Starting phenix.real_space_refine on Thu Sep 26 03:48:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uvt_42628/09_2024/8uvt_42628.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uvt_42628/09_2024/8uvt_42628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uvt_42628/09_2024/8uvt_42628.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uvt_42628/09_2024/8uvt_42628.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uvt_42628/09_2024/8uvt_42628.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uvt_42628/09_2024/8uvt_42628.cif" } resolution = 2.9 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= 0.003 sd= 0.114 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 132 5.16 5 C 7892 2.51 5 N 2024 2.21 5 O 2056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12104 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3026 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 13, 'TRANS': 372} Chain breaks: 2 Restraints were copied for chains: C, B, D Time building chain proxies: 6.26, per 1000 atoms: 0.52 Number of scatterers: 12104 At special positions: 0 Unit cell: (110.004, 110.004, 91.848, 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 132 16.00 O 2056 8.00 N 2024 7.00 C 7892 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: 3.05 Conformation dependent library (CDL) restraints added in 1.7 seconds 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2912 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 4 sheets defined 83.2% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 20 through 32 removed outlier: 3.874A pdb=" N PHE A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 79 Processing helix chain 'A' and resid 89 through 113 Processing helix chain 'A' and resid 113 through 136 removed outlier: 4.379A pdb=" N ASN A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 175 removed outlier: 3.802A pdb=" N LYS A 175 " --> pdb=" O MET A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 227 removed outlier: 5.030A pdb=" N GLY A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N PHE A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 340 removed outlier: 3.719A pdb=" N GLY A 292 " --> pdb=" O CYS A 288 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) Proline residue: A 315 - end of helix Proline residue: A 331 - end of helix removed outlier: 3.704A pdb=" N VAL A 340 " --> pdb=" O MET A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 389 Proline residue: A 368 - end of helix Processing helix chain 'A' and resid 394 through 410 removed outlier: 3.752A pdb=" N SER A 398 " --> pdb=" O GLY A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 423 through 445 removed outlier: 3.529A pdb=" N MET A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 444 " --> pdb=" O ILE A 440 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 32 removed outlier: 3.875A pdb=" N PHE B 31 " --> pdb=" O LYS B 27 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 79 Processing helix chain 'B' and resid 89 through 113 Processing helix chain 'B' and resid 113 through 136 removed outlier: 4.379A pdb=" N ASN B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 175 removed outlier: 3.802A pdb=" N LYS B 175 " --> pdb=" O MET B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 227 removed outlier: 5.030A pdb=" N GLY B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N PHE B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 340 removed outlier: 3.718A pdb=" N GLY B 292 " --> pdb=" O CYS B 288 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) Proline residue: B 315 - end of helix Proline residue: B 331 - end of helix removed outlier: 3.704A pdb=" N VAL B 340 " --> pdb=" O MET B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 389 Proline residue: B 368 - end of helix Processing helix chain 'B' and resid 394 through 410 removed outlier: 3.753A pdb=" N SER B 398 " --> pdb=" O GLY B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 423 through 445 removed outlier: 3.528A pdb=" N MET B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE B 444 " --> pdb=" O ILE B 440 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 32 removed outlier: 3.875A pdb=" N PHE C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS C 32 " --> pdb=" O ILE C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 79 Processing helix chain 'C' and resid 89 through 113 Processing helix chain 'C' and resid 113 through 136 removed outlier: 4.379A pdb=" N ASN C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 175 removed outlier: 3.802A pdb=" N LYS C 175 " --> pdb=" O MET C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 227 removed outlier: 5.030A pdb=" N GLY C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N PHE C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 340 removed outlier: 3.718A pdb=" N GLY C 292 " --> pdb=" O CYS C 288 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU C 314 " --> pdb=" O ASP C 310 " (cutoff:3.500A) Proline residue: C 315 - end of helix Proline residue: C 331 - end of helix removed outlier: 3.704A pdb=" N VAL C 340 " --> pdb=" O MET C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 389 Proline residue: C 368 - end of helix Processing helix chain 'C' and resid 394 through 410 removed outlier: 3.752A pdb=" N SER C 398 " --> pdb=" O GLY C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 423 through 445 removed outlier: 3.529A pdb=" N MET C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE C 444 " --> pdb=" O ILE C 440 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN C 445 " --> pdb=" O LEU C 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 32 removed outlier: 3.875A pdb=" N PHE D 31 " --> pdb=" O LYS D 27 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS D 32 " --> pdb=" O ILE D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 79 Processing helix chain 'D' and resid 89 through 113 Processing helix chain 'D' and resid 113 through 136 removed outlier: 4.380A pdb=" N ASN D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 175 removed outlier: 3.803A pdb=" N LYS D 175 " --> pdb=" O MET D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 227 removed outlier: 5.029A pdb=" N GLY D 188 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N PHE D 189 " --> pdb=" O ASN D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 340 removed outlier: 3.718A pdb=" N GLY D 292 " --> pdb=" O CYS D 288 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU D 314 " --> pdb=" O ASP D 310 " (cutoff:3.500A) Proline residue: D 315 - end of helix Proline residue: D 331 - end of helix removed outlier: 3.704A pdb=" N VAL D 340 " --> pdb=" O MET D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 389 Proline residue: D 368 - end of helix Processing helix chain 'D' and resid 394 through 410 removed outlier: 3.752A pdb=" N SER D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 423 through 445 removed outlier: 3.528A pdb=" N MET D 427 " --> pdb=" O ASP D 423 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE D 444 " --> pdb=" O ILE D 440 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN D 445 " --> pdb=" O LEU D 441 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 41 Processing sheet with id=AA2, first strand: chain 'B' and resid 37 through 41 Processing sheet with id=AA3, first strand: chain 'C' and resid 37 through 41 Processing sheet with id=AA4, first strand: chain 'D' and resid 37 through 41 1040 hydrogen bonds defined for protein. 3096 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: 3.50 Time building geometry restraints manager: 3.53 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: 3754 1.34 - 1.46: 2268 1.46 - 1.58: 6118 1.58 - 1.69: 0 1.69 - 1.81: 200 Bond restraints: 12340 Sorted by residual: bond pdb=" C GLU C 367 " pdb=" N PRO C 368 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.36e-02 5.41e+03 1.96e+00 bond pdb=" C GLU A 367 " pdb=" N PRO A 368 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.36e-02 5.41e+03 1.92e+00 bond pdb=" C GLU D 367 " pdb=" N PRO D 368 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.36e-02 5.41e+03 1.88e+00 bond pdb=" C GLU B 367 " pdb=" N PRO B 368 " ideal model delta sigma weight residual 1.335 1.354 -0.018 1.36e-02 5.41e+03 1.80e+00 bond pdb=" C LEU A 122 " pdb=" O LEU A 122 " ideal model delta sigma weight residual 1.237 1.247 -0.011 1.17e-02 7.31e+03 8.31e-01 ... (remaining 12335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 16163 1.00 - 1.99: 422 1.99 - 2.99: 81 2.99 - 3.99: 38 3.99 - 4.99: 32 Bond angle restraints: 16736 Sorted by residual: angle pdb=" N GLY B 313 " pdb=" CA GLY B 313 " pdb=" C GLY B 313 " ideal model delta sigma weight residual 112.50 116.40 -3.90 1.16e+00 7.43e-01 1.13e+01 angle pdb=" N GLY C 313 " pdb=" CA GLY C 313 " pdb=" C GLY C 313 " ideal model delta sigma weight residual 112.50 116.40 -3.90 1.16e+00 7.43e-01 1.13e+01 angle pdb=" N GLY D 313 " pdb=" CA GLY D 313 " pdb=" C GLY D 313 " ideal model delta sigma weight residual 112.50 116.40 -3.90 1.16e+00 7.43e-01 1.13e+01 angle pdb=" N GLY A 313 " pdb=" CA GLY A 313 " pdb=" C GLY A 313 " ideal model delta sigma weight residual 112.50 116.38 -3.88 1.16e+00 7.43e-01 1.12e+01 angle pdb=" C VAL D 366 " pdb=" N GLU D 367 " pdb=" CA GLU D 367 " ideal model delta sigma weight residual 120.26 124.59 -4.33 1.34e+00 5.57e-01 1.04e+01 ... (remaining 16731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 6562 17.80 - 35.60: 662 35.60 - 53.40: 108 53.40 - 71.20: 28 71.20 - 89.01: 20 Dihedral angle restraints: 7380 sinusoidal: 2876 harmonic: 4504 Sorted by residual: dihedral pdb=" CB GLU B 40 " pdb=" CG GLU B 40 " pdb=" CD GLU B 40 " pdb=" OE1 GLU B 40 " ideal model delta sinusoidal sigma weight residual 0.00 86.33 -86.33 1 3.00e+01 1.11e-03 9.98e+00 dihedral pdb=" CB GLU D 40 " pdb=" CG GLU D 40 " pdb=" CD GLU D 40 " pdb=" OE1 GLU D 40 " ideal model delta sinusoidal sigma weight residual 0.00 86.32 -86.32 1 3.00e+01 1.11e-03 9.98e+00 dihedral pdb=" CB GLU A 40 " pdb=" CG GLU A 40 " pdb=" CD GLU A 40 " pdb=" OE1 GLU A 40 " ideal model delta sinusoidal sigma weight residual 0.00 86.32 -86.32 1 3.00e+01 1.11e-03 9.98e+00 ... (remaining 7377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1330 0.027 - 0.054: 448 0.054 - 0.081: 186 0.081 - 0.108: 77 0.108 - 0.134: 15 Chirality restraints: 2056 Sorted by residual: chirality pdb=" CG LEU B 386 " pdb=" CB LEU B 386 " pdb=" CD1 LEU B 386 " pdb=" CD2 LEU B 386 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CG LEU D 386 " pdb=" CB LEU D 386 " pdb=" CD1 LEU D 386 " pdb=" CD2 LEU D 386 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CG LEU C 386 " pdb=" CB LEU C 386 " pdb=" CD1 LEU C 386 " pdb=" CD2 LEU C 386 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 2053 not shown) Planarity restraints: 2020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 424 " 0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO B 425 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 425 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 425 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 424 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO D 425 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO D 425 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 425 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 424 " -0.019 5.00e-02 4.00e+02 2.91e-02 1.35e+00 pdb=" N PRO A 425 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 425 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 425 " -0.016 5.00e-02 4.00e+02 ... (remaining 2017 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2125 2.77 - 3.30: 12287 3.30 - 3.83: 21314 3.83 - 4.37: 23750 4.37 - 4.90: 42212 Nonbonded interactions: 101688 Sorted by model distance: nonbonded pdb=" OG SER A 84 " pdb=" O MET A 87 " model vdw 2.233 3.040 nonbonded pdb=" OG SER C 84 " pdb=" O MET C 87 " model vdw 2.233 3.040 nonbonded pdb=" OG SER D 84 " pdb=" O MET D 87 " model vdw 2.233 3.040 nonbonded pdb=" OG SER B 84 " pdb=" O MET B 87 " model vdw 2.233 3.040 nonbonded pdb=" OD2 ASP D 165 " pdb=" OH TYR D 190 " model vdw 2.253 3.040 ... (remaining 101683 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' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.440 Find NCS groups from input model: 0.550 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:11.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12340 Z= 0.185 Angle : 0.474 4.985 16736 Z= 0.260 Chirality : 0.036 0.134 2056 Planarity : 0.003 0.029 2020 Dihedral : 15.275 89.006 4468 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: 2.31 (0.21), residues: 1520 helix: 2.32 (0.14), residues: 1228 sheet: -0.45 (0.55), residues: 40 loop : -2.38 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 193 HIS 0.004 0.001 HIS C 392 PHE 0.014 0.001 PHE D 205 TYR 0.008 0.001 TYR C 124 ARG 0.003 0.000 ARG D 405 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.238 Fit side-chains REVERT: A 296 ARG cc_start: 0.8233 (mtt90) cc_final: 0.7900 (mtt90) REVERT: A 310 ASP cc_start: 0.8256 (m-30) cc_final: 0.7970 (m-30) REVERT: B 310 ASP cc_start: 0.8288 (m-30) cc_final: 0.7960 (m-30) REVERT: B 387 MET cc_start: 0.8775 (mtm) cc_final: 0.8573 (mtm) REVERT: C 427 MET cc_start: 0.8635 (ptt) cc_final: 0.8348 (ptt) REVERT: D 427 MET cc_start: 0.8631 (ptt) cc_final: 0.8352 (ptt) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 1.0755 time to fit residues: 284.8466 Evaluate side-chains 183 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS A 392 HIS A 443 GLN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 HIS B 392 HIS C 358 HIS C 392 HIS ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS D 392 HIS D 443 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12340 Z= 0.247 Angle : 0.546 6.125 16736 Z= 0.283 Chirality : 0.038 0.155 2056 Planarity : 0.004 0.030 2020 Dihedral : 3.859 15.578 1688 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.29 % Allowed : 10.50 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.21), residues: 1520 helix: 2.85 (0.13), residues: 1228 sheet: 0.06 (0.54), residues: 40 loop : -2.09 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 193 HIS 0.005 0.001 HIS B 392 PHE 0.019 0.002 PHE A 205 TYR 0.030 0.002 TYR B 124 ARG 0.004 0.001 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 195 time to evaluate : 1.379 Fit side-chains REVERT: A 171 MET cc_start: 0.7764 (mmp) cc_final: 0.7513 (mmm) REVERT: A 296 ARG cc_start: 0.8199 (mtt90) cc_final: 0.7853 (mtt90) REVERT: A 310 ASP cc_start: 0.8351 (m-30) cc_final: 0.8110 (m-30) REVERT: A 385 ARG cc_start: 0.8106 (ttm110) cc_final: 0.7872 (ttp-110) REVERT: A 387 MET cc_start: 0.9204 (mtm) cc_final: 0.8974 (mtm) REVERT: B 306 ARG cc_start: 0.7888 (mtm-85) cc_final: 0.7680 (mtp180) REVERT: B 310 ASP cc_start: 0.8361 (m-30) cc_final: 0.8044 (m-30) REVERT: B 387 MET cc_start: 0.9173 (mtm) cc_final: 0.8924 (mtm) REVERT: C 143 THR cc_start: 0.8655 (m) cc_final: 0.8321 (m) REVERT: C 310 ASP cc_start: 0.8395 (m-30) cc_final: 0.8155 (m-30) REVERT: C 427 MET cc_start: 0.8458 (ptt) cc_final: 0.8215 (ptt) REVERT: D 143 THR cc_start: 0.8656 (m) cc_final: 0.8323 (m) REVERT: D 310 ASP cc_start: 0.8367 (m-30) cc_final: 0.8134 (m-30) REVERT: D 385 ARG cc_start: 0.8118 (ttm110) cc_final: 0.7849 (ttp-110) REVERT: D 427 MET cc_start: 0.8496 (ptt) cc_final: 0.8243 (ptt) outliers start: 31 outliers final: 16 residues processed: 210 average time/residue: 1.2813 time to fit residues: 291.3944 Evaluate side-chains 197 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 181 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 224 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 138 optimal weight: 0.4980 chunk 149 optimal weight: 1.9990 chunk 123 optimal weight: 0.0970 chunk 137 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 443 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12340 Z= 0.201 Angle : 0.505 6.203 16736 Z= 0.263 Chirality : 0.036 0.125 2056 Planarity : 0.004 0.032 2020 Dihedral : 3.756 13.659 1688 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.74 % Allowed : 13.31 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.25 (0.21), residues: 1520 helix: 3.01 (0.13), residues: 1236 sheet: 0.47 (0.50), residues: 40 loop : -2.53 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 193 HIS 0.003 0.001 HIS C 392 PHE 0.016 0.001 PHE A 205 TYR 0.026 0.001 TYR B 124 ARG 0.004 0.000 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 203 time to evaluate : 1.476 Fit side-chains REVERT: A 296 ARG cc_start: 0.8172 (mtt90) cc_final: 0.7805 (mtt90) REVERT: A 310 ASP cc_start: 0.8329 (m-30) cc_final: 0.8067 (m-30) REVERT: A 385 ARG cc_start: 0.8108 (ttm110) cc_final: 0.7881 (ttp-110) REVERT: A 387 MET cc_start: 0.9176 (mtm) cc_final: 0.8961 (mtm) REVERT: B 284 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.7243 (mp10) REVERT: B 306 ARG cc_start: 0.7931 (mtm-85) cc_final: 0.7705 (mtp180) REVERT: B 310 ASP cc_start: 0.8325 (m-30) cc_final: 0.7912 (m-30) REVERT: B 387 MET cc_start: 0.9163 (mtm) cc_final: 0.8901 (mtm) REVERT: B 401 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7821 (tm-30) REVERT: C 87 MET cc_start: 0.4205 (mtt) cc_final: 0.3233 (mtt) REVERT: C 143 THR cc_start: 0.8606 (m) cc_final: 0.8252 (m) REVERT: C 310 ASP cc_start: 0.8362 (m-30) cc_final: 0.8130 (m-30) REVERT: C 427 MET cc_start: 0.8448 (ptt) cc_final: 0.8220 (ptt) REVERT: D 143 THR cc_start: 0.8610 (m) cc_final: 0.8255 (m) REVERT: D 310 ASP cc_start: 0.8365 (m-30) cc_final: 0.8131 (m-30) REVERT: D 385 ARG cc_start: 0.8102 (ttm110) cc_final: 0.7765 (ttm110) REVERT: D 427 MET cc_start: 0.8446 (ptt) cc_final: 0.8209 (ptt) outliers start: 37 outliers final: 16 residues processed: 224 average time/residue: 1.2315 time to fit residues: 299.5965 Evaluate side-chains 205 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 188 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 224 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 0.0170 chunk 103 optimal weight: 0.6980 chunk 71 optimal weight: 0.0020 chunk 15 optimal weight: 0.8980 chunk 65 optimal weight: 0.0970 chunk 92 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.2624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12340 Z= 0.154 Angle : 0.484 6.798 16736 Z= 0.250 Chirality : 0.035 0.173 2056 Planarity : 0.003 0.030 2020 Dihedral : 3.647 14.102 1688 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.11 % Allowed : 15.38 % Favored : 81.51 % 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: 3.59 (0.21), residues: 1520 helix: 3.28 (0.14), residues: 1224 sheet: 1.04 (0.55), residues: 40 loop : -2.44 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 193 HIS 0.002 0.001 HIS D 139 PHE 0.014 0.001 PHE A 205 TYR 0.022 0.001 TYR B 124 ARG 0.002 0.000 ARG B 405 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 201 time to evaluate : 1.344 Fit side-chains REVERT: A 296 ARG cc_start: 0.8136 (mtt90) cc_final: 0.7765 (mtt90) REVERT: B 284 GLN cc_start: 0.7375 (OUTLIER) cc_final: 0.7140 (mp10) REVERT: B 310 ASP cc_start: 0.8243 (m-30) cc_final: 0.7959 (m-30) REVERT: B 387 MET cc_start: 0.9102 (mtm) cc_final: 0.8846 (mtm) REVERT: B 401 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7804 (tm-30) REVERT: C 87 MET cc_start: 0.4196 (mtt) cc_final: 0.3153 (mtt) REVERT: C 143 THR cc_start: 0.8525 (m) cc_final: 0.8156 (m) REVERT: C 427 MET cc_start: 0.8455 (ptt) cc_final: 0.8186 (ptt) REVERT: D 87 MET cc_start: 0.4011 (mtt) cc_final: 0.3252 (mtt) REVERT: D 143 THR cc_start: 0.8527 (m) cc_final: 0.8155 (m) REVERT: D 385 ARG cc_start: 0.7945 (ttm110) cc_final: 0.7543 (ttm110) REVERT: D 427 MET cc_start: 0.8442 (ptt) cc_final: 0.8170 (ptt) outliers start: 42 outliers final: 22 residues processed: 222 average time/residue: 1.2499 time to fit residues: 301.0383 Evaluate side-chains 209 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 186 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 431 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 109 optimal weight: 0.0000 chunk 60 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 101 optimal weight: 0.0870 chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 0.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 443 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12340 Z= 0.217 Angle : 0.525 6.771 16736 Z= 0.269 Chirality : 0.037 0.139 2056 Planarity : 0.004 0.031 2020 Dihedral : 3.738 13.949 1688 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.33 % Allowed : 15.38 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.40 (0.21), residues: 1520 helix: 3.13 (0.13), residues: 1236 sheet: 1.32 (0.58), residues: 40 loop : -2.71 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 193 HIS 0.003 0.001 HIS B 392 PHE 0.017 0.002 PHE A 205 TYR 0.024 0.001 TYR C 124 ARG 0.004 0.000 ARG B 405 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 197 time to evaluate : 1.345 Fit side-chains REVERT: A 171 MET cc_start: 0.7841 (mmm) cc_final: 0.7552 (mmp) REVERT: A 310 ASP cc_start: 0.8331 (m-30) cc_final: 0.8057 (m-30) REVERT: B 310 ASP cc_start: 0.8335 (m-30) cc_final: 0.8044 (m-30) REVERT: B 387 MET cc_start: 0.9197 (mtm) cc_final: 0.8853 (mtm) REVERT: B 401 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7881 (tm-30) REVERT: C 52 LYS cc_start: 0.7708 (mmtm) cc_final: 0.7343 (pttp) REVERT: C 87 MET cc_start: 0.4098 (mtt) cc_final: 0.3066 (mtt) REVERT: C 143 THR cc_start: 0.8568 (m) cc_final: 0.8200 (m) REVERT: C 151 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8006 (tt) REVERT: C 224 THR cc_start: 0.7315 (OUTLIER) cc_final: 0.7031 (p) REVERT: C 310 ASP cc_start: 0.8340 (m-30) cc_final: 0.8063 (m-30) REVERT: C 427 MET cc_start: 0.8452 (ptt) cc_final: 0.8202 (ptt) REVERT: D 52 LYS cc_start: 0.7706 (mmtm) cc_final: 0.7347 (pttp) REVERT: D 143 THR cc_start: 0.8569 (m) cc_final: 0.8202 (m) REVERT: D 151 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8012 (tt) REVERT: D 224 THR cc_start: 0.7304 (OUTLIER) cc_final: 0.7021 (p) REVERT: D 310 ASP cc_start: 0.8340 (m-30) cc_final: 0.8064 (m-30) REVERT: D 385 ARG cc_start: 0.8120 (ttm110) cc_final: 0.7716 (ttm110) REVERT: D 427 MET cc_start: 0.8440 (ptt) cc_final: 0.8187 (ptt) outliers start: 45 outliers final: 29 residues processed: 226 average time/residue: 1.2420 time to fit residues: 304.0366 Evaluate side-chains 219 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 186 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 431 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 chunk 36 optimal weight: 0.0980 chunk 147 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 12 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12340 Z= 0.200 Angle : 0.512 6.930 16736 Z= 0.263 Chirality : 0.036 0.124 2056 Planarity : 0.003 0.031 2020 Dihedral : 3.728 13.749 1688 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.66 % Allowed : 17.23 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.39 (0.21), residues: 1520 helix: 3.10 (0.13), residues: 1236 sheet: 1.61 (0.62), residues: 40 loop : -2.71 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 193 HIS 0.002 0.001 HIS B 392 PHE 0.016 0.001 PHE A 205 TYR 0.022 0.001 TYR D 124 ARG 0.004 0.000 ARG B 405 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 192 time to evaluate : 1.223 Fit side-chains REVERT: A 310 ASP cc_start: 0.8324 (m-30) cc_final: 0.8049 (m-30) REVERT: B 129 VAL cc_start: 0.8377 (t) cc_final: 0.7969 (m) REVERT: B 310 ASP cc_start: 0.8338 (m-30) cc_final: 0.8060 (m-30) REVERT: B 387 MET cc_start: 0.9177 (mtm) cc_final: 0.8855 (mtm) REVERT: B 401 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7904 (tm-30) REVERT: C 52 LYS cc_start: 0.7726 (mmtm) cc_final: 0.7372 (pttp) REVERT: C 87 MET cc_start: 0.4032 (mtt) cc_final: 0.3032 (mtt) REVERT: C 143 THR cc_start: 0.8558 (m) cc_final: 0.8218 (m) REVERT: C 224 THR cc_start: 0.7261 (OUTLIER) cc_final: 0.6972 (p) REVERT: C 310 ASP cc_start: 0.8331 (m-30) cc_final: 0.8058 (m-30) REVERT: C 427 MET cc_start: 0.8446 (ptt) cc_final: 0.8186 (ptt) REVERT: D 52 LYS cc_start: 0.7728 (mmtm) cc_final: 0.7375 (pttp) REVERT: D 87 MET cc_start: 0.4086 (mtt) cc_final: 0.2927 (mtt) REVERT: D 143 THR cc_start: 0.8515 (m) cc_final: 0.8177 (m) REVERT: D 310 ASP cc_start: 0.8332 (m-30) cc_final: 0.8057 (m-30) REVERT: D 427 MET cc_start: 0.8446 (ptt) cc_final: 0.8186 (ptt) outliers start: 36 outliers final: 25 residues processed: 213 average time/residue: 1.2526 time to fit residues: 288.6344 Evaluate side-chains 215 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 189 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 431 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 chunk 82 optimal weight: 0.3980 chunk 146 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 202 GLN B 445 GLN C 202 GLN D 202 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12340 Z= 0.233 Angle : 0.542 9.290 16736 Z= 0.276 Chirality : 0.037 0.127 2056 Planarity : 0.004 0.031 2020 Dihedral : 3.801 13.887 1688 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.81 % Allowed : 17.68 % Favored : 79.51 % 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: 3.24 (0.21), residues: 1520 helix: 3.00 (0.13), residues: 1236 sheet: 1.67 (0.64), residues: 40 loop : -2.75 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 193 HIS 0.003 0.001 HIS B 392 PHE 0.017 0.002 PHE A 205 TYR 0.023 0.001 TYR B 124 ARG 0.004 0.000 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 195 time to evaluate : 1.374 Fit side-chains REVERT: A 296 ARG cc_start: 0.8164 (mtt90) cc_final: 0.7922 (mtt-85) REVERT: A 310 ASP cc_start: 0.8360 (m-30) cc_final: 0.8129 (m-30) REVERT: B 87 MET cc_start: 0.4043 (mtt) cc_final: 0.2946 (mtt) REVERT: B 310 ASP cc_start: 0.8344 (m-30) cc_final: 0.8053 (m-30) REVERT: B 387 MET cc_start: 0.9193 (mtm) cc_final: 0.8897 (mtm) REVERT: B 401 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7931 (tm-30) REVERT: C 87 MET cc_start: 0.3903 (mtt) cc_final: 0.2898 (mtt) REVERT: C 143 THR cc_start: 0.8557 (m) cc_final: 0.8208 (m) REVERT: C 151 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7949 (tt) REVERT: C 224 THR cc_start: 0.7370 (OUTLIER) cc_final: 0.7133 (p) REVERT: C 296 ARG cc_start: 0.8154 (mtt90) cc_final: 0.7908 (mtt-85) REVERT: C 310 ASP cc_start: 0.8361 (m-30) cc_final: 0.8130 (m-30) REVERT: C 427 MET cc_start: 0.8438 (ptt) cc_final: 0.8192 (ptt) REVERT: D 87 MET cc_start: 0.4102 (mtt) cc_final: 0.2967 (mtt) REVERT: D 143 THR cc_start: 0.8565 (m) cc_final: 0.8215 (m) REVERT: D 151 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7962 (tt) REVERT: D 296 ARG cc_start: 0.8168 (mtt90) cc_final: 0.7926 (mtt-85) REVERT: D 310 ASP cc_start: 0.8365 (m-30) cc_final: 0.8129 (m-30) REVERT: D 385 ARG cc_start: 0.8162 (ttm110) cc_final: 0.7753 (ttm110) REVERT: D 427 MET cc_start: 0.8438 (ptt) cc_final: 0.8188 (ptt) outliers start: 38 outliers final: 26 residues processed: 220 average time/residue: 1.3172 time to fit residues: 313.0447 Evaluate side-chains 211 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 182 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 431 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 99 optimal weight: 0.3980 chunk 72 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 445 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12340 Z= 0.254 Angle : 0.564 9.424 16736 Z= 0.287 Chirality : 0.037 0.135 2056 Planarity : 0.004 0.031 2020 Dihedral : 3.873 13.721 1688 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.59 % Allowed : 17.97 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.16 (0.21), residues: 1520 helix: 2.94 (0.13), residues: 1236 sheet: 1.73 (0.65), residues: 40 loop : -2.78 (0.34), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 193 HIS 0.003 0.001 HIS B 392 PHE 0.024 0.002 PHE A 444 TYR 0.023 0.001 TYR B 124 ARG 0.005 0.000 ARG D 405 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 186 time to evaluate : 1.418 Fit side-chains REVERT: A 171 MET cc_start: 0.7727 (mmp) cc_final: 0.7412 (mmm) REVERT: A 296 ARG cc_start: 0.8166 (mtt90) cc_final: 0.7928 (mtt-85) REVERT: A 310 ASP cc_start: 0.8362 (m-30) cc_final: 0.8142 (m-30) REVERT: B 87 MET cc_start: 0.4011 (mtt) cc_final: 0.2977 (mtt) REVERT: B 310 ASP cc_start: 0.8345 (m-30) cc_final: 0.8065 (m-30) REVERT: B 387 MET cc_start: 0.9197 (mtm) cc_final: 0.8897 (mtm) REVERT: B 401 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7901 (tm-30) REVERT: C 87 MET cc_start: 0.3871 (mtt) cc_final: 0.2869 (mtt) REVERT: C 143 THR cc_start: 0.8551 (m) cc_final: 0.8194 (m) REVERT: C 151 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7948 (tt) REVERT: C 224 THR cc_start: 0.7430 (OUTLIER) cc_final: 0.7168 (p) REVERT: C 296 ARG cc_start: 0.8164 (mtt90) cc_final: 0.7916 (mtt-85) REVERT: C 310 ASP cc_start: 0.8367 (m-30) cc_final: 0.8134 (m-30) REVERT: C 427 MET cc_start: 0.8441 (ptt) cc_final: 0.8197 (ptt) REVERT: D 87 MET cc_start: 0.4098 (mtt) cc_final: 0.2973 (mtt) REVERT: D 143 THR cc_start: 0.8559 (m) cc_final: 0.8201 (m) REVERT: D 151 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7952 (tt) REVERT: D 296 ARG cc_start: 0.8172 (mtt90) cc_final: 0.7924 (mtt-85) REVERT: D 310 ASP cc_start: 0.8371 (m-30) cc_final: 0.8131 (m-30) REVERT: D 385 ARG cc_start: 0.8176 (ttm110) cc_final: 0.7866 (ttp-110) REVERT: D 427 MET cc_start: 0.8439 (ptt) cc_final: 0.8197 (ptt) outliers start: 35 outliers final: 24 residues processed: 211 average time/residue: 1.3975 time to fit residues: 317.1954 Evaluate side-chains 209 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 182 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 431 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 129 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 144 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12340 Z= 0.255 Angle : 0.569 9.308 16736 Z= 0.290 Chirality : 0.038 0.140 2056 Planarity : 0.004 0.031 2020 Dihedral : 3.903 13.818 1688 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.66 % Allowed : 18.12 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.13 (0.21), residues: 1520 helix: 2.91 (0.13), residues: 1236 sheet: 1.74 (0.64), residues: 40 loop : -2.79 (0.33), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 193 HIS 0.003 0.001 HIS C 392 PHE 0.026 0.002 PHE A 444 TYR 0.023 0.002 TYR B 124 ARG 0.005 0.000 ARG B 405 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 187 time to evaluate : 1.224 Fit side-chains REVERT: A 171 MET cc_start: 0.7741 (mmp) cc_final: 0.7443 (mmm) REVERT: A 296 ARG cc_start: 0.8168 (mtt90) cc_final: 0.7927 (mtt-85) REVERT: A 310 ASP cc_start: 0.8352 (m-30) cc_final: 0.8128 (m-30) REVERT: B 310 ASP cc_start: 0.8344 (m-30) cc_final: 0.8049 (m-30) REVERT: B 387 MET cc_start: 0.9195 (mtm) cc_final: 0.8895 (mtm) REVERT: B 401 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7911 (tm-30) REVERT: C 52 LYS cc_start: 0.7652 (mmtm) cc_final: 0.7333 (pttp) REVERT: C 87 MET cc_start: 0.3860 (mtt) cc_final: 0.2866 (mtt) REVERT: C 143 THR cc_start: 0.8519 (m) cc_final: 0.8172 (m) REVERT: C 151 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7950 (tt) REVERT: C 224 THR cc_start: 0.7433 (OUTLIER) cc_final: 0.7175 (p) REVERT: C 296 ARG cc_start: 0.8168 (mtt90) cc_final: 0.7917 (mtt-85) REVERT: C 310 ASP cc_start: 0.8359 (m-30) cc_final: 0.8124 (m-30) REVERT: C 427 MET cc_start: 0.8439 (ptt) cc_final: 0.8197 (ptt) REVERT: C 445 GLN cc_start: 0.6749 (mp-120) cc_final: 0.6446 (mp10) REVERT: D 52 LYS cc_start: 0.7653 (mmtm) cc_final: 0.7334 (pttp) REVERT: D 87 MET cc_start: 0.4079 (mtt) cc_final: 0.2939 (mtt) REVERT: D 143 THR cc_start: 0.8526 (m) cc_final: 0.8179 (m) REVERT: D 151 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7956 (tt) REVERT: D 296 ARG cc_start: 0.8175 (mtt90) cc_final: 0.7927 (mtt-85) REVERT: D 310 ASP cc_start: 0.8361 (m-30) cc_final: 0.8121 (m-30) REVERT: D 385 ARG cc_start: 0.8179 (ttm110) cc_final: 0.7869 (ttp-110) REVERT: D 427 MET cc_start: 0.8438 (ptt) cc_final: 0.8197 (ptt) outliers start: 36 outliers final: 23 residues processed: 209 average time/residue: 1.3569 time to fit residues: 304.7898 Evaluate side-chains 207 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 181 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 431 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 93 optimal weight: 0.5980 chunk 73 optimal weight: 0.0770 chunk 95 optimal weight: 0.6980 chunk 128 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12340 Z= 0.238 Angle : 0.558 10.144 16736 Z= 0.286 Chirality : 0.037 0.144 2056 Planarity : 0.004 0.031 2020 Dihedral : 3.883 13.625 1688 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.92 % Allowed : 18.79 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.14 (0.21), residues: 1520 helix: 2.92 (0.14), residues: 1236 sheet: 1.79 (0.64), residues: 40 loop : -2.79 (0.33), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 193 HIS 0.003 0.001 HIS B 392 PHE 0.023 0.002 PHE A 444 TYR 0.022 0.001 TYR A 124 ARG 0.004 0.000 ARG A 405 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 186 time to evaluate : 1.282 Fit side-chains REVERT: A 52 LYS cc_start: 0.7635 (mmtm) cc_final: 0.7312 (pttp) REVERT: A 171 MET cc_start: 0.7649 (mmp) cc_final: 0.7354 (mmm) REVERT: A 296 ARG cc_start: 0.8163 (mtt90) cc_final: 0.7919 (mtt-85) REVERT: A 310 ASP cc_start: 0.8355 (m-30) cc_final: 0.8128 (m-30) REVERT: B 52 LYS cc_start: 0.7644 (mmtm) cc_final: 0.7313 (pttp) REVERT: B 310 ASP cc_start: 0.8340 (m-30) cc_final: 0.8054 (m-30) REVERT: B 387 MET cc_start: 0.9185 (mtm) cc_final: 0.8879 (mtm) REVERT: B 401 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7909 (tm-30) REVERT: C 52 LYS cc_start: 0.7684 (mmtm) cc_final: 0.7361 (pttp) REVERT: C 87 MET cc_start: 0.3843 (mtt) cc_final: 0.2855 (mtt) REVERT: C 143 THR cc_start: 0.8515 (m) cc_final: 0.8176 (m) REVERT: C 151 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7941 (tt) REVERT: C 224 THR cc_start: 0.7375 (OUTLIER) cc_final: 0.7135 (p) REVERT: C 296 ARG cc_start: 0.8164 (mtt90) cc_final: 0.7912 (mtt-85) REVERT: C 310 ASP cc_start: 0.8364 (m-30) cc_final: 0.8136 (m-30) REVERT: C 427 MET cc_start: 0.8438 (ptt) cc_final: 0.8190 (ptt) REVERT: D 52 LYS cc_start: 0.7683 (mmtm) cc_final: 0.7362 (pttp) REVERT: D 87 MET cc_start: 0.4059 (mtt) cc_final: 0.2914 (mtt) REVERT: D 143 THR cc_start: 0.8521 (m) cc_final: 0.8183 (m) REVERT: D 151 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7947 (tt) REVERT: D 296 ARG cc_start: 0.8171 (mtt90) cc_final: 0.7924 (mtt-85) REVERT: D 310 ASP cc_start: 0.8366 (m-30) cc_final: 0.8135 (m-30) REVERT: D 385 ARG cc_start: 0.8159 (ttm110) cc_final: 0.7856 (ttp-110) REVERT: D 427 MET cc_start: 0.8436 (ptt) cc_final: 0.8191 (ptt) outliers start: 26 outliers final: 22 residues processed: 202 average time/residue: 1.4607 time to fit residues: 318.3955 Evaluate side-chains 206 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 181 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 431 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 0.0040 chunk 106 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.152096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.125141 restraints weight = 12750.114| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.29 r_work: 0.3274 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12340 Z= 0.217 Angle : 0.544 9.783 16736 Z= 0.279 Chirality : 0.037 0.140 2056 Planarity : 0.004 0.031 2020 Dihedral : 3.834 13.523 1688 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.00 % Allowed : 18.86 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.18 (0.21), residues: 1520 helix: 2.96 (0.14), residues: 1236 sheet: 1.81 (0.64), residues: 40 loop : -2.84 (0.33), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 193 HIS 0.002 0.001 HIS B 392 PHE 0.022 0.002 PHE B 444 TYR 0.021 0.001 TYR A 124 ARG 0.004 0.000 ARG D 405 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4864.59 seconds wall clock time: 86 minutes 24.63 seconds (5184.63 seconds total)