484 (tpt170) cc_final: 0.6077 (tpp-160) REVERT: B 59 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7199 (mp) REVERT: B 78 VAL cc_start: 0.8217 (t) cc_final: 0.7788 (p) REVERT: B 110 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7700 (m-30) REVERT: B 120 ASN cc_start: 0.7490 (p0) cc_final: 0.6545 (t0) REVERT: B 159 GLN cc_start: 0.6196 (OUTLIER) cc_final: 0.5834 (mt0) REVERT: B 328 TRP cc_start: 0.6463 (m100) cc_final: 0.5712 (m-10) REVERT: C 26 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.7172 (ttm170) REVERT: C 57 ARG cc_start: 0.7472 (tpt170) cc_final: 0.6066 (tpp-160) REVERT: C 59 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7188 (mp) REVERT: C 78 VAL cc_start: 0.8223 (t) cc_final: 0.7794 (p) REVERT: C 110 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7705 (m-30) REVERT: C 120 ASN cc_start: 0.7474 (p0) cc_final: 0.6524 (t0) REVERT: C 159 GLN cc_start: 0.6198 (OUTLIER) cc_final: 0.5835 (mt0) REVERT: C 328 TRP cc_start: 0.6461 (m100) cc_final: 0.5712 (m-10) REVERT: D 26 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.7174 (ttm170) REVERT: D 57 ARG cc_start: 0.7483 (tpt170) cc_final: 0.6077 (tpp-160) REVERT: D 59 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7192 (mp) REVERT: D 78 VAL cc_start: 0.8219 (t) cc_final: 0.7790 (p) REVERT: D 110 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7704 (m-30) REVERT: D 120 ASN cc_start: 0.7491 (p0) cc_final: 0.6544 (t0) REVERT: D 159 GLN cc_start: 0.6197 (OUTLIER) cc_final: 0.5834 (mt0) REVERT: D 328 TRP cc_start: 0.6467 (m100) cc_final: 0.5714 (m-10) outliers start: 37 outliers final: 8 residues processed: 194 average time/residue: 2.6283 time to fit residues: 557.6457 Evaluate side-chains 202 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ARG Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 159 GLN Chi-restraints excluded: chain D residue 345 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 134 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.136442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.094917 restraints weight = 37819.623| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.92 r_work: 0.2881 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12280 Z= 0.215 Angle : 0.489 4.886 16656 Z= 0.271 Chirality : 0.036 0.131 1996 Planarity : 0.004 0.057 2040 Dihedral : 3.548 11.602 1660 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.58 % Allowed : 13.83 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.21), residues: 1508 helix: 2.46 (0.13), residues: 1260 sheet: 0.17 (0.70), residues: 48 loop : -1.49 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 154 HIS 0.003 0.001 HIS A 278 PHE 0.041 0.002 PHE D 422 TYR 0.009 0.001 TYR D 56 ARG 0.009 0.001 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.04937 ( 1080) hydrogen bonds : angle 4.02976 ( 3228) covalent geometry : bond 0.00478 (12280) covalent geometry : angle 0.48932 (16656) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 1.808 Fit side-chains REVERT: A 26 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.7142 (ttm170) REVERT: A 57 ARG cc_start: 0.7481 (tpt170) cc_final: 0.6100 (tpp-160) REVERT: A 59 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7229 (mp) REVERT: A 78 VAL cc_start: 0.8234 (t) cc_final: 0.7809 (p) REVERT: A 110 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7696 (m-30) REVERT: A 120 ASN cc_start: 0.7465 (p0) cc_final: 0.6498 (t0) REVERT: A 159 GLN cc_start: 0.6192 (OUTLIER) cc_final: 0.5815 (mt0) REVERT: A 328 TRP cc_start: 0.6453 (m100) cc_final: 0.5722 (m-10) REVERT: A 399 ARG cc_start: 0.8147 (mtm110) cc_final: 0.7713 (mtt90) REVERT: B 26 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.7137 (ttm170) REVERT: B 57 ARG cc_start: 0.7484 (tpt170) cc_final: 0.6101 (tpp-160) REVERT: B 59 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7222 (mp) REVERT: B 78 VAL cc_start: 0.8240 (t) cc_final: 0.7815 (p) REVERT: B 110 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7691 (m-30) REVERT: B 120 ASN cc_start: 0.7468 (p0) cc_final: 0.6500 (t0) REVERT: B 159 GLN cc_start: 0.6197 (OUTLIER) cc_final: 0.5819 (mt0) REVERT: B 328 TRP cc_start: 0.6452 (m100) cc_final: 0.5725 (m-10) REVERT: B 399 ARG cc_start: 0.8148 (mtm110) cc_final: 0.7710 (mtt90) REVERT: C 26 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.7129 (ttm170) REVERT: C 57 ARG cc_start: 0.7481 (tpt170) cc_final: 0.6099 (tpp-160) REVERT: C 59 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7220 (mp) REVERT: C 78 VAL cc_start: 0.8213 (t) cc_final: 0.7785 (p) REVERT: C 110 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7697 (m-30) REVERT: C 120 ASN cc_start: 0.7453 (p0) cc_final: 0.6481 (t0) REVERT: C 159 GLN cc_start: 0.6195 (OUTLIER) cc_final: 0.5815 (mt0) REVERT: C 328 TRP cc_start: 0.6442 (m100) cc_final: 0.5707 (m-10) REVERT: C 399 ARG cc_start: 0.8134 (mtm110) cc_final: 0.7705 (mtt90) REVERT: D 26 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.7155 (ttm170) REVERT: D 57 ARG cc_start: 0.7475 (tpt170) cc_final: 0.6082 (tpp-160) REVERT: D 59 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7227 (mp) REVERT: D 78 VAL cc_start: 0.8228 (t) cc_final: 0.7805 (p) REVERT: D 110 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7698 (m-30) REVERT: D 120 ASN cc_start: 0.7475 (p0) cc_final: 0.6508 (t0) REVERT: D 159 GLN cc_start: 0.6193 (OUTLIER) cc_final: 0.5813 (mt0) REVERT: D 328 TRP cc_start: 0.6457 (m100) cc_final: 0.5728 (m-10) REVERT: D 399 ARG cc_start: 0.8149 (mtm110) cc_final: 0.7715 (mtt90) outliers start: 34 outliers final: 8 residues processed: 202 average time/residue: 2.5552 time to fit residues: 563.9068 Evaluate side-chains 200 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ARG Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 26 ARG Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 159 GLN Chi-restraints excluded: chain D residue 345 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 96 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.139257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.098127 restraints weight = 37725.499| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.90 r_work: 0.2905 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12280 Z= 0.157 Angle : 0.463 6.007 16656 Z= 0.255 Chirality : 0.034 0.131 1996 Planarity : 0.003 0.054 2040 Dihedral : 3.455 11.200 1660 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.20 % Allowed : 14.21 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.14 (0.21), residues: 1508 helix: 2.63 (0.14), residues: 1260 sheet: 0.25 (0.72), residues: 48 loop : -1.27 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 154 HIS 0.002 0.001 HIS B 278 PHE 0.038 0.002 PHE C 422 TYR 0.006 0.001 TYR D 56 ARG 0.007 0.000 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.04595 ( 1080) hydrogen bonds : angle 3.91663 ( 3228) covalent geometry : bond 0.00331 (12280) covalent geometry : angle 0.46276 (16656) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 1.902 Fit side-chains REVERT: A 26 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.7125 (ttm170) REVERT: A 57 ARG cc_start: 0.7412 (tpt170) cc_final: 0.5995 (tpp-160) REVERT: A 59 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7137 (mp) REVERT: A 67 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7660 (tt) REVERT: A 78 VAL cc_start: 0.8177 (t) cc_final: 0.7748 (p) REVERT: A 110 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7659 (m-30) REVERT: A 120 ASN cc_start: 0.7418 (p0) cc_final: 0.6452 (t0) REVERT: A 159 GLN cc_start: 0.6257 (OUTLIER) cc_final: 0.5871 (mt0) REVERT: A 328 TRP cc_start: 0.6404 (m100) cc_final: 0.5723 (m-10) REVERT: A 399 ARG cc_start: 0.8094 (mtm110) cc_final: 0.7654 (mtt90) REVERT: B 26 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.7146 (ttm170) REVERT: B 57 ARG cc_start: 0.7410 (tpt170) cc_final: 0.5992 (tpp-160) REVERT: B 59 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7131 (mp) REVERT: B 67 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7662 (tt) REVERT: B 78 VAL cc_start: 0.8176 (t) cc_final: 0.7748 (p) REVERT: B 110 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7646 (m-30) REVERT: B 120 ASN cc_start: 0.7424 (p0) cc_final: 0.6456 (t0) REVERT: B 159 GLN cc_start: 0.6262 (OUTLIER) cc_final: 0.5876 (mt0) REVERT: B 328 TRP cc_start: 0.6398 (m100) cc_final: 0.5720 (m-10) REVERT: B 399 ARG cc_start: 0.8095 (mtm110) cc_final: 0.7652 (mtt90) REVERT: C 57 ARG cc_start: 0.7404 (tpt170) cc_final: 0.5985 (tpp-160) REVERT: C 59 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7125 (mp) REVERT: C 67 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7661 (tt) REVERT: C 78 VAL cc_start: 0.8172 (t) cc_final: 0.7741 (p) REVERT: C 110 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7651 (m-30) REVERT: C 120 ASN cc_start: 0.7410 (p0) cc_final: 0.6440 (t0) REVERT: C 159 GLN cc_start: 0.6264 (OUTLIER) cc_final: 0.5873 (mt0) REVERT: C 328 TRP cc_start: 0.6394 (m100) cc_final: 0.5717 (m-10) REVERT: C 399 ARG cc_start: 0.8084 (mtm110) cc_final: 0.7650 (mtt90) REVERT: D 26 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.7131 (ttm170) REVERT: D 57 ARG cc_start: 0.7403 (tpt170) cc_final: 0.5988 (tpp-160) REVERT: D 59 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7128 (mp) REVERT: D 67 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7662 (tt) REVERT: D 78 VAL cc_start: 0.8173 (t) cc_final: 0.7744 (p) REVERT: D 110 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7659 (m-30) REVERT: D 120 ASN cc_start: 0.7423 (p0) cc_final: 0.6456 (t0) REVERT: D 159 GLN cc_start: 0.6257 (OUTLIER) cc_final: 0.5868 (mt0) REVERT: D 328 TRP cc_start: 0.6398 (m100) cc_final: 0.5717 (m-10) REVERT: D 399 ARG cc_start: 0.8099 (mtm110) cc_final: 0.7657 (mtt90) outliers start: 29 outliers final: 4 residues processed: 181 average time/residue: 2.6472 time to fit residues: 522.0383 Evaluate side-chains 199 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ARG Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 159 GLN Chi-restraints excluded: chain D residue 345 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 146 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.138711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.097423 restraints weight = 37692.142| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.92 r_work: 0.2889 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12280 Z= 0.178 Angle : 0.470 5.609 16656 Z= 0.259 Chirality : 0.034 0.130 1996 Planarity : 0.004 0.052 2040 Dihedral : 3.475 11.377 1660 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.75 % Allowed : 14.67 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.21), residues: 1508 helix: 2.59 (0.13), residues: 1260 sheet: 0.19 (0.71), residues: 48 loop : -1.34 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 154 HIS 0.002 0.001 HIS A 278 PHE 0.038 0.002 PHE D 422 TYR 0.008 0.001 TYR D 56 ARG 0.007 0.000 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.04719 ( 1080) hydrogen bonds : angle 3.94457 ( 3228) covalent geometry : bond 0.00386 (12280) covalent geometry : angle 0.47013 (16656) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 1.774 Fit side-chains REVERT: A 26 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.7153 (ttm170) REVERT: A 57 ARG cc_start: 0.7449 (tpt170) cc_final: 0.6022 (tpp-160) REVERT: A 59 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7160 (mp) REVERT: A 67 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7668 (tt) REVERT: A 78 VAL cc_start: 0.8217 (t) cc_final: 0.7790 (p) REVERT: A 110 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7689 (m-30) REVERT: A 120 ASN cc_start: 0.7438 (p0) cc_final: 0.6473 (t0) REVERT: A 159 GLN cc_start: 0.6179 (OUTLIER) cc_final: 0.5804 (mt0) REVERT: A 399 ARG cc_start: 0.8141 (mtm110) cc_final: 0.7699 (mtt90) REVERT: B 26 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.7142 (ttm170) REVERT: B 57 ARG cc_start: 0.7445 (tpt170) cc_final: 0.6018 (tpp-160) REVERT: B 59 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7189 (mp) REVERT: B 67 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7672 (tt) REVERT: B 78 VAL cc_start: 0.8212 (t) cc_final: 0.7785 (p) REVERT: B 110 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7684 (m-30) REVERT: B 159 GLN cc_start: 0.6189 (OUTLIER) cc_final: 0.5813 (mt0) REVERT: B 399 ARG cc_start: 0.8133 (mtm110) cc_final: 0.7691 (mtt90) REVERT: C 26 ARG cc_start: 0.7172 (ttm170) cc_final: 0.6972 (ttm170) REVERT: C 57 ARG cc_start: 0.7443 (tpt170) cc_final: 0.6017 (tpp-160) REVERT: C 59 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7186 (mp) REVERT: C 67 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7667 (tt) REVERT: C 78 VAL cc_start: 0.8211 (t) cc_final: 0.7783 (p) REVERT: C 110 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7694 (m-30) REVERT: C 120 ASN cc_start: 0.7430 (p0) cc_final: 0.6459 (t0) REVERT: C 159 GLN cc_start: 0.6187 (OUTLIER) cc_final: 0.5809 (mt0) REVERT: C 399 ARG cc_start: 0.8124 (mtm110) cc_final: 0.7686 (mtt90) REVERT: D 26 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.7165 (ttm170) REVERT: D 57 ARG cc_start: 0.7444 (tpt170) cc_final: 0.6020 (tpp-160) REVERT: D 59 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7151 (mp) REVERT: D 67 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7673 (tt) REVERT: D 78 VAL cc_start: 0.8210 (t) cc_final: 0.7782 (p) REVERT: D 110 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7690 (m-30) REVERT: D 120 ASN cc_start: 0.7447 (p0) cc_final: 0.6481 (t0) REVERT: D 159 GLN cc_start: 0.6182 (OUTLIER) cc_final: 0.5804 (mt0) REVERT: D 399 ARG cc_start: 0.8142 (mtm110) cc_final: 0.7699 (mtt90) outliers start: 23 outliers final: 4 residues processed: 184 average time/residue: 2.6440 time to fit residues: 530.5360 Evaluate side-chains 193 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ARG Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 159 GLN Chi-restraints excluded: chain D residue 345 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 86 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN C 117 ASN D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.137882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.096450 restraints weight = 37735.540| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.92 r_work: 0.2882 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12280 Z= 0.214 Angle : 0.493 5.584 16656 Z= 0.273 Chirality : 0.035 0.131 1996 Planarity : 0.004 0.050 2040 Dihedral : 3.571 11.752 1660 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.05 % Allowed : 14.36 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.21), residues: 1508 helix: 2.44 (0.13), residues: 1260 sheet: 0.18 (0.71), residues: 48 loop : -1.47 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 154 HIS 0.003 0.001 HIS C 278 PHE 0.044 0.002 PHE B 422 TYR 0.009 0.001 TYR C 56 ARG 0.007 0.001 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.04934 ( 1080) hydrogen bonds : angle 4.02570 ( 3228) covalent geometry : bond 0.00476 (12280) covalent geometry : angle 0.49326 (16656) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16990.89 seconds wall clock time: 291 minutes 0.69 seconds (17460.69 seconds total)