Starting phenix.real_space_refine on Tue Sep 24 12:50:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pxb_18002/09_2024/8pxb_18002.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pxb_18002/09_2024/8pxb_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pxb_18002/09_2024/8pxb_18002.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pxb_18002/09_2024/8pxb_18002.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pxb_18002/09_2024/8pxb_18002.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pxb_18002/09_2024/8pxb_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-5461/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: 4.89, per 1000 atoms: 0.60 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: 1.88 Conformation dependent library (CDL) restraints added in 1.1 seconds 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1892 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 1 sheets defined 72.5% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 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: 2.14 Time building geometry restraints manager: 2.22 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: 0.00 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: 0.570 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.340 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.450 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 4 poor density : 326 time to evaluate : 0.947 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: 0.1833 time to fit residues: 81.3968 Evaluate side-chains 212 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 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 fitting. rotamer outliers: 30 poor density : 209 time to evaluate : 0.851 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 outliers start: 30 outliers final: 22 residues processed: 225 average time/residue: 0.1664 time to fit residues: 52.7233 Evaluate side-chains 190 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 168 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 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 50 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 98 optimal weight: 30.0000 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS B 243 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 ASN B 430 ASN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8338 Z= 0.198 Angle : 0.719 10.025 11320 Z= 0.358 Chirality : 0.045 0.246 1276 Planarity : 0.004 0.034 1402 Dihedral : 3.742 16.822 1078 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.09 % Allowed : 19.72 % 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: 1.16 (0.27), residues: 1010 helix: 1.67 (0.19), residues: 702 sheet: 4.81 (0.86), residues: 24 loop : -1.99 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 321 HIS 0.004 0.001 HIS A 18 PHE 0.030 0.002 PHE B 377 TYR 0.020 0.001 TYR A 68 ARG 0.008 0.001 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 213 time to evaluate : 0.855 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: 0.8548 (tt) cc_final: 0.7740 (tp) REVERT: B 294 VAL cc_start: 0.8441 (m) cc_final: 0.8183 (p) REVERT: A 148 TYR cc_start: 0.7026 (t80) cc_final: 0.5845 (t80) REVERT: A 420 ASN cc_start: 0.7378 (m-40) cc_final: 0.7136 (m-40) outliers start: 18 outliers final: 11 residues processed: 223 average time/residue: 0.1621 time to fit residues: 52.2134 Evaluate side-chains 199 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 188 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 430 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 374 ASN ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.5042 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= 0.191 Angle : 0.743 13.346 11320 Z= 0.364 Chirality : 0.045 0.252 1276 Planarity : 0.004 0.035 1402 Dihedral : 3.797 16.149 1078 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.20 % Allowed : 19.03 % Favored : 78.77 % 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: 1.07 (0.27), residues: 1010 helix: 1.58 (0.19), residues: 702 sheet: 4.92 (0.86), residues: 24 loop : -1.98 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 321 HIS 0.003 0.001 HIS A 18 PHE 0.029 0.002 PHE B 365 TYR 0.012 0.001 TYR A 58 ARG 0.005 0.001 ARG A 67 *********************** 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 233 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 214 time to evaluate : 0.927 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 29 PHE cc_start: 0.6593 (OUTLIER) cc_final: 0.5944 (t80) REVERT: A 420 ASN cc_start: 0.7342 (m-40) cc_final: 0.7097 (m-40) outliers start: 19 outliers final: 11 residues processed: 225 average time/residue: 0.1504 time to fit residues: 48.9883 Evaluate side-chains 202 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 190 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 430 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 87 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8338 Z= 0.191 Angle : 0.764 10.080 11320 Z= 0.376 Chirality : 0.045 0.207 1276 Planarity : 0.004 0.035 1402 Dihedral : 3.897 16.421 1078 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.20 % Allowed : 21.46 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.27), residues: 1010 helix: 1.48 (0.19), residues: 702 sheet: 4.95 (0.86), residues: 24 loop : -2.01 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 321 HIS 0.003 0.000 HIS A 18 PHE 0.025 0.002 PHE B 370 TYR 0.014 0.001 TYR B 58 ARG 0.004 0.000 ARG A 360 *********************** 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 236 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 217 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 PHE cc_start: 0.6543 (OUTLIER) cc_final: 0.5861 (t80) REVERT: A 321 TRP cc_start: 0.6624 (t60) cc_final: 0.5708 (t60) REVERT: A 420 ASN cc_start: 0.7263 (m-40) cc_final: 0.7017 (m-40) outliers start: 19 outliers final: 13 residues processed: 226 average time/residue: 0.1537 time to fit residues: 49.6941 Evaluate side-chains 211 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 197 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 336 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 430 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 10 optimal weight: 30.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.5870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8338 Z= 0.234 Angle : 0.792 11.626 11320 Z= 0.394 Chirality : 0.047 0.302 1276 Planarity : 0.004 0.054 1402 Dihedral : 4.056 17.945 1078 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.48 % Allowed : 21.93 % 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: 0.78 (0.27), residues: 1010 helix: 1.34 (0.19), residues: 702 sheet: 4.86 (0.86), residues: 24 loop : -2.05 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 39 HIS 0.003 0.001 HIS A 224 PHE 0.048 0.002 PHE A 223 TYR 0.031 0.001 TYR A 350 ARG 0.003 0.001 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 234 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 204 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 PHE cc_start: 0.6793 (OUTLIER) cc_final: 0.6093 (t80) REVERT: A 41 PHE cc_start: 0.7173 (OUTLIER) cc_final: 0.6946 (t80) REVERT: A 420 ASN cc_start: 0.7448 (m-40) cc_final: 0.7231 (m-40) outliers start: 30 outliers final: 18 residues processed: 222 average time/residue: 0.1601 time to fit residues: 51.1989 Evaluate side-chains 211 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 191 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 VAL 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 316 PHE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain B residue 453 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 96 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.6082 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= 0.207 Angle : 0.811 13.004 11320 Z= 0.402 Chirality : 0.047 0.224 1276 Planarity : 0.004 0.053 1402 Dihedral : 4.092 14.699 1078 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.44 % Allowed : 24.59 % Favored : 72.97 % 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: 0.60 (0.27), residues: 1010 helix: 1.20 (0.19), residues: 702 sheet: 4.91 (0.87), residues: 24 loop : -2.10 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 39 HIS 0.003 0.001 HIS A 50 PHE 0.041 0.002 PHE A 223 TYR 0.020 0.001 TYR A 350 ARG 0.004 0.000 ARG B 441 *********************** 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 224 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 203 time to evaluate : 0.908 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: B 29 PHE cc_start: 0.6621 (OUTLIER) cc_final: 0.5898 (t80) REVERT: A 41 PHE cc_start: 0.7114 (OUTLIER) cc_final: 0.6897 (t80) REVERT: A 351 ASN cc_start: 0.7831 (OUTLIER) cc_final: 0.7593 (p0) REVERT: A 420 ASN cc_start: 0.7300 (m-40) cc_final: 0.7080 (m-40) outliers start: 21 outliers final: 13 residues processed: 212 average time/residue: 0.1629 time to fit residues: 49.3898 Evaluate side-chains 203 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 187 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 41 PHE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 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 350 TYR 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 29 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 61 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 87 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.6280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8338 Z= 0.209 Angle : 0.864 13.578 11320 Z= 0.423 Chirality : 0.049 0.252 1276 Planarity : 0.004 0.054 1402 Dihedral : 4.067 15.464 1078 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.44 % Allowed : 24.94 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.27), residues: 1010 helix: 1.19 (0.19), residues: 704 sheet: 4.93 (0.87), residues: 24 loop : -2.02 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 321 HIS 0.003 0.001 HIS B 347 PHE 0.037 0.002 PHE A 223 TYR 0.018 0.001 TYR A 350 ARG 0.003 0.000 ARG B 441 *********************** 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 fitting. rotamer outliers: 21 poor density : 202 time to evaluate : 0.854 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 29 PHE cc_start: 0.6737 (OUTLIER) cc_final: 0.5980 (t80) REVERT: B 62 MET cc_start: 0.7081 (mmp) cc_final: 0.6842 (mpp) REVERT: A 351 ASN cc_start: 0.7855 (OUTLIER) cc_final: 0.7620 (p0) REVERT: A 420 ASN cc_start: 0.7277 (m-40) cc_final: 0.7047 (m-40) outliers start: 21 outliers final: 15 residues processed: 215 average time/residue: 0.1564 time to fit residues: 48.2626 Evaluate side-chains 208 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 191 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 336 VAL Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain A residue 29 PHE 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 350 TYR Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 430 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.6521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8338 Z= 0.229 Angle : 0.906 13.561 11320 Z= 0.442 Chirality : 0.050 0.261 1276 Planarity : 0.005 0.057 1402 Dihedral : 4.109 15.295 1078 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.09 % Allowed : 25.17 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.26), residues: 1010 helix: 1.07 (0.19), residues: 702 sheet: 4.90 (0.87), residues: 24 loop : -2.02 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 39 HIS 0.004 0.001 HIS B 347 PHE 0.034 0.002 PHE A 223 TYR 0.017 0.001 TYR B 58 ARG 0.005 0.000 ARG A 47 *********************** 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 217 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 199 time to evaluate : 0.849 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 29 PHE cc_start: 0.6720 (OUTLIER) cc_final: 0.6000 (t80) REVERT: B 460 MET cc_start: 0.6854 (ptp) cc_final: 0.6547 (ptp) REVERT: A 351 ASN cc_start: 0.7845 (OUTLIER) cc_final: 0.7618 (p0) REVERT: A 420 ASN cc_start: 0.7331 (m-40) cc_final: 0.7116 (m-40) outliers start: 18 outliers final: 15 residues processed: 208 average time/residue: 0.1625 time to fit residues: 48.2461 Evaluate side-chains 208 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 191 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 VAL 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 244 ASP Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain A residue 29 PHE Chi-restraints excluded: chain A residue 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 350 TYR Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 430 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 63 optimal weight: 0.0370 chunk 84 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 overall best weight: 2.1864 ------------------------------------------------------------------------------- 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 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.6793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8338 Z= 0.245 Angle : 0.933 13.551 11320 Z= 0.462 Chirality : 0.051 0.267 1276 Planarity : 0.005 0.058 1402 Dihedral : 4.168 16.169 1078 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 20.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.09 % Allowed : 25.41 % Favored : 72.51 % 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: 0.43 (0.27), residues: 1010 helix: 1.03 (0.19), residues: 702 sheet: 4.79 (0.87), residues: 24 loop : -2.03 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 321 HIS 0.004 0.001 HIS B 347 PHE 0.035 0.002 PHE A 396 TYR 0.016 0.001 TYR A 350 ARG 0.007 0.001 ARG B 451 ********************** 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 207 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 189 time to evaluate : 0.910 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: B 460 MET cc_start: 0.6773 (ptp) cc_final: 0.6461 (ptp) REVERT: A 351 ASN cc_start: 0.7804 (OUTLIER) cc_final: 0.7584 (p0) REVERT: A 420 ASN cc_start: 0.7372 (m-40) cc_final: 0.7164 (m-40) REVERT: A 460 MET cc_start: 0.7048 (ptp) cc_final: 0.6758 (ptp) outliers start: 18 outliers final: 16 residues processed: 199 average time/residue: 0.1601 time to fit residues: 45.7583 Evaluate side-chains 204 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 187 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 VAL 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 336 VAL Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain A residue 29 PHE 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 350 TYR Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 430 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 0.0770 chunk 33 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.2744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN ** 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 = 0.3964 r_free = 0.3964 target = 0.086124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.069054 restraints weight = 35099.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.070811 restraints weight = 24546.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.072026 restraints weight = 18748.718| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.6900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8338 Z= 0.219 Angle : 0.953 13.671 11320 Z= 0.462 Chirality : 0.050 0.260 1276 Planarity : 0.005 0.058 1402 Dihedral : 4.161 15.560 1078 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.74 % Allowed : 26.10 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.26), residues: 1010 helix: 0.99 (0.19), residues: 702 sheet: 4.78 (0.86), residues: 24 loop : -2.05 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 39 HIS 0.005 0.001 HIS A 50 PHE 0.035 0.002 PHE A 396 TYR 0.020 0.001 TYR A 58 ARG 0.011 0.001 ARG A 451 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1763.23 seconds wall clock time: 32 minutes 12.01 seconds (1932.01 seconds total)