Starting phenix.real_space_refine on Wed Feb 12 15:59:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pxb_18002/02_2025/8pxb_18002.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pxb_18002/02_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_18002/02_2025/8pxb_18002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pxb_18002/02_2025/8pxb_18002.map" model { file = "/net/cci-nas-00/data/ceres_data/8pxb_18002/02_2025/8pxb_18002.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pxb_18002/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.76, per 1000 atoms: 0.59 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: 2.05 Conformation dependent library (CDL) restraints added in 1.2 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: 0.64 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: 2.07 Time building geometry restraints manager: 2.36 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: 0.07 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: 0.780 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: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.550 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.920 ------------------------------------------------------------------------------- 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 : 0.862 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: 0.1929 time to fit residues: 85.5138 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 : 0.953 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.085163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.067864 restraints weight = 35896.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.069606 restraints weight = 25084.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.070964 restraints weight = 19204.040| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 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 : 0.961 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: 0.9710 (mt) cc_final: 0.9251 (tt) REVERT: B 28 ASN cc_start: 0.9739 (m110) cc_final: 0.9461 (m110) REVERT: B 211 MET cc_start: 0.9425 (tpp) cc_final: 0.9139 (tpp) REVERT: B 310 MET cc_start: 0.9251 (tpp) cc_final: 0.8745 (tmm) REVERT: B 332 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7140 (pp) REVERT: B 365 PHE cc_start: 0.9187 (m-80) cc_final: 0.8861 (m-80) REVERT: B 434 MET cc_start: 0.9350 (tpp) cc_final: 0.9077 (tpp) REVERT: B 452 ASP cc_start: 0.8664 (t0) cc_final: 0.8420 (t0) REVERT: B 483 MET cc_start: 0.9405 (tpp) cc_final: 0.9140 (tpp) REVERT: A 360 ARG cc_start: 0.8974 (ttm110) cc_final: 0.8690 (ttm110) REVERT: A 368 MET cc_start: 0.9139 (mtp) cc_final: 0.8933 (ptp) REVERT: A 373 GLU cc_start: 0.8854 (pt0) cc_final: 0.8594 (pt0) REVERT: A 374 ASN cc_start: 0.9479 (m-40) cc_final: 0.8948 (m110) REVERT: A 378 CYS cc_start: 0.9295 (t) cc_final: 0.8858 (m) REVERT: A 454 GLU cc_start: 0.6834 (pp20) cc_final: 0.6476 (tp30) outliers start: 30 outliers final: 22 residues processed: 225 average time/residue: 0.1833 time to fit residues: 57.6438 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 : 0.884 ------------------------------------------------------------------------------- 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: 2.9990 chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.085283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.067849 restraints weight = 36032.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.069733 restraints weight = 24159.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.071155 restraints weight = 17958.919| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4803 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= 0.210 Angle : 0.696 9.731 11320 Z= 0.353 Chirality : 0.045 0.263 1276 Planarity : 0.004 0.032 1402 Dihedral : 3.772 17.259 1078 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.44 % Allowed : 19.37 % 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: 1.20 (0.27), residues: 1010 helix: 1.72 (0.19), residues: 702 sheet: 4.79 (0.86), residues: 24 loop : -2.04 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 474 HIS 0.004 0.001 HIS A 18 PHE 0.028 0.002 PHE B 377 TYR 0.019 0.001 TYR A 68 ARG 0.002 0.000 ARG B 67 *********************** 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 231 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 210 time to evaluate : 0.887 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: 0.9681 (mt) cc_final: 0.9108 (tp) REVERT: B 28 ASN cc_start: 0.9708 (m110) cc_final: 0.9357 (m-40) REVERT: B 58 TYR cc_start: 0.9178 (m-10) cc_final: 0.8907 (m-10) REVERT: B 132 GLU cc_start: 0.8407 (pt0) cc_final: 0.8096 (pp20) REVERT: B 133 ILE cc_start: 0.9652 (mt) cc_final: 0.9099 (mp) REVERT: B 332 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7368 (pp) REVERT: B 452 ASP cc_start: 0.8736 (t0) cc_final: 0.8501 (t0) REVERT: B 483 MET cc_start: 0.9394 (tpp) cc_final: 0.9091 (tpp) REVERT: A 58 TYR cc_start: 0.8909 (m-10) cc_final: 0.8701 (m-10) REVERT: A 67 ARG cc_start: 0.9141 (tpt90) cc_final: 0.8608 (tmm160) REVERT: A 127 MET cc_start: 0.7295 (tpp) cc_final: 0.7010 (tpp) REVERT: A 148 TYR cc_start: 0.9115 (t80) cc_final: 0.8424 (t80) REVERT: A 321 TRP cc_start: 0.9185 (t60) cc_final: 0.8766 (t60) REVERT: A 373 GLU cc_start: 0.8681 (pt0) cc_final: 0.8461 (pt0) REVERT: A 374 ASN cc_start: 0.9432 (m-40) cc_final: 0.8881 (m110) REVERT: A 380 MET cc_start: 0.9414 (mtt) cc_final: 0.8948 (mtp) REVERT: A 420 ASN cc_start: 0.8727 (m-40) cc_final: 0.8507 (m-40) REVERT: A 446 PHE cc_start: 0.9105 (t80) cc_final: 0.8882 (t80) REVERT: A 454 GLU cc_start: 0.6953 (pp20) cc_final: 0.6697 (tp30) REVERT: A 483 MET cc_start: 0.9449 (tpp) cc_final: 0.9045 (tpp) outliers start: 21 outliers final: 13 residues processed: 221 average time/residue: 0.1626 time to fit residues: 51.5582 Evaluate side-chains 198 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 184 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 203 ASP 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: 0.9980 chunk 97 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS ** 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 = 0.3959 r_free = 0.3959 target = 0.086120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.068416 restraints weight = 35575.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.070151 restraints weight = 24673.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.071475 restraints weight = 18845.083| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.5095 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= 0.197 Angle : 0.708 11.729 11320 Z= 0.353 Chirality : 0.044 0.238 1276 Planarity : 0.004 0.034 1402 Dihedral : 3.770 16.990 1078 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.32 % Allowed : 18.79 % Favored : 78.89 % 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: 1.66 (0.19), residues: 702 sheet: 4.82 (0.86), residues: 24 loop : -1.96 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 228 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 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: B 24 LEU cc_start: 0.9673 (mt) cc_final: 0.9176 (tp) REVERT: B 28 ASN cc_start: 0.9683 (m110) cc_final: 0.9420 (m-40) REVERT: B 64 LEU cc_start: 0.9612 (tp) cc_final: 0.9390 (pp) REVERT: B 127 MET cc_start: 0.6839 (tpp) cc_final: 0.6243 (tpp) REVERT: B 132 GLU cc_start: 0.8179 (pt0) cc_final: 0.7817 (pp20) REVERT: B 310 MET cc_start: 0.9071 (tpp) cc_final: 0.8791 (tmm) REVERT: B 332 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7547 (pp) REVERT: B 377 PHE cc_start: 0.9418 (m-80) cc_final: 0.9169 (m-10) REVERT: B 378 CYS cc_start: 0.9056 (m) cc_final: 0.8822 (m) REVERT: B 452 ASP cc_start: 0.8660 (t0) cc_final: 0.8420 (t0) REVERT: B 483 MET cc_start: 0.9415 (tpp) cc_final: 0.9085 (tpp) REVERT: A 67 ARG cc_start: 0.9131 (tpt90) cc_final: 0.8690 (ttp80) REVERT: A 127 MET cc_start: 0.7304 (tpp) cc_final: 0.7032 (tpp) REVERT: A 199 PHE cc_start: 0.7362 (m-80) cc_final: 0.7086 (m-80) REVERT: A 310 MET cc_start: 0.8931 (tpp) cc_final: 0.8622 (tmm) REVERT: A 373 GLU cc_start: 0.8615 (pt0) cc_final: 0.8321 (pt0) REVERT: A 374 ASN cc_start: 0.9387 (m-40) cc_final: 0.9033 (m110) REVERT: A 380 MET cc_start: 0.9483 (mtt) cc_final: 0.9013 (mtp) REVERT: A 390 HIS cc_start: 0.7378 (t-90) cc_final: 0.7101 (t-90) REVERT: A 420 ASN cc_start: 0.8660 (m-40) cc_final: 0.8433 (m-40) REVERT: A 483 MET cc_start: 0.9435 (tpp) cc_final: 0.8973 (tpp) outliers start: 20 outliers final: 11 residues processed: 219 average time/residue: 0.1749 time to fit residues: 54.7498 Evaluate side-chains 200 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 188 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 65 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3942 r_free = 0.3942 target = 0.084232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.066981 restraints weight = 35636.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.068678 restraints weight = 24559.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.069872 restraints weight = 18690.230| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.5481 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= 0.200 Angle : 0.717 8.724 11320 Z= 0.358 Chirality : 0.045 0.214 1276 Planarity : 0.003 0.034 1402 Dihedral : 3.857 16.141 1078 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.02 % Allowed : 20.19 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.27), residues: 1010 helix: 1.60 (0.19), residues: 702 sheet: 4.83 (0.87), residues: 24 loop : -1.91 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 39 HIS 0.003 0.001 HIS A 18 PHE 0.019 0.002 PHE A 266 TYR 0.013 0.001 TYR A 58 ARG 0.003 0.000 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 235 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 0.921 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: 0.9676 (mt) cc_final: 0.9140 (tp) REVERT: B 28 ASN cc_start: 0.9675 (m110) cc_final: 0.9320 (m110) REVERT: B 29 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.7330 (t80) REVERT: B 58 TYR cc_start: 0.9023 (m-10) cc_final: 0.8789 (m-10) REVERT: B 64 LEU cc_start: 0.9605 (tp) cc_final: 0.9368 (pp) REVERT: B 127 MET cc_start: 0.6907 (tpp) cc_final: 0.6357 (tpp) REVERT: B 132 GLU cc_start: 0.8135 (pt0) cc_final: 0.7699 (pp20) REVERT: B 133 ILE cc_start: 0.9647 (mt) cc_final: 0.9207 (mp) REVERT: B 332 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7533 (pp) REVERT: B 365 PHE cc_start: 0.9137 (m-80) cc_final: 0.8924 (m-80) REVERT: B 377 PHE cc_start: 0.9510 (m-80) cc_final: 0.9292 (m-80) REVERT: B 378 CYS cc_start: 0.8966 (m) cc_final: 0.8754 (m) REVERT: B 452 ASP cc_start: 0.8823 (t0) cc_final: 0.8473 (t0) REVERT: B 483 MET cc_start: 0.9424 (tpp) cc_final: 0.8992 (tpp) REVERT: A 67 ARG cc_start: 0.9144 (tpt90) cc_final: 0.8683 (tpt90) REVERT: A 127 MET cc_start: 0.7333 (tpp) cc_final: 0.7099 (tpp) REVERT: A 199 PHE cc_start: 0.7446 (m-80) cc_final: 0.7141 (m-80) REVERT: A 310 MET cc_start: 0.8863 (tpp) cc_final: 0.8583 (tmm) REVERT: A 321 TRP cc_start: 0.9133 (t60) cc_final: 0.8576 (t60) REVERT: A 374 ASN cc_start: 0.9424 (m-40) cc_final: 0.8926 (m110) REVERT: A 380 MET cc_start: 0.9493 (mtt) cc_final: 0.9069 (mtp) REVERT: A 390 HIS cc_start: 0.7289 (t-90) cc_final: 0.6969 (t-90) REVERT: A 420 ASN cc_start: 0.8689 (m-40) cc_final: 0.8482 (m-40) REVERT: A 446 PHE cc_start: 0.9200 (t80) cc_final: 0.8921 (t80) outliers start: 26 outliers final: 16 residues processed: 224 average time/residue: 0.1704 time to fit residues: 53.9592 Evaluate side-chains 211 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 193 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE 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 332 LEU 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 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 351 ASN 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: 0.6980 chunk 26 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 48 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.085109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.067467 restraints weight = 35009.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.069231 restraints weight = 24302.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.070601 restraints weight = 18530.457| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.5664 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= 0.187 Angle : 0.753 10.138 11320 Z= 0.370 Chirality : 0.045 0.192 1276 Planarity : 0.004 0.050 1402 Dihedral : 3.848 15.565 1078 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.55 % Allowed : 22.85 % Favored : 74.59 % 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: 0.95 (0.27), residues: 1010 helix: 1.45 (0.19), residues: 702 sheet: 4.94 (0.87), residues: 24 loop : -1.91 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 39 HIS 0.003 0.001 HIS A 18 PHE 0.032 0.002 PHE A 405 TYR 0.020 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 225 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 203 time to evaluate : 1.037 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: 0.9667 (mt) cc_final: 0.9132 (tp) REVERT: B 28 ASN cc_start: 0.9657 (m110) cc_final: 0.9285 (m110) REVERT: B 29 PHE cc_start: 0.7751 (OUTLIER) cc_final: 0.7219 (t80) REVERT: B 64 LEU cc_start: 0.9617 (tp) cc_final: 0.9372 (pp) REVERT: B 181 MET cc_start: 0.8862 (tmm) cc_final: 0.8358 (ppp) REVERT: B 332 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7648 (pp) REVERT: B 373 GLU cc_start: 0.8197 (pp20) cc_final: 0.7971 (pp20) REVERT: B 390 HIS cc_start: 0.7570 (t-90) cc_final: 0.7293 (t-90) REVERT: B 405 PHE cc_start: 0.9105 (m-10) cc_final: 0.8898 (m-10) REVERT: B 452 ASP cc_start: 0.8747 (t0) cc_final: 0.8370 (t0) REVERT: B 483 MET cc_start: 0.9395 (tpp) cc_final: 0.9009 (tpp) REVERT: A 41 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.8162 (t80) REVERT: A 67 ARG cc_start: 0.9138 (tpt90) cc_final: 0.8649 (tpt90) REVERT: A 127 MET cc_start: 0.7318 (tpp) cc_final: 0.7095 (tpp) REVERT: A 199 PHE cc_start: 0.7431 (m-80) cc_final: 0.7118 (m-80) REVERT: A 310 MET cc_start: 0.8748 (tpp) cc_final: 0.8511 (tmm) REVERT: A 321 TRP cc_start: 0.9072 (t60) cc_final: 0.8522 (t60) REVERT: A 374 ASN cc_start: 0.9334 (m-40) cc_final: 0.8878 (m110) REVERT: A 380 MET cc_start: 0.9487 (mtt) cc_final: 0.9200 (mtp) REVERT: A 390 HIS cc_start: 0.7207 (t-90) cc_final: 0.6860 (t-90) REVERT: A 420 ASN cc_start: 0.8657 (m-40) cc_final: 0.8441 (m-40) REVERT: A 483 MET cc_start: 0.9345 (mmm) cc_final: 0.9015 (mmp) outliers start: 22 outliers final: 16 residues processed: 217 average time/residue: 0.1726 time to fit residues: 52.9466 Evaluate side-chains 211 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 192 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 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 332 LEU 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 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 354 SER 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: 6.9990 chunk 32 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 243 ASN ** 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 = 0.3959 r_free = 0.3959 target = 0.085614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.067897 restraints weight = 35255.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.069647 restraints weight = 24494.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.070939 restraints weight = 18728.778| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.5854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8338 Z= 0.196 Angle : 0.788 13.032 11320 Z= 0.383 Chirality : 0.045 0.195 1276 Planarity : 0.004 0.051 1402 Dihedral : 3.869 16.419 1078 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.55 % Allowed : 23.09 % Favored : 74.36 % 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: 0.90 (0.27), residues: 1010 helix: 1.43 (0.19), residues: 702 sheet: 4.96 (0.87), residues: 24 loop : -2.00 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 39 HIS 0.003 0.001 HIS A 18 PHE 0.034 0.002 PHE A 401 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 227 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.860 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: 0.9664 (mt) cc_final: 0.9110 (tp) REVERT: B 28 ASN cc_start: 0.9651 (m110) cc_final: 0.9265 (m110) REVERT: B 29 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.7281 (t80) REVERT: B 64 LEU cc_start: 0.9595 (tp) cc_final: 0.9349 (pp) REVERT: B 127 MET cc_start: 0.6398 (mmt) cc_final: 0.6128 (mmm) REVERT: B 332 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7621 (pp) REVERT: B 452 ASP cc_start: 0.8742 (t0) cc_final: 0.8399 (t0) REVERT: B 461 MET cc_start: 0.9222 (mmm) cc_final: 0.8791 (mtt) REVERT: A 41 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.8153 (t80) REVERT: A 127 MET cc_start: 0.7388 (tpp) cc_final: 0.7077 (tpp) REVERT: A 199 PHE cc_start: 0.7418 (m-80) cc_final: 0.7074 (m-80) REVERT: A 310 MET cc_start: 0.8701 (tpp) cc_final: 0.8470 (tmm) REVERT: A 321 TRP cc_start: 0.9032 (t60) cc_final: 0.8469 (t60) REVERT: A 374 ASN cc_start: 0.9307 (m-40) cc_final: 0.8867 (m110) REVERT: A 380 MET cc_start: 0.9459 (mtt) cc_final: 0.9172 (mtp) REVERT: A 390 HIS cc_start: 0.7228 (t-90) cc_final: 0.6914 (t-90) REVERT: A 420 ASN cc_start: 0.8635 (m-40) cc_final: 0.8417 (m-40) REVERT: A 446 PHE cc_start: 0.9075 (t80) cc_final: 0.8809 (t80) REVERT: A 483 MET cc_start: 0.9460 (mmm) cc_final: 0.9131 (mmp) outliers start: 22 outliers final: 14 residues processed: 218 average time/residue: 0.1766 time to fit residues: 54.2138 Evaluate side-chains 204 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 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 332 LEU 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 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: 1.9990 chunk 84 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 43 optimal weight: 0.0370 chunk 52 optimal weight: 7.9990 chunk 70 optimal weight: 0.0040 chunk 5 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 overall best weight: 0.7674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 ASN ** A 345 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 = 0.3958 r_free = 0.3958 target = 0.085270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.068085 restraints weight = 34927.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.069870 restraints weight = 24098.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.071262 restraints weight = 18212.148| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.5965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8338 Z= 0.195 Angle : 0.814 14.064 11320 Z= 0.398 Chirality : 0.047 0.220 1276 Planarity : 0.004 0.054 1402 Dihedral : 3.893 15.309 1078 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.44 % Allowed : 24.13 % Favored : 73.43 % 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: 0.77 (0.27), residues: 1010 helix: 1.33 (0.19), residues: 702 sheet: 4.97 (0.87), residues: 24 loop : -2.02 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 39 HIS 0.003 0.001 HIS A 18 PHE 0.033 0.002 PHE A 396 TYR 0.015 0.001 TYR A 58 ARG 0.008 0.001 ARG A 67 *********************** 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 223 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 0.870 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: 0.9167 (tp) REVERT: B 28 ASN cc_start: 0.9657 (m110) cc_final: 0.9368 (m110) REVERT: B 29 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.7304 (t80) REVERT: B 64 LEU cc_start: 0.9599 (tp) cc_final: 0.9346 (pp) REVERT: B 167 PHE cc_start: 0.9302 (m-10) cc_final: 0.9020 (m-80) REVERT: B 188 MET cc_start: 0.8515 (tmm) cc_final: 0.8283 (tmm) REVERT: B 312 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7408 (mp0) REVERT: B 332 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7666 (pp) REVERT: B 390 HIS cc_start: 0.7623 (t-90) cc_final: 0.7277 (t-90) REVERT: B 434 MET cc_start: 0.9197 (tpp) cc_final: 0.8390 (mmm) REVERT: B 452 ASP cc_start: 0.8796 (t0) cc_final: 0.8453 (t0) REVERT: B 483 MET cc_start: 0.9462 (tpp) cc_final: 0.9021 (tpp) REVERT: A 41 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.8129 (t80) REVERT: A 58 TYR cc_start: 0.8971 (m-10) cc_final: 0.8564 (m-10) REVERT: A 62 MET cc_start: 0.9420 (mmp) cc_final: 0.8996 (tpt) REVERT: A 127 MET cc_start: 0.7349 (tpp) cc_final: 0.7054 (tpp) REVERT: A 167 PHE cc_start: 0.9347 (m-10) cc_final: 0.9039 (m-80) REVERT: A 199 PHE cc_start: 0.7374 (m-80) cc_final: 0.7032 (m-80) REVERT: A 374 ASN cc_start: 0.9306 (m110) cc_final: 0.8925 (m110) REVERT: A 380 MET cc_start: 0.9405 (mtt) cc_final: 0.9189 (mtp) REVERT: A 390 HIS cc_start: 0.7137 (t-90) cc_final: 0.6719 (t-90) REVERT: A 420 ASN cc_start: 0.8604 (m-40) cc_final: 0.8388 (m-40) REVERT: A 446 PHE cc_start: 0.9061 (t80) cc_final: 0.8853 (t80) REVERT: A 483 MET cc_start: 0.9435 (mmm) cc_final: 0.9091 (mmp) outliers start: 21 outliers final: 17 residues processed: 214 average time/residue: 0.1648 time to fit residues: 50.5011 Evaluate side-chains 214 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 194 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 40 LEU 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 295 VAL Chi-restraints excluded: chain B residue 332 LEU 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 430 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 41 optimal weight: 0.7980 chunk 46 optimal weight: 0.0770 chunk 44 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 33 optimal weight: 0.3980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 28 ASN ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.086718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.068791 restraints weight = 35736.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.070560 restraints weight = 25111.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.071972 restraints weight = 19270.119| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.6123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8338 Z= 0.203 Angle : 0.859 13.292 11320 Z= 0.418 Chirality : 0.047 0.245 1276 Planarity : 0.004 0.056 1402 Dihedral : 3.883 15.691 1078 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.97 % Allowed : 24.25 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.27), residues: 1010 helix: 1.31 (0.19), residues: 700 sheet: 4.94 (0.87), residues: 24 loop : -2.11 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 39 HIS 0.003 0.000 HIS B 347 PHE 0.030 0.002 PHE B 223 TYR 0.018 0.001 TYR B 58 ARG 0.006 0.000 ARG A 67 *********************** 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 223 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 206 time to evaluate : 0.886 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: 0.9634 (mt) cc_final: 0.9107 (tp) REVERT: B 28 ASN cc_start: 0.9644 (m110) cc_final: 0.9313 (m110) REVERT: B 64 LEU cc_start: 0.9598 (tp) cc_final: 0.9339 (pp) REVERT: B 167 PHE cc_start: 0.9269 (m-10) cc_final: 0.8999 (m-80) REVERT: B 188 MET cc_start: 0.8538 (tmm) cc_final: 0.8294 (tmm) REVERT: B 332 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7632 (pp) REVERT: B 390 HIS cc_start: 0.7481 (t-90) cc_final: 0.7162 (t-90) REVERT: B 434 MET cc_start: 0.9234 (tpp) cc_final: 0.8328 (mmm) REVERT: B 451 ARG cc_start: 0.9497 (tpp-160) cc_final: 0.9254 (mmt90) REVERT: B 452 ASP cc_start: 0.8764 (t0) cc_final: 0.8397 (t0) REVERT: B 461 MET cc_start: 0.9144 (tpp) cc_final: 0.8819 (tpp) REVERT: B 483 MET cc_start: 0.9453 (tpp) cc_final: 0.8875 (tpp) REVERT: A 41 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.8075 (t80) REVERT: A 58 TYR cc_start: 0.8902 (m-10) cc_final: 0.8525 (m-10) REVERT: A 62 MET cc_start: 0.9394 (mmp) cc_final: 0.8939 (tpt) REVERT: A 127 MET cc_start: 0.7420 (tpp) cc_final: 0.6956 (tpp) REVERT: A 167 PHE cc_start: 0.9293 (m-10) cc_final: 0.8949 (m-80) REVERT: A 199 PHE cc_start: 0.7347 (m-80) cc_final: 0.6938 (m-80) REVERT: A 223 PHE cc_start: 0.9469 (m-80) cc_final: 0.9090 (m-80) REVERT: A 312 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7658 (mp0) REVERT: A 380 MET cc_start: 0.9427 (mtt) cc_final: 0.9109 (mtp) REVERT: A 390 HIS cc_start: 0.6979 (t-90) cc_final: 0.6655 (t-90) REVERT: A 420 ASN cc_start: 0.8573 (m-40) cc_final: 0.8359 (m-40) REVERT: A 446 PHE cc_start: 0.9057 (t80) cc_final: 0.8830 (t80) REVERT: A 483 MET cc_start: 0.9459 (mmm) cc_final: 0.9095 (mmp) outliers start: 17 outliers final: 14 residues processed: 216 average time/residue: 0.1643 time to fit residues: 50.7655 Evaluate side-chains 215 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 332 LEU 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 430 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 55 optimal weight: 0.1980 chunk 83 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 74 optimal weight: 40.0000 chunk 84 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 345 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 = 0.3953 r_free = 0.3953 target = 0.085779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.068920 restraints weight = 35168.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.070707 restraints weight = 24377.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.072088 restraints weight = 18498.064| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.6366 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= 0.223 Angle : 0.873 13.269 11320 Z= 0.430 Chirality : 0.050 0.245 1276 Planarity : 0.004 0.058 1402 Dihedral : 3.937 15.924 1078 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.32 % Allowed : 24.83 % Favored : 72.85 % 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: 0.53 (0.26), residues: 1010 helix: 1.14 (0.19), residues: 702 sheet: 4.90 (0.87), residues: 24 loop : -2.10 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 39 HIS 0.004 0.001 HIS B 347 PHE 0.046 0.002 PHE B 223 TYR 0.011 0.001 TYR B 58 ARG 0.006 0.001 ARG A 67 ********************** 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 214 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 194 time to evaluate : 0.893 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: 0.9643 (mt) cc_final: 0.9163 (tp) REVERT: B 28 ASN cc_start: 0.9644 (m110) cc_final: 0.9328 (m110) REVERT: B 29 PHE cc_start: 0.7791 (OUTLIER) cc_final: 0.7281 (t80) REVERT: B 64 LEU cc_start: 0.9606 (tp) cc_final: 0.9344 (pp) REVERT: B 188 MET cc_start: 0.8597 (tmm) cc_final: 0.8358 (tmm) REVERT: B 332 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7498 (pp) REVERT: B 378 CYS cc_start: 0.9072 (m) cc_final: 0.8825 (m) REVERT: B 390 HIS cc_start: 0.7533 (t-90) cc_final: 0.7166 (t-90) REVERT: B 451 ARG cc_start: 0.9518 (tpp-160) cc_final: 0.9088 (mtt-85) REVERT: B 452 ASP cc_start: 0.8642 (t0) cc_final: 0.8174 (t0) REVERT: B 461 MET cc_start: 0.9203 (tpp) cc_final: 0.8623 (tpp) REVERT: A 41 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.8071 (t80) REVERT: A 58 TYR cc_start: 0.8915 (m-10) cc_final: 0.8450 (m-10) REVERT: A 62 MET cc_start: 0.9428 (mmp) cc_final: 0.8924 (tpt) REVERT: A 127 MET cc_start: 0.7561 (tpp) cc_final: 0.7115 (tpp) REVERT: A 199 PHE cc_start: 0.7467 (m-80) cc_final: 0.7120 (m-80) REVERT: A 223 PHE cc_start: 0.9462 (m-80) cc_final: 0.9069 (m-80) REVERT: A 312 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7646 (mp0) REVERT: A 380 MET cc_start: 0.9514 (mtt) cc_final: 0.9098 (mtp) REVERT: A 390 HIS cc_start: 0.6886 (t-90) cc_final: 0.5984 (t-90) REVERT: A 446 PHE cc_start: 0.9181 (t80) cc_final: 0.8943 (t80) REVERT: A 460 MET cc_start: 0.8107 (ptp) cc_final: 0.7634 (ptp) REVERT: A 483 MET cc_start: 0.9504 (mmm) cc_final: 0.9090 (mmp) outliers start: 20 outliers final: 17 residues processed: 207 average time/residue: 0.1682 time to fit residues: 49.7855 Evaluate side-chains 207 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 29 PHE 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 295 VAL Chi-restraints excluded: chain B residue 332 LEU 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 430 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 13 optimal weight: 0.0470 chunk 52 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 chunk 82 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 overall best weight: 1.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** A 420 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 = 0.3967 r_free = 0.3967 target = 0.085875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.068906 restraints weight = 36154.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.070716 restraints weight = 25076.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.072146 restraints weight = 19004.986| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.6420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.216 8338 Z= 0.393 Angle : 1.163 59.128 11320 Z= 0.664 Chirality : 0.056 0.907 1276 Planarity : 0.005 0.066 1402 Dihedral : 4.091 35.011 1078 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.20 % Allowed : 24.83 % Favored : 72.97 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.50 (0.26), residues: 1010 helix: 1.11 (0.19), residues: 702 sheet: 4.90 (0.87), residues: 24 loop : -2.10 (0.36), 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 0.059 0.002 PHE B 223 TYR 0.010 0.001 TYR B 58 ARG 0.005 0.001 ARG A 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2641.57 seconds wall clock time: 48 minutes 8.50 seconds (2888.50 seconds total)