Starting phenix.real_space_refine on Wed Mar 12 16:31:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pxb_18002/03_2025/8pxb_18002.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pxb_18002/03_2025/8pxb_18002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pxb_18002/03_2025/8pxb_18002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pxb_18002/03_2025/8pxb_18002.map" model { file = "/net/cci-nas-00/data/ceres_data/8pxb_18002/03_2025/8pxb_18002.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pxb_18002/03_2025/8pxb_18002.cif" } resolution = 3.6 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= 0.004 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 5388 2.51 5 N 1280 2.21 5 O 1384 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8102 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4051 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 18, 'TRANS': 490} Chain breaks: 1 Chain: "A" Number of atoms: 4051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4051 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 18, 'TRANS': 490} Chain breaks: 1 Time building chain proxies: 6.26, per 1000 atoms: 0.77 Number of scatterers: 8102 At special positions: 0 Unit cell: (80.925, 106.862, 88.1875, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1384 8.00 N 1280 7.00 C 5388 6.00 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: 2.10 Conformation dependent library (CDL) restraints added in 1.1 seconds 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1892 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 1 sheets defined 72.5% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'B' and resid 19 through 45 removed outlier: 4.045A pdb=" N GLU B 23 " --> pdb=" O GLN B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 68 removed outlier: 3.591A pdb=" N TYR B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 121 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 138 through 149 removed outlier: 3.729A pdb=" N ILE B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 192 removed outlier: 4.380A pdb=" N THR B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 171 " --> pdb=" O PHE B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 211 Processing helix chain 'B' and resid 216 through 227 Processing helix chain 'B' and resid 229 through 257 removed outlier: 3.558A pdb=" N TYR B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA B 245 " --> pdb=" O VAL B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 303 Processing helix chain 'B' and resid 304 through 307 removed outlier: 3.824A pdb=" N GLU B 307 " --> pdb=" O LYS B 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 304 through 307' Processing helix chain 'B' and resid 308 through 330 Processing helix chain 'B' and resid 333 through 349 removed outlier: 3.594A pdb=" N ALA B 337 " --> pdb=" O THR B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 354 through 381 removed outlier: 3.711A pdb=" N MET B 359 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 422 removed outlier: 3.618A pdb=" N ILE B 412 " --> pdb=" O ARG B 408 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) Proline residue: B 414 - end of helix removed outlier: 3.807A pdb=" N GLY B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 438 Processing helix chain 'B' and resid 442 through 452 removed outlier: 3.901A pdb=" N PHE B 446 " --> pdb=" O GLY B 442 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP B 452 " --> pdb=" O LEU B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 487 removed outlier: 3.647A pdb=" N TRP B 474 " --> pdb=" O PHE B 470 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N THR B 481 " --> pdb=" O GLY B 477 " (cutoff:3.500A) Proline residue: B 482 - end of helix Processing helix chain 'B' and resid 524 through 535 Processing helix chain 'B' and resid 535 through 541 removed outlier: 3.869A pdb=" N ILE B 539 " --> pdb=" O TYR B 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 45 removed outlier: 3.990A pdb=" N GLU A 23 " --> pdb=" O GLN A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 68 removed outlier: 3.518A pdb=" N TYR A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 121 Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 138 through 149 removed outlier: 3.717A pdb=" N ILE A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 192 removed outlier: 4.380A pdb=" N THR A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 171 " --> pdb=" O PHE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 211 Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 229 through 257 removed outlier: 3.561A pdb=" N TYR A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 303 Processing helix chain 'A' and resid 304 through 307 removed outlier: 3.761A pdb=" N GLU A 307 " --> pdb=" O LYS A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 304 through 307' Processing helix chain 'A' and resid 308 through 330 Processing helix chain 'A' and resid 333 through 349 removed outlier: 3.628A pdb=" N ALA A 337 " --> pdb=" O THR A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 354 through 381 removed outlier: 3.706A pdb=" N MET A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 422 removed outlier: 3.586A pdb=" N ILE A 412 " --> pdb=" O ARG A 408 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Proline residue: A 414 - end of helix removed outlier: 3.778A pdb=" N GLY A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 438 Processing helix chain 'A' and resid 442 through 452 removed outlier: 3.902A pdb=" N PHE A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 487 removed outlier: 3.645A pdb=" N TRP A 474 " --> pdb=" O PHE A 470 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N THR A 481 " --> pdb=" O GLY A 477 " (cutoff:3.500A) Proline residue: A 482 - end of helix Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 535 through 541 removed outlier: 3.874A pdb=" N ILE A 539 " --> pdb=" O TYR A 535 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 97 removed outlier: 7.373A pdb=" N VAL B 101 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N GLU A 109 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLU B 103 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS B 107 " --> pdb=" O GLU A 103 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N GLU A 103 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLU B 109 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL A 101 " --> pdb=" O GLU B 109 " (cutoff:3.500A) 539 hydrogen bonds defined for protein. 1611 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.18 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2442 1.34 - 1.46: 2105 1.46 - 1.58: 3705 1.58 - 1.69: 0 1.69 - 1.81: 86 Bond restraints: 8338 Sorted by residual: bond pdb=" CA ASN A 430 " pdb=" CB ASN A 430 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 7.07e-01 bond pdb=" N GLU B 454 " pdb=" CA GLU B 454 " ideal model delta sigma weight residual 1.460 1.471 -0.011 1.42e-02 4.96e+03 6.46e-01 bond pdb=" CA ASN B 430 " pdb=" CB ASN B 430 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.69e-02 3.50e+03 6.12e-01 bond pdb=" N SER A 258 " pdb=" CA SER A 258 " ideal model delta sigma weight residual 1.463 1.456 0.007 8.80e-03 1.29e+04 6.02e-01 bond pdb=" N GLU A 454 " pdb=" CA GLU A 454 " ideal model delta sigma weight residual 1.460 1.471 -0.011 1.42e-02 4.96e+03 5.83e-01 ... (remaining 8333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 11155 1.45 - 2.90: 122 2.90 - 4.35: 25 4.35 - 5.80: 16 5.80 - 7.24: 2 Bond angle restraints: 11320 Sorted by residual: angle pdb=" C TRP A 429 " pdb=" N ASN A 430 " pdb=" CA ASN A 430 " ideal model delta sigma weight residual 121.54 128.78 -7.24 1.91e+00 2.74e-01 1.44e+01 angle pdb=" C TRP B 429 " pdb=" N ASN B 430 " pdb=" CA ASN B 430 " ideal model delta sigma weight residual 121.54 128.75 -7.21 1.91e+00 2.74e-01 1.42e+01 angle pdb=" N ILE B 115 " pdb=" CA ILE B 115 " pdb=" C ILE B 115 " ideal model delta sigma weight residual 112.29 109.17 3.12 9.40e-01 1.13e+00 1.10e+01 angle pdb=" N ILE A 115 " pdb=" CA ILE A 115 " pdb=" C ILE A 115 " ideal model delta sigma weight residual 112.29 109.21 3.08 9.40e-01 1.13e+00 1.08e+01 angle pdb=" N PHE B 155 " pdb=" CA PHE B 155 " pdb=" CB PHE B 155 " ideal model delta sigma weight residual 113.65 110.30 3.35 1.47e+00 4.63e-01 5.19e+00 ... (remaining 11315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.98: 4305 9.98 - 19.95: 307 19.95 - 29.93: 90 29.93 - 39.91: 41 39.91 - 49.88: 21 Dihedral angle restraints: 4764 sinusoidal: 1818 harmonic: 2946 Sorted by residual: dihedral pdb=" CA GLU A 51 " pdb=" CB GLU A 51 " pdb=" CG GLU A 51 " pdb=" CD GLU A 51 " ideal model delta sinusoidal sigma weight residual -60.00 -109.88 49.88 3 1.50e+01 4.44e-03 8.83e+00 dihedral pdb=" CA GLU B 51 " pdb=" CB GLU B 51 " pdb=" CG GLU B 51 " pdb=" CD GLU B 51 " ideal model delta sinusoidal sigma weight residual -60.00 -107.90 47.90 3 1.50e+01 4.44e-03 8.56e+00 dihedral pdb=" CA GLN A 19 " pdb=" CB GLN A 19 " pdb=" CG GLN A 19 " pdb=" CD GLN A 19 " ideal model delta sinusoidal sigma weight residual 60.00 106.95 -46.95 3 1.50e+01 4.44e-03 8.42e+00 ... (remaining 4761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 772 0.024 - 0.048: 307 0.048 - 0.072: 127 0.072 - 0.097: 45 0.097 - 0.121: 25 Chirality restraints: 1276 Sorted by residual: chirality pdb=" CA ILE B 97 " pdb=" N ILE B 97 " pdb=" C ILE B 97 " pdb=" CB ILE B 97 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.64e-01 chirality pdb=" CA ILE B 110 " pdb=" N ILE B 110 " pdb=" C ILE B 110 " pdb=" CB ILE B 110 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.44e-01 chirality pdb=" CA ILE A 97 " pdb=" N ILE A 97 " pdb=" C ILE A 97 " pdb=" CB ILE A 97 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.43e-01 ... (remaining 1273 not shown) Planarity restraints: 1402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 140 " -0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO A 141 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 141 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 141 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 140 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO B 141 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 141 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 141 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 139 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO A 140 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 140 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 140 " 0.017 5.00e-02 4.00e+02 ... (remaining 1399 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1848 2.79 - 3.32: 8135 3.32 - 3.84: 13236 3.84 - 4.37: 14142 4.37 - 4.90: 25290 Nonbonded interactions: 62651 Sorted by model distance: nonbonded pdb=" O PHE A 370 " pdb=" ND2 ASN A 374 " model vdw 2.259 3.120 nonbonded pdb=" O PHE B 370 " pdb=" ND2 ASN B 374 " model vdw 2.262 3.120 nonbonded pdb=" O TRP B 429 " pdb=" ND2 ASN B 430 " model vdw 2.270 3.120 nonbonded pdb=" O TRP A 429 " pdb=" ND2 ASN A 430 " model vdw 2.274 3.120 nonbonded pdb=" OE2 GLU A 312 " pdb=" OG SER A 357 " model vdw 2.279 3.040 ... (remaining 62646 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.690 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 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 : 0.002 0.024 8338 Z= 0.105 Angle : 0.446 7.244 11320 Z= 0.252 Chirality : 0.035 0.121 1276 Planarity : 0.003 0.033 1402 Dihedral : 9.092 49.883 2872 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.46 % Allowed : 6.15 % Favored : 93.39 % 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: 2.65 (0.28), residues: 1010 helix: 3.00 (0.19), residues: 696 sheet: 3.48 (0.82), residues: 24 loop : -1.76 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 429 HIS 0.002 0.000 HIS B 18 PHE 0.008 0.001 PHE A 278 TYR 0.004 0.001 TYR A 165 ARG 0.002 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 326 time to evaluate : 0.832 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: symmetry clash 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: symmetry clash REVERT: B 37 THR cc_start: 0.7926 (p) cc_final: 0.7450 (p) REVERT: A 180 ILE cc_start: 0.8279 (mt) cc_final: 0.7987 (mt) REVERT: A 378 CYS cc_start: 0.6785 (t) cc_final: 0.5598 (t) REVERT: A 420 ASN cc_start: 0.7178 (m-40) cc_final: 0.6910 (m-40) outliers start: 4 outliers final: 0 residues processed: 326 average time/residue: 0.1830 time to fit residues: 81.7346 Evaluate side-chains 212 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN A 432 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.086403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.069277 restraints weight = 35824.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.071009 restraints weight = 25003.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.072219 restraints weight = 19125.023| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8338 Z= 0.345 Angle : 0.771 11.949 11320 Z= 0.402 Chirality : 0.046 0.175 1276 Planarity : 0.004 0.027 1402 Dihedral : 3.850 16.375 1078 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.48 % Allowed : 17.29 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.27), residues: 1010 helix: 2.00 (0.19), residues: 700 sheet: 4.65 (0.85), residues: 24 loop : -2.11 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 474 HIS 0.005 0.001 HIS A 433 PHE 0.024 0.003 PHE A 201 TYR 0.024 0.002 TYR A 68 ARG 0.005 0.001 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 0.848 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LEU cc_start: 0.9709 (mt) cc_final: 0.9252 (tt) REVERT: B 28 ASN cc_start: 0.9741 (m110) cc_final: 0.9463 (m110) REVERT: B 211 MET cc_start: 0.9418 (tpp) cc_final: 0.9134 (tpp) REVERT: B 310 MET cc_start: 0.9250 (tpp) cc_final: 0.8745 (tmm) REVERT: B 332 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7141 (pp) REVERT: B 365 PHE cc_start: 0.9199 (m-80) cc_final: 0.8871 (m-80) REVERT: B 434 MET cc_start: 0.9350 (tpp) cc_final: 0.9077 (tpp) REVERT: B 452 ASP cc_start: 0.8689 (t0) cc_final: 0.8445 (t0) REVERT: B 483 MET cc_start: 0.9412 (tpp) cc_final: 0.9146 (tpp) REVERT: A 360 ARG cc_start: 0.8982 (ttm110) cc_final: 0.8699 (ttm110) REVERT: A 368 MET cc_start: 0.9141 (mtp) cc_final: 0.8936 (ptp) REVERT: A 373 GLU cc_start: 0.8869 (pt0) cc_final: 0.8610 (pt0) REVERT: A 374 ASN cc_start: 0.9481 (m-40) cc_final: 0.8947 (m110) REVERT: A 378 CYS cc_start: 0.9301 (t) cc_final: 0.8859 (m) REVERT: A 454 GLU cc_start: 0.6836 (pp20) cc_final: 0.6471 (tp30) outliers start: 30 outliers final: 22 residues processed: 225 average time/residue: 0.1789 time to fit residues: 56.7872 Evaluate side-chains 194 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 430 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 57 optimal weight: 30.0000 chunk 27 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 ASN B 430 ASN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.085391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.067941 restraints weight = 35981.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.069826 restraints weight = 24138.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.071112 restraints weight = 17913.687| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8338 Z= 0.205 Angle : 0.690 9.714 11320 Z= 0.350 Chirality : 0.044 0.257 1276 Planarity : 0.004 0.032 1402 Dihedral : 3.763 17.124 1078 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.20 % Allowed : 19.61 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.27), residues: 1010 helix: 1.70 (0.19), residues: 702 sheet: 4.77 (0.86), residues: 24 loop : -2.02 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 474 HIS 0.004 0.001 HIS A 18 PHE 0.029 0.002 PHE B 377 TYR 0.019 0.001 TYR A 68 ARG 0.002 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 211 time to evaluate : 0.859 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: symmetry clash revert: symmetry clash REVERT: B 24 LEU cc_start: 0.9691 (mt) cc_final: 0.9090 (tp) REVERT: B 28 ASN cc_start: 0.9707 (m110) cc_final: 0.9348 (m-40) REVERT: B 58 TYR cc_start: 0.9196 (m-10) cc_final: 0.8970 (m-10) REVERT: B 132 GLU cc_start: 0.8442 (pt0) cc_final: 0.8112 (pp20) REVERT: B 133 ILE cc_start: 0.9655 (mt) cc_final: 0.9098 (mp) REVERT: B 332 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7367 (pp) REVERT: B 452 ASP cc_start: 0.8751 (t0) cc_final: 0.8519 (t0) REVERT: B 483 MET cc_start: 0.9397 (tpp) cc_final: 0.9098 (tpp) REVERT: A 58 TYR cc_start: 0.8900 (m-10) cc_final: 0.8688 (m-10) REVERT: A 67 ARG cc_start: 0.9133 (tpt90) cc_final: 0.8593 (tmm160) REVERT: A 127 MET cc_start: 0.7243 (tpp) cc_final: 0.6957 (tpp) REVERT: A 148 TYR cc_start: 0.9102 (t80) cc_final: 0.8411 (t80) REVERT: A 321 TRP cc_start: 0.9180 (t60) cc_final: 0.8760 (t60) REVERT: A 373 GLU cc_start: 0.8671 (pt0) cc_final: 0.8288 (pt0) REVERT: A 374 ASN cc_start: 0.9428 (m-40) cc_final: 0.8859 (m110) REVERT: A 377 PHE cc_start: 0.9523 (m-80) cc_final: 0.9301 (m-10) REVERT: A 380 MET cc_start: 0.9410 (mtt) cc_final: 0.8890 (mtp) REVERT: A 420 ASN cc_start: 0.8719 (m-40) cc_final: 0.8496 (m-40) REVERT: A 446 PHE cc_start: 0.9092 (t80) cc_final: 0.8880 (t80) REVERT: A 454 GLU cc_start: 0.6962 (pp20) cc_final: 0.6706 (tp30) REVERT: A 483 MET cc_start: 0.9455 (tpp) cc_final: 0.9052 (tpp) outliers start: 19 outliers final: 11 residues processed: 222 average time/residue: 0.1557 time to fit residues: 49.8221 Evaluate side-chains 197 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 185 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 430 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 22 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 99 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 84 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS B 243 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.086725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.068741 restraints weight = 35478.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.070493 restraints weight = 24613.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.071800 restraints weight = 18845.970| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8338 Z= 0.192 Angle : 0.709 11.819 11320 Z= 0.352 Chirality : 0.044 0.234 1276 Planarity : 0.004 0.034 1402 Dihedral : 3.767 16.599 1078 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.44 % Allowed : 19.03 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.27), residues: 1010 helix: 1.65 (0.19), residues: 702 sheet: 4.84 (0.86), residues: 24 loop : -1.94 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 39 HIS 0.003 0.001 HIS A 18 PHE 0.025 0.002 PHE A 266 TYR 0.011 0.001 TYR A 68 ARG 0.004 0.000 ARG B 451 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 209 time to evaluate : 0.874 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: B 24 LEU cc_start: 0.9676 (mt) cc_final: 0.9183 (tp) REVERT: B 28 ASN cc_start: 0.9680 (m110) cc_final: 0.9416 (m-40) REVERT: B 58 TYR cc_start: 0.9153 (m-10) cc_final: 0.8925 (m-10) REVERT: B 64 LEU cc_start: 0.9615 (tp) cc_final: 0.9399 (pp) REVERT: B 127 MET cc_start: 0.6818 (tpp) cc_final: 0.6229 (tpp) REVERT: B 132 GLU cc_start: 0.8174 (pt0) cc_final: 0.7821 (pp20) REVERT: B 310 MET cc_start: 0.9071 (tpp) cc_final: 0.8790 (tmm) REVERT: B 332 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7630 (pp) REVERT: B 452 ASP cc_start: 0.8676 (t0) cc_final: 0.8430 (t0) REVERT: B 483 MET cc_start: 0.9419 (tpp) cc_final: 0.9064 (tpp) REVERT: A 67 ARG cc_start: 0.9133 (tpt90) cc_final: 0.8703 (ttp80) REVERT: A 127 MET cc_start: 0.7251 (tpp) cc_final: 0.6966 (tpp) REVERT: A 199 PHE cc_start: 0.7314 (m-80) cc_final: 0.7037 (m-80) REVERT: A 310 MET cc_start: 0.8922 (tpp) cc_final: 0.8615 (tmm) REVERT: A 373 GLU cc_start: 0.8598 (pt0) cc_final: 0.8304 (pt0) REVERT: A 374 ASN cc_start: 0.9382 (m-40) cc_final: 0.9022 (m110) REVERT: A 380 MET cc_start: 0.9482 (mtt) cc_final: 0.9067 (mtp) REVERT: A 390 HIS cc_start: 0.7288 (t-90) cc_final: 0.7038 (t-90) REVERT: A 420 ASN cc_start: 0.8650 (m-40) cc_final: 0.8421 (m-40) REVERT: A 483 MET cc_start: 0.9437 (tpp) cc_final: 0.9032 (tpp) outliers start: 21 outliers final: 12 residues processed: 221 average time/residue: 0.1534 time to fit residues: 48.8490 Evaluate side-chains 201 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 430 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 86 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 HIS ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.082099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.065564 restraints weight = 36601.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.067301 restraints weight = 24641.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.068650 restraints weight = 18503.909| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8338 Z= 0.260 Angle : 0.738 9.294 11320 Z= 0.375 Chirality : 0.046 0.232 1276 Planarity : 0.004 0.033 1402 Dihedral : 3.956 17.089 1078 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.13 % Allowed : 20.53 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.27), residues: 1010 helix: 1.48 (0.19), residues: 702 sheet: 4.68 (0.87), residues: 24 loop : -1.95 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 39 HIS 0.003 0.001 HIS A 433 PHE 0.019 0.002 PHE B 365 TYR 0.011 0.001 TYR A 58 ARG 0.003 0.001 ARG B 441 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 203 time to evaluate : 0.864 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: symmetry clash REVERT: B 24 LEU cc_start: 0.9681 (mt) cc_final: 0.9156 (tp) REVERT: B 28 ASN cc_start: 0.9680 (m110) cc_final: 0.9340 (m110) REVERT: B 64 LEU cc_start: 0.9598 (tp) cc_final: 0.9366 (pp) REVERT: B 127 MET cc_start: 0.7086 (tpp) cc_final: 0.6591 (tpp) REVERT: B 132 GLU cc_start: 0.8347 (pt0) cc_final: 0.7864 (pp20) REVERT: B 133 ILE cc_start: 0.9675 (mt) cc_final: 0.9306 (mp) REVERT: B 452 ASP cc_start: 0.8831 (t0) cc_final: 0.8487 (t0) REVERT: B 483 MET cc_start: 0.9410 (tpp) cc_final: 0.9107 (tpp) REVERT: A 58 TYR cc_start: 0.8801 (m-10) cc_final: 0.8599 (m-10) REVERT: A 67 ARG cc_start: 0.9165 (tpt90) cc_final: 0.8712 (tpt90) REVERT: A 127 MET cc_start: 0.7460 (tpp) cc_final: 0.7106 (tpp) REVERT: A 310 MET cc_start: 0.8836 (tpp) cc_final: 0.8579 (tmm) REVERT: A 321 TRP cc_start: 0.9179 (t60) cc_final: 0.8550 (t60) REVERT: A 374 ASN cc_start: 0.9446 (m-40) cc_final: 0.8990 (m110) REVERT: A 380 MET cc_start: 0.9522 (mtt) cc_final: 0.9118 (mtp) REVERT: A 420 ASN cc_start: 0.8719 (m-40) cc_final: 0.8518 (m-40) REVERT: A 446 PHE cc_start: 0.9178 (t80) cc_final: 0.8920 (t80) REVERT: A 458 LYS cc_start: 0.9235 (tptm) cc_final: 0.9024 (tptm) outliers start: 27 outliers final: 19 residues processed: 219 average time/residue: 0.1659 time to fit residues: 51.8462 Evaluate side-chains 209 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 430 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 31 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 12 optimal weight: 0.0970 chunk 14 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.084078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.066508 restraints weight = 35682.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.068248 restraints weight = 24603.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.069536 restraints weight = 18712.290| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.5876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8338 Z= 0.197 Angle : 0.763 9.950 11320 Z= 0.378 Chirality : 0.046 0.211 1276 Planarity : 0.004 0.052 1402 Dihedral : 3.928 16.236 1078 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.44 % Allowed : 22.74 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.27), residues: 1010 helix: 1.41 (0.19), residues: 702 sheet: 4.77 (0.87), residues: 24 loop : -1.96 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 39 HIS 0.005 0.001 HIS A 50 PHE 0.020 0.002 PHE A 144 TYR 0.011 0.001 TYR A 58 ARG 0.003 0.000 ARG B 441 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 207 time to evaluate : 0.861 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LEU cc_start: 0.9680 (mt) cc_final: 0.9227 (tp) REVERT: B 28 ASN cc_start: 0.9662 (m110) cc_final: 0.9401 (m110) REVERT: B 29 PHE cc_start: 0.7819 (OUTLIER) cc_final: 0.7303 (t80) REVERT: B 41 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.8093 (t80) REVERT: B 58 TYR cc_start: 0.9077 (m-10) cc_final: 0.8859 (m-10) REVERT: B 64 LEU cc_start: 0.9606 (tp) cc_final: 0.9364 (pp) REVERT: B 390 HIS cc_start: 0.7555 (t-90) cc_final: 0.7310 (t-90) REVERT: B 452 ASP cc_start: 0.8790 (t0) cc_final: 0.8447 (t0) REVERT: B 483 MET cc_start: 0.9392 (tpp) cc_final: 0.9025 (tpp) REVERT: A 41 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.8202 (t80) REVERT: A 67 ARG cc_start: 0.9155 (tpt90) cc_final: 0.8667 (tpt90) REVERT: A 127 MET cc_start: 0.7397 (tpp) cc_final: 0.7165 (tpp) REVERT: A 310 MET cc_start: 0.8750 (tpp) cc_final: 0.8491 (tmm) REVERT: A 374 ASN cc_start: 0.9338 (m-40) cc_final: 0.8856 (m110) REVERT: A 380 MET cc_start: 0.9479 (mtt) cc_final: 0.9196 (mtp) REVERT: A 432 GLN cc_start: 0.9163 (mt0) cc_final: 0.8821 (mp10) REVERT: A 483 MET cc_start: 0.9368 (mmm) cc_final: 0.9067 (mmp) outliers start: 21 outliers final: 13 residues processed: 218 average time/residue: 0.1667 time to fit residues: 51.9088 Evaluate side-chains 207 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 430 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 51 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 28 ASN A 243 ASN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.084631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.067157 restraints weight = 35568.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.068923 restraints weight = 24494.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.070125 restraints weight = 18629.196| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.6014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8338 Z= 0.188 Angle : 0.782 9.212 11320 Z= 0.382 Chirality : 0.047 0.207 1276 Planarity : 0.004 0.036 1402 Dihedral : 3.934 15.581 1078 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.55 % Allowed : 23.32 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1010 helix: 1.27 (0.19), residues: 704 sheet: 4.75 (0.87), residues: 24 loop : -1.96 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 39 HIS 0.005 0.001 HIS A 50 PHE 0.025 0.001 PHE B 370 TYR 0.013 0.001 TYR A 58 ARG 0.004 0.000 ARG B 451 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.942 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LEU cc_start: 0.9662 (mt) cc_final: 0.9119 (tp) REVERT: B 28 ASN cc_start: 0.9650 (m110) cc_final: 0.9275 (m110) REVERT: B 29 PHE cc_start: 0.7791 (OUTLIER) cc_final: 0.7303 (t80) REVERT: B 41 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.8153 (t80) REVERT: B 64 LEU cc_start: 0.9613 (tp) cc_final: 0.9366 (pp) REVERT: B 378 CYS cc_start: 0.8915 (m) cc_final: 0.8714 (m) REVERT: B 390 HIS cc_start: 0.7608 (t-90) cc_final: 0.7305 (t-90) REVERT: B 452 ASP cc_start: 0.8725 (t0) cc_final: 0.8367 (t0) REVERT: A 41 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.8160 (t80) REVERT: A 58 TYR cc_start: 0.9093 (m-10) cc_final: 0.8725 (m-10) REVERT: A 62 MET cc_start: 0.9484 (mmp) cc_final: 0.9033 (tpt) REVERT: A 67 ARG cc_start: 0.9164 (tpt90) cc_final: 0.8649 (tpt90) REVERT: A 127 MET cc_start: 0.7420 (tpp) cc_final: 0.7016 (tpp) REVERT: A 194 LEU cc_start: 0.5557 (OUTLIER) cc_final: 0.4265 (pt) REVERT: A 211 MET cc_start: 0.9321 (tpp) cc_final: 0.9110 (tpp) REVERT: A 310 MET cc_start: 0.8689 (tpp) cc_final: 0.8450 (tmm) REVERT: A 321 TRP cc_start: 0.9064 (t60) cc_final: 0.8496 (t60) REVERT: A 374 ASN cc_start: 0.9312 (m-40) cc_final: 0.8849 (m110) REVERT: A 380 MET cc_start: 0.9476 (mtt) cc_final: 0.9200 (mtp) REVERT: A 405 PHE cc_start: 0.9069 (m-10) cc_final: 0.8868 (m-10) REVERT: A 483 MET cc_start: 0.9473 (mmm) cc_final: 0.9132 (mmp) outliers start: 22 outliers final: 15 residues processed: 218 average time/residue: 0.1767 time to fit residues: 54.5611 Evaluate side-chains 213 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 194 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 430 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 44 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.080114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.064169 restraints weight = 37696.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.065887 restraints weight = 25112.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.067207 restraints weight = 18667.964| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.6659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8338 Z= 0.289 Angle : 0.855 11.793 11320 Z= 0.429 Chirality : 0.050 0.277 1276 Planarity : 0.005 0.059 1402 Dihedral : 4.177 17.200 1078 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.67 % Allowed : 25.06 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.26), residues: 1010 helix: 1.01 (0.19), residues: 704 sheet: 4.51 (0.88), residues: 24 loop : -2.05 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 39 HIS 0.003 0.001 HIS A 224 PHE 0.029 0.002 PHE A 223 TYR 0.015 0.002 TYR B 58 ARG 0.003 0.001 ARG A 423 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 0.882 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LEU cc_start: 0.9661 (mt) cc_final: 0.9178 (tp) REVERT: B 28 ASN cc_start: 0.9658 (m110) cc_final: 0.9381 (m110) REVERT: B 29 PHE cc_start: 0.7686 (OUTLIER) cc_final: 0.7173 (t80) REVERT: B 41 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.8127 (t80) REVERT: B 64 LEU cc_start: 0.9606 (tp) cc_final: 0.9361 (pp) REVERT: B 188 MET cc_start: 0.8493 (tmm) cc_final: 0.8264 (tmm) REVERT: B 220 LEU cc_start: 0.9587 (pp) cc_final: 0.9337 (mp) REVERT: B 312 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7645 (mp0) REVERT: B 321 TRP cc_start: 0.8996 (t-100) cc_final: 0.8711 (t-100) REVERT: B 378 CYS cc_start: 0.9061 (m) cc_final: 0.8834 (m) REVERT: B 380 MET cc_start: 0.9371 (mtm) cc_final: 0.8906 (mtp) REVERT: B 390 HIS cc_start: 0.7768 (t-90) cc_final: 0.7472 (t-90) REVERT: B 451 ARG cc_start: 0.9444 (tpp-160) cc_final: 0.9016 (mtt-85) REVERT: B 452 ASP cc_start: 0.8798 (t0) cc_final: 0.8429 (t0) REVERT: B 458 LYS cc_start: 0.9616 (mmtm) cc_final: 0.9395 (mmmm) REVERT: A 41 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.8169 (t80) REVERT: A 58 TYR cc_start: 0.9140 (m-10) cc_final: 0.8719 (m-10) REVERT: A 62 MET cc_start: 0.9484 (mmp) cc_final: 0.9030 (tpt) REVERT: A 67 ARG cc_start: 0.9232 (tpt90) cc_final: 0.8735 (tpt90) REVERT: A 127 MET cc_start: 0.7737 (tpp) cc_final: 0.7390 (tpp) REVERT: A 310 MET cc_start: 0.8689 (tpp) cc_final: 0.8470 (tmm) REVERT: A 354 SER cc_start: 0.9025 (OUTLIER) cc_final: 0.8702 (p) REVERT: A 374 ASN cc_start: 0.9399 (m-40) cc_final: 0.8929 (m110) REVERT: A 380 MET cc_start: 0.9497 (mtt) cc_final: 0.9258 (mtt) REVERT: A 483 MET cc_start: 0.9530 (mmm) cc_final: 0.9139 (mmp) outliers start: 23 outliers final: 18 residues processed: 209 average time/residue: 0.1596 time to fit residues: 47.7418 Evaluate side-chains 210 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 430 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 41 optimal weight: 0.0870 chunk 46 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 overall best weight: 1.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 ASN ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.081647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.065061 restraints weight = 37171.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.066870 restraints weight = 24717.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.068107 restraints weight = 18293.948| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.6723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8338 Z= 0.219 Angle : 0.872 13.325 11320 Z= 0.425 Chirality : 0.050 0.278 1276 Planarity : 0.004 0.058 1402 Dihedral : 4.120 16.632 1078 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.32 % Allowed : 24.94 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.26), residues: 1010 helix: 0.99 (0.19), residues: 702 sheet: 4.47 (0.87), residues: 24 loop : -2.05 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 39 HIS 0.004 0.001 HIS B 347 PHE 0.026 0.002 PHE A 223 TYR 0.012 0.001 TYR B 58 ARG 0.002 0.000 ARG B 441 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 199 time to evaluate : 0.911 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LEU cc_start: 0.9645 (mt) cc_final: 0.9169 (tp) REVERT: B 28 ASN cc_start: 0.9666 (m110) cc_final: 0.9377 (m110) REVERT: B 29 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.7087 (t80) REVERT: B 39 TRP cc_start: 0.8549 (t60) cc_final: 0.8312 (t60) REVERT: B 41 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.8158 (t80) REVERT: B 64 LEU cc_start: 0.9629 (tp) cc_final: 0.9374 (pp) REVERT: B 220 LEU cc_start: 0.9578 (pp) cc_final: 0.9329 (mp) REVERT: B 312 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7579 (mp0) REVERT: B 321 TRP cc_start: 0.8940 (t-100) cc_final: 0.8625 (t-100) REVERT: B 364 LEU cc_start: 0.9767 (tp) cc_final: 0.9363 (tp) REVERT: B 390 HIS cc_start: 0.7644 (t-90) cc_final: 0.7405 (t-90) REVERT: B 451 ARG cc_start: 0.9485 (tpp-160) cc_final: 0.9068 (mtt-85) REVERT: B 452 ASP cc_start: 0.8809 (t0) cc_final: 0.8413 (t0) REVERT: A 41 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.8179 (t80) REVERT: A 58 TYR cc_start: 0.9121 (m-10) cc_final: 0.8709 (m-10) REVERT: A 62 MET cc_start: 0.9513 (mmp) cc_final: 0.8970 (tpt) REVERT: A 67 ARG cc_start: 0.9222 (tpt90) cc_final: 0.8710 (tpt90) REVERT: A 127 MET cc_start: 0.7714 (tpp) cc_final: 0.7364 (tpp) REVERT: A 312 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7601 (mp0) REVERT: A 354 SER cc_start: 0.9005 (OUTLIER) cc_final: 0.8797 (p) REVERT: A 374 ASN cc_start: 0.9348 (m-40) cc_final: 0.8894 (m110) REVERT: A 380 MET cc_start: 0.9470 (mtt) cc_final: 0.9181 (mtp) REVERT: A 460 MET cc_start: 0.8580 (ptp) cc_final: 0.8369 (ptp) REVERT: A 483 MET cc_start: 0.9552 (mmm) cc_final: 0.9138 (mmp) outliers start: 20 outliers final: 14 residues processed: 212 average time/residue: 0.1678 time to fit residues: 50.6340 Evaluate side-chains 212 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 430 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 55 optimal weight: 20.0000 chunk 83 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 52 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 74 optimal weight: 0.0070 chunk 84 optimal weight: 6.9990 overall best weight: 1.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 ASN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.082455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.065646 restraints weight = 35951.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.067420 restraints weight = 24411.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.068633 restraints weight = 18291.005| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.6865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8338 Z= 0.215 Angle : 0.908 15.107 11320 Z= 0.443 Chirality : 0.052 0.296 1276 Planarity : 0.004 0.058 1402 Dihedral : 4.163 16.326 1078 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.09 % Allowed : 25.29 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.26), residues: 1010 helix: 0.88 (0.19), residues: 702 sheet: 4.52 (0.87), residues: 24 loop : -2.03 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 39 HIS 0.004 0.001 HIS B 347 PHE 0.029 0.002 PHE A 199 TYR 0.015 0.001 TYR B 348 ARG 0.002 0.000 ARG B 441 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 0.928 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: symmetry clash revert: symmetry clash REVERT: B 24 LEU cc_start: 0.9635 (mt) cc_final: 0.9135 (tp) REVERT: B 28 ASN cc_start: 0.9628 (m110) cc_final: 0.9313 (m110) REVERT: B 29 PHE cc_start: 0.7711 (OUTLIER) cc_final: 0.7168 (t80) REVERT: B 39 TRP cc_start: 0.8481 (t60) cc_final: 0.8058 (t60) REVERT: B 41 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.8156 (t80) REVERT: B 64 LEU cc_start: 0.9634 (tp) cc_final: 0.9366 (pp) REVERT: B 220 LEU cc_start: 0.9557 (pp) cc_final: 0.9279 (mp) REVERT: B 390 HIS cc_start: 0.7593 (t-90) cc_final: 0.7307 (t-90) REVERT: B 452 ASP cc_start: 0.8810 (t0) cc_final: 0.8514 (t0) REVERT: B 458 LYS cc_start: 0.9591 (mmtm) cc_final: 0.9387 (mmmm) REVERT: A 41 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.8170 (t80) REVERT: A 56 MET cc_start: 0.9079 (mmp) cc_final: 0.8162 (mmp) REVERT: A 58 TYR cc_start: 0.9070 (m-10) cc_final: 0.8657 (m-10) REVERT: A 62 MET cc_start: 0.9478 (mmp) cc_final: 0.8936 (tpt) REVERT: A 67 ARG cc_start: 0.9199 (tpt90) cc_final: 0.8694 (tpt90) REVERT: A 127 MET cc_start: 0.7699 (tpp) cc_final: 0.7338 (tpp) REVERT: A 312 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7542 (mp0) REVERT: A 351 ASN cc_start: 0.9334 (OUTLIER) cc_final: 0.8826 (p0) REVERT: A 354 SER cc_start: 0.8968 (OUTLIER) cc_final: 0.8759 (p) REVERT: A 374 ASN cc_start: 0.9373 (m-40) cc_final: 0.9009 (m110) REVERT: A 451 ARG cc_start: 0.9395 (tpp-160) cc_final: 0.9180 (mmt-90) REVERT: A 483 MET cc_start: 0.9556 (mmm) cc_final: 0.9196 (mmp) outliers start: 18 outliers final: 11 residues processed: 214 average time/residue: 0.1662 time to fit residues: 50.5665 Evaluate side-chains 210 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 194 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 430 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 13 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 84 optimal weight: 0.0270 overall best weight: 1.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 ASN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.083590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.066870 restraints weight = 36075.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.068711 restraints weight = 24401.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.070170 restraints weight = 18184.892| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.6972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8338 Z= 0.209 Angle : 0.912 13.644 11320 Z= 0.446 Chirality : 0.051 0.305 1276 Planarity : 0.005 0.058 1402 Dihedral : 4.146 15.812 1078 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.20 % Allowed : 25.52 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.26), residues: 1010 helix: 0.89 (0.19), residues: 702 sheet: 4.59 (0.88), residues: 24 loop : -2.02 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 39 HIS 0.004 0.001 HIS A 50 PHE 0.033 0.002 PHE B 144 TYR 0.017 0.001 TYR A 379 ARG 0.002 0.000 ARG B 441 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2713.41 seconds wall clock time: 47 minutes 51.09 seconds (2871.09 seconds total)