Starting phenix.real_space_refine on Wed Aug 5 13:05:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/31ew_58351/08_2026/31ew_58351.cif Found real_map, /net/cci-nas-00/data/ceres_data/31ew_58351/08_2026/31ew_58351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/31ew_58351/08_2026/31ew_58351.map" default_real_map = "/net/cci-nas-00/data/ceres_data/31ew_58351/08_2026/31ew_58351.map" model { file = "/net/cci-nas-00/data/ceres_data/31ew_58351/08_2026/31ew_58351.cif" } default_model = "/net/cci-nas-00/data/ceres_data/31ew_58351/08_2026/31ew_58351.cif" } resolution = 2.06 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.007 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 72 5.16 5 C 6344 2.51 5 N 1246 2.21 5 O 2028 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9690 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3866 Classifications: {'peptide': 519} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 485} Chain: "B" Number of atoms: 3866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3866 Classifications: {'peptide': 519} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 485} Chain: "A" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 777 Unusual residues: {'DAO': 7, 'DGA': 2, 'ERG': 4, 'LMT': 7, 'MYR': 11, 'PLM': 3} Classifications: {'undetermined': 34} Link IDs: {None: 33} Chain: "B" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 777 Unusual residues: {'DAO': 7, 'DGA': 2, 'ERG': 4, 'LMT': 7, 'MYR': 11, 'PLM': 3} Classifications: {'undetermined': 34} Link IDs: {None: 33} Chain: "A" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 202 Classifications: {'water': 202} Link IDs: {None: 201} Chain: "B" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 202 Classifications: {'water': 202} Link IDs: {None: 201} Time building chain proxies: 1.73, per 1000 atoms: 0.18 Number of scatterers: 9690 At special positions: 0 Unit cell: (105.248, 109.664, 78.752, 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 72 16.00 O 2028 8.00 N 1246 7.00 C 6344 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 174 " - pdb=" SG CYS A 185 " distance=2.04 Simple disulfide: pdb=" SG CYS A 248 " - pdb=" SG CYS A 255 " distance=2.04 Simple disulfide: pdb=" SG CYS B 174 " - pdb=" SG CYS B 185 " distance=2.04 Simple disulfide: pdb=" SG CYS B 248 " - pdb=" SG CYS B 255 " distance=2.04 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: 0.84 Conformation dependent library (CDL) restraints added in 198.9 milliseconds 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 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: 48 helices and 4 sheets defined 72.2% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 28 through 36 removed outlier: 3.577A pdb=" N ALA A 32 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 46 through 52 removed outlier: 3.648A pdb=" N ARG A 52 " --> pdb=" O PHE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 105 removed outlier: 4.816A pdb=" N ALA A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N GLY A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Proline residue: A 97 - end of helix removed outlier: 3.533A pdb=" N LEU A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 133 Processing helix chain 'A' and resid 155 through 171 removed outlier: 3.718A pdb=" N SER A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 200 removed outlier: 3.823A pdb=" N TYR A 189 " --> pdb=" O CYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 207 removed outlier: 3.515A pdb=" N ILE A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'A' and resid 219 through 243 Proline residue: A 225 - end of helix removed outlier: 3.962A pdb=" N GLY A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N THR A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 289 Processing helix chain 'A' and resid 290 through 295 removed outlier: 3.754A pdb=" N SER A 295 " --> pdb=" O PRO A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 312 Processing helix chain 'A' and resid 316 through 323 removed outlier: 4.196A pdb=" N ILE A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 342 through 368 Processing helix chain 'A' and resid 374 through 398 removed outlier: 3.740A pdb=" N VAL A 393 " --> pdb=" O GLY A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 417 Processing helix chain 'A' and resid 420 through 437 Processing helix chain 'A' and resid 437 through 446 removed outlier: 4.264A pdb=" N ALA A 441 " --> pdb=" O PHE A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 472 removed outlier: 3.546A pdb=" N MET A 455 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 495 removed outlier: 3.794A pdb=" N THR A 495 " --> pdb=" O GLY A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 526 Processing helix chain 'A' and resid 526 through 542 removed outlier: 3.786A pdb=" N VAL A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 36 removed outlier: 3.710A pdb=" N THR B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 46 through 52 removed outlier: 3.654A pdb=" N ARG B 52 " --> pdb=" O PHE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 105 removed outlier: 4.865A pdb=" N ALA B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N GLY B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Proline residue: B 97 - end of helix removed outlier: 3.566A pdb=" N LEU B 105 " --> pdb=" O ILE B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 133 Processing helix chain 'B' and resid 155 through 171 removed outlier: 3.708A pdb=" N SER B 159 " --> pdb=" O PHE B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 200 removed outlier: 3.826A pdb=" N TYR B 189 " --> pdb=" O CYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 207 removed outlier: 3.509A pdb=" N ILE B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 Processing helix chain 'B' and resid 219 through 243 Proline residue: B 225 - end of helix removed outlier: 3.982A pdb=" N GLY B 236 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR B 237 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 289 Processing helix chain 'B' and resid 290 through 295 removed outlier: 3.725A pdb=" N SER B 295 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 312 Processing helix chain 'B' and resid 316 through 323 removed outlier: 4.215A pdb=" N ILE B 320 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'B' and resid 342 through 368 Processing helix chain 'B' and resid 374 through 398 removed outlier: 3.733A pdb=" N VAL B 393 " --> pdb=" O GLY B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 417 Processing helix chain 'B' and resid 420 through 437 Processing helix chain 'B' and resid 437 through 446 removed outlier: 4.248A pdb=" N ALA B 441 " --> pdb=" O PHE B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 472 removed outlier: 3.552A pdb=" N MET B 455 " --> pdb=" O VAL B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 495 removed outlier: 3.821A pdb=" N THR B 495 " --> pdb=" O GLY B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 526 Processing helix chain 'B' and resid 526 through 542 removed outlier: 3.821A pdb=" N VAL B 530 " --> pdb=" O THR B 526 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 152 Processing sheet with id=AA3, first strand: chain 'B' and resid 134 through 135 Processing sheet with id=AA4, first strand: chain 'B' and resid 151 through 152 522 hydrogen bonds defined for protein. 1536 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: 1.00 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1374 1.32 - 1.45: 2244 1.45 - 1.57: 5738 1.57 - 1.69: 0 1.69 - 1.81: 106 Bond restraints: 9462 Sorted by residual: bond pdb=" CG1 ILE A 307 " pdb=" CD1 ILE A 307 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.17e+00 bond pdb=" CG1 ILE B 307 " pdb=" CD1 ILE B 307 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.15e+00 bond pdb=" N LYS A 138 " pdb=" CA LYS A 138 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.55e+00 bond pdb=" N LYS B 138 " pdb=" CA LYS B 138 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.43e+00 bond pdb=" CB GLU A 178 " pdb=" CG GLU A 178 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.24e+00 ... (remaining 9457 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 12407 1.76 - 3.52: 197 3.52 - 5.28: 31 5.28 - 7.04: 10 7.04 - 8.80: 1 Bond angle restraints: 12646 Sorted by residual: angle pdb=" CA ILE A 307 " pdb=" CB ILE A 307 " pdb=" CG1 ILE A 307 " ideal model delta sigma weight residual 110.40 116.77 -6.37 1.70e+00 3.46e-01 1.40e+01 angle pdb=" CA ILE B 307 " pdb=" CB ILE B 307 " pdb=" CG1 ILE B 307 " ideal model delta sigma weight residual 110.40 116.72 -6.32 1.70e+00 3.46e-01 1.38e+01 angle pdb=" N ILE B 307 " pdb=" CA ILE B 307 " pdb=" CB ILE B 307 " ideal model delta sigma weight residual 110.54 115.47 -4.93 1.36e+00 5.41e-01 1.31e+01 angle pdb=" N ILE A 307 " pdb=" CA ILE A 307 " pdb=" CB ILE A 307 " ideal model delta sigma weight residual 110.54 115.40 -4.86 1.36e+00 5.41e-01 1.28e+01 angle pdb=" CB MET A 58 " pdb=" CG MET A 58 " pdb=" SD MET A 58 " ideal model delta sigma weight residual 112.70 121.50 -8.80 3.00e+00 1.11e-01 8.61e+00 ... (remaining 12641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 5957 17.65 - 35.30: 607 35.30 - 52.96: 137 52.96 - 70.61: 27 70.61 - 88.26: 8 Dihedral angle restraints: 6736 sinusoidal: 3784 harmonic: 2952 Sorted by residual: dihedral pdb=" CG ARG A 262 " pdb=" CD ARG A 262 " pdb=" NE ARG A 262 " pdb=" CZ ARG A 262 " ideal model delta sinusoidal sigma weight residual 90.00 40.08 49.92 2 1.50e+01 4.44e-03 1.25e+01 dihedral pdb=" CA MET A 90 " pdb=" C MET A 90 " pdb=" N LEU A 91 " pdb=" CA LEU A 91 " ideal model delta harmonic sigma weight residual -180.00 -164.07 -15.93 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA GLU B 521 " pdb=" CB GLU B 521 " pdb=" CG GLU B 521 " pdb=" CD GLU B 521 " ideal model delta sinusoidal sigma weight residual -60.00 -118.93 58.93 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 6733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1382 0.069 - 0.139: 112 0.139 - 0.208: 2 0.208 - 0.277: 0 0.277 - 0.346: 2 Chirality restraints: 1498 Sorted by residual: chirality pdb=" C1B LMT B 627 " pdb=" C2B LMT B 627 " pdb=" O1B LMT B 627 " pdb=" O5B LMT B 627 " both_signs ideal model delta sigma weight residual False -2.20 -1.85 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C1B LMT A 625 " pdb=" C2B LMT A 625 " pdb=" O1B LMT A 625 " pdb=" O5B LMT A 625 " both_signs ideal model delta sigma weight residual False -2.20 -1.86 -0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CB ILE B 307 " pdb=" CA ILE B 307 " pdb=" CG1 ILE B 307 " pdb=" CG2 ILE B 307 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.20e-01 ... (remaining 1495 not shown) Planarity restraints: 1418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 139 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO B 140 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 140 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 140 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 340 " 0.030 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO A 341 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 341 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 341 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 340 " -0.029 5.00e-02 4.00e+02 4.40e-02 3.09e+00 pdb=" N PRO B 341 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 341 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 341 " -0.025 5.00e-02 4.00e+02 ... (remaining 1415 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 4759 2.99 - 3.47: 9493 3.47 - 3.95: 16785 3.95 - 4.42: 19699 4.42 - 4.90: 28928 Nonbonded interactions: 79664 Sorted by model distance: nonbonded pdb=" O5' LMT A 625 " pdb=" O6' LMT A 625 " model vdw 2.513 2.432 nonbonded pdb=" O1B LMT B 627 " pdb=" O2B LMT B 627 " model vdw 2.540 2.432 nonbonded pdb=" O1B LMT A 625 " pdb=" O2B LMT A 625 " model vdw 2.542 2.432 nonbonded pdb=" N GLU A 178 " pdb=" OE1 GLU A 178 " model vdw 2.573 3.120 nonbonded pdb=" O GLN B 167 " pdb=" OD1 ASN B 171 " model vdw 2.588 3.040 ... (remaining 79659 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 601 or resid 609 or resid 611 or resid 613 thro \ ugh 614 or resid 623 or resid 629 through 630 or resid 632)) selection = (chain 'B' and (resid 28 through 601 or resid 609 or resid 611 or resid 613 thro \ ugh 614 or resid 623 or resid 629 through 630 or resid 632)) } 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: 3.640 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.510 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 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:8.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 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 0.069 9466 Z= 0.156 Angle : 0.584 8.801 12654 Z= 0.303 Chirality : 0.041 0.346 1498 Planarity : 0.005 0.051 1418 Dihedral : 14.038 88.259 4832 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.68 % Favored : 99.13 % Rotamer: Outliers : 0.72 % Allowed : 13.25 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.25), residues: 1034 helix: 1.93 (0.19), residues: 698 sheet: None (None), residues: 0 loop : 0.26 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 262 TYR 0.012 0.002 TYR B 137 PHE 0.017 0.002 PHE B 528 TRP 0.015 0.001 TRP B 242 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 ( 9462) covalent geometry : angle 0.58430 / 0.30 (12646) SS BOND : bond 0.00572 / 0.27 ( 4) SS BOND : angle 0.45865 / 0.25 ( 8) hydrogen bonds : bond 0.13471 / 8.65 ( 522) hydrogen bonds : angle 4.61173 / 3.31 ( 1536) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.224 Fit side-chains REVERT: A 525 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7821 (mt-10) REVERT: B 212 LYS cc_start: 0.8788 (mttm) cc_final: 0.8150 (mppt) REVERT: B 525 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7801 (mt-10) outliers start: 6 outliers final: 4 residues processed: 73 average time/residue: 0.6164 time to fit residues: 47.7142 Evaluate side-chains 72 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain B residue 526 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.120651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.086221 restraints weight = 11696.741| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.68 r_work: 0.2953 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.0418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9466 Z= 0.137 Angle : 0.529 6.733 12654 Z= 0.268 Chirality : 0.040 0.340 1498 Planarity : 0.005 0.047 1418 Dihedral : 10.640 67.981 3158 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.68 % Favored : 99.13 % Rotamer: Outliers : 0.84 % Allowed : 12.05 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.25), residues: 1034 helix: 2.14 (0.19), residues: 716 sheet: None (None), residues: 0 loop : 0.27 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 262 TYR 0.010 0.001 TYR B 492 PHE 0.014 0.001 PHE B 528 TRP 0.013 0.001 TRP B 242 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 ( 9462) covalent geometry : angle 0.52870 / 0.27 (12646) SS BOND : bond 0.00394 / 0.18 ( 4) SS BOND : angle 0.40155 / 0.22 ( 8) hydrogen bonds : bond 0.06888 / 4.53 ( 522) hydrogen bonds : angle 4.09113 / 2.93 ( 1536) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.349 Fit side-chains REVERT: B 212 LYS cc_start: 0.8876 (mttm) cc_final: 0.8206 (mppt) outliers start: 7 outliers final: 2 residues processed: 71 average time/residue: 0.6541 time to fit residues: 49.5554 Evaluate side-chains 64 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 87 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 171 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.122533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.089455 restraints weight = 11680.153| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.61 r_work: 0.3034 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.0638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9466 Z= 0.125 Angle : 0.510 6.644 12654 Z= 0.256 Chirality : 0.039 0.330 1498 Planarity : 0.005 0.049 1418 Dihedral : 10.013 59.665 3150 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.77 % Favored : 99.03 % Rotamer: Outliers : 0.60 % Allowed : 12.41 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.25), residues: 1034 helix: 2.30 (0.19), residues: 718 sheet: None (None), residues: 0 loop : 0.26 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 262 TYR 0.009 0.001 TYR A 492 PHE 0.015 0.001 PHE B 528 TRP 0.010 0.001 TRP B 242 HIS 0.002 0.000 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.13 ( 9462) covalent geometry : angle 0.50964 / 0.26 (12646) SS BOND : bond 0.00330 / 0.15 ( 4) SS BOND : angle 0.33029 / 0.18 ( 8) hydrogen bonds : bond 0.06171 / 4.07 ( 522) hydrogen bonds : angle 3.91977 / 2.82 ( 1536) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.338 Fit side-chains REVERT: B 38 ARG cc_start: 0.7328 (tpp-160) cc_final: 0.7109 (tmt170) REVERT: B 212 LYS cc_start: 0.8963 (mttm) cc_final: 0.8339 (mppt) outliers start: 5 outliers final: 3 residues processed: 67 average time/residue: 0.7312 time to fit residues: 52.1374 Evaluate side-chains 65 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 35 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.119031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.084406 restraints weight = 11655.696| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.69 r_work: 0.2922 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.0544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9466 Z= 0.152 Angle : 0.547 7.439 12654 Z= 0.279 Chirality : 0.041 0.329 1498 Planarity : 0.005 0.049 1418 Dihedral : 9.975 59.927 3150 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.87 % Favored : 98.94 % Rotamer: Outliers : 0.96 % Allowed : 11.81 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.25), residues: 1034 helix: 2.26 (0.19), residues: 716 sheet: None (None), residues: 0 loop : 0.28 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 262 TYR 0.012 0.002 TYR B 492 PHE 0.016 0.001 PHE B 528 TRP 0.011 0.001 TRP B 242 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 ( 9462) covalent geometry : angle 0.54688 / 0.28 (12646) SS BOND : bond 0.00533 / 0.25 ( 4) SS BOND : angle 0.45550 / 0.25 ( 8) hydrogen bonds : bond 0.07458 / 4.90 ( 522) hydrogen bonds : angle 4.05680 / 2.91 ( 1536) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.313 Fit side-chains REVERT: B 212 LYS cc_start: 0.8882 (mttm) cc_final: 0.8202 (mppt) outliers start: 8 outliers final: 4 residues processed: 67 average time/residue: 0.7270 time to fit residues: 51.7461 Evaluate side-chains 65 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 97 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.120613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.086417 restraints weight = 11665.321| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.70 r_work: 0.2959 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.0671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9466 Z= 0.130 Angle : 0.519 7.289 12654 Z= 0.263 Chirality : 0.039 0.325 1498 Planarity : 0.005 0.049 1418 Dihedral : 9.624 59.481 3150 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.68 % Favored : 99.13 % Rotamer: Outliers : 0.72 % Allowed : 11.81 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.25), residues: 1034 helix: 2.33 (0.19), residues: 718 sheet: None (None), residues: 0 loop : 0.25 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 262 TYR 0.010 0.001 TYR B 492 PHE 0.015 0.001 PHE A 528 TRP 0.008 0.001 TRP B 242 HIS 0.001 0.000 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 ( 9462) covalent geometry : angle 0.51957 / 0.26 (12646) SS BOND : bond 0.00369 / 0.17 ( 4) SS BOND : angle 0.35654 / 0.20 ( 8) hydrogen bonds : bond 0.06483 / 4.27 ( 522) hydrogen bonds : angle 3.93915 / 2.83 ( 1536) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.346 Fit side-chains REVERT: B 38 ARG cc_start: 0.7341 (tpp-160) cc_final: 0.7115 (tmt170) REVERT: B 212 LYS cc_start: 0.8883 (mttm) cc_final: 0.8208 (mppt) outliers start: 6 outliers final: 4 residues processed: 70 average time/residue: 0.6629 time to fit residues: 49.4163 Evaluate side-chains 65 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.118050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.083285 restraints weight = 11628.699| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.69 r_work: 0.2902 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.0636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9466 Z= 0.164 Angle : 0.567 7.420 12654 Z= 0.290 Chirality : 0.042 0.325 1498 Planarity : 0.005 0.050 1418 Dihedral : 9.799 58.774 3150 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.87 % Favored : 98.94 % Rotamer: Outliers : 0.96 % Allowed : 12.05 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.25), residues: 1034 helix: 2.20 (0.19), residues: 716 sheet: None (None), residues: 0 loop : 0.27 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 262 TYR 0.012 0.002 TYR B 492 PHE 0.016 0.002 PHE A 528 TRP 0.009 0.001 TRP A 242 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 9462) covalent geometry : angle 0.56671 / 0.29 (12646) SS BOND : bond 0.00619 / 0.29 ( 4) SS BOND : angle 0.50585 / 0.28 ( 8) hydrogen bonds : bond 0.07964 / 5.23 ( 522) hydrogen bonds : angle 4.11061 / 2.94 ( 1536) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.232 Fit side-chains REVERT: B 38 ARG cc_start: 0.7304 (tpp-160) cc_final: 0.7026 (tmt170) REVERT: B 212 LYS cc_start: 0.8880 (mttm) cc_final: 0.8196 (mppt) outliers start: 8 outliers final: 7 residues processed: 71 average time/residue: 0.5864 time to fit residues: 44.3062 Evaluate side-chains 68 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 526 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 30 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 15 optimal weight: 0.0970 chunk 56 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.121715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.087656 restraints weight = 11804.039| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.69 r_work: 0.2984 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 9466 Z= 0.123 Angle : 0.517 8.152 12654 Z= 0.260 Chirality : 0.039 0.319 1498 Planarity : 0.005 0.049 1418 Dihedral : 9.339 57.893 3150 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.68 % Favored : 99.13 % Rotamer: Outliers : 0.60 % Allowed : 12.65 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.25), residues: 1034 helix: 2.38 (0.19), residues: 718 sheet: None (None), residues: 0 loop : 0.28 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 262 TYR 0.009 0.001 TYR A 492 PHE 0.014 0.001 PHE A 528 TRP 0.007 0.001 TRP B 242 HIS 0.001 0.000 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 ( 9462) covalent geometry : angle 0.51698 / 0.26 (12646) SS BOND : bond 0.00314 / 0.15 ( 4) SS BOND : angle 0.29555 / 0.16 ( 8) hydrogen bonds : bond 0.05934 / 3.92 ( 522) hydrogen bonds : angle 3.87542 / 2.79 ( 1536) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.217 Fit side-chains REVERT: A 36 THR cc_start: 0.8471 (OUTLIER) cc_final: 0.8233 (t) REVERT: B 38 ARG cc_start: 0.7349 (tpp-160) cc_final: 0.7069 (ttt180) REVERT: B 212 LYS cc_start: 0.8878 (mttm) cc_final: 0.8208 (mppt) outliers start: 5 outliers final: 4 residues processed: 68 average time/residue: 0.5840 time to fit residues: 42.3396 Evaluate side-chains 67 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 96 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 317 HIS B 510 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.123794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.091923 restraints weight = 11813.008| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.51 r_work: 0.3091 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9466 Z= 0.132 Angle : 0.532 9.017 12654 Z= 0.268 Chirality : 0.039 0.316 1498 Planarity : 0.005 0.049 1418 Dihedral : 9.295 57.150 3150 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.77 % Favored : 99.03 % Rotamer: Outliers : 0.60 % Allowed : 12.89 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.25), residues: 1034 helix: 2.36 (0.19), residues: 718 sheet: None (None), residues: 0 loop : 0.30 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 262 TYR 0.010 0.001 TYR B 492 PHE 0.015 0.001 PHE A 528 TRP 0.008 0.001 TRP B 242 HIS 0.001 0.000 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 ( 9462) covalent geometry : angle 0.53186 / 0.27 (12646) SS BOND : bond 0.00368 / 0.17 ( 4) SS BOND : angle 0.35653 / 0.20 ( 8) hydrogen bonds : bond 0.06438 / 4.24 ( 522) hydrogen bonds : angle 3.92053 / 2.82 ( 1536) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.314 Fit side-chains REVERT: A 36 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8310 (t) REVERT: B 38 ARG cc_start: 0.7444 (tpp-160) cc_final: 0.7205 (tmt170) REVERT: B 212 LYS cc_start: 0.8994 (mttm) cc_final: 0.8410 (mppt) outliers start: 5 outliers final: 4 residues processed: 66 average time/residue: 0.5986 time to fit residues: 42.1259 Evaluate side-chains 66 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 31 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 50 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.122507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.089881 restraints weight = 11695.830| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.54 r_work: 0.3063 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9466 Z= 0.145 Angle : 0.553 8.974 12654 Z= 0.281 Chirality : 0.040 0.316 1498 Planarity : 0.005 0.049 1418 Dihedral : 9.384 58.391 3150 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.87 % Favored : 98.94 % Rotamer: Outliers : 0.72 % Allowed : 12.53 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.25), residues: 1034 helix: 2.32 (0.19), residues: 716 sheet: None (None), residues: 0 loop : 0.32 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 262 TYR 0.011 0.001 TYR B 492 PHE 0.016 0.001 PHE A 528 TRP 0.009 0.001 TRP B 242 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 9462) covalent geometry : angle 0.55303 / 0.28 (12646) SS BOND : bond 0.00463 / 0.22 ( 4) SS BOND : angle 0.41456 / 0.23 ( 8) hydrogen bonds : bond 0.07094 / 4.67 ( 522) hydrogen bonds : angle 4.01360 / 2.88 ( 1536) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.203 Fit side-chains REVERT: A 36 THR cc_start: 0.8566 (OUTLIER) cc_final: 0.8324 (t) REVERT: B 38 ARG cc_start: 0.7447 (tpp-160) cc_final: 0.7205 (tmt170) REVERT: B 212 LYS cc_start: 0.8999 (mttm) cc_final: 0.8397 (mppt) outliers start: 6 outliers final: 5 residues processed: 68 average time/residue: 0.6412 time to fit residues: 46.4799 Evaluate side-chains 67 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 526 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 47 optimal weight: 0.2980 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.121443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.088299 restraints weight = 11728.259| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.68 r_work: 0.2983 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9466 Z= 0.128 Angle : 0.529 9.510 12654 Z= 0.266 Chirality : 0.039 0.312 1498 Planarity : 0.005 0.048 1418 Dihedral : 9.124 57.354 3150 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.68 % Favored : 99.13 % Rotamer: Outliers : 0.60 % Allowed : 13.01 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.25), residues: 1034 helix: 2.38 (0.19), residues: 718 sheet: None (None), residues: 0 loop : 0.31 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 262 TYR 0.009 0.001 TYR A 492 PHE 0.015 0.001 PHE A 528 TRP 0.007 0.001 TRP B 242 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 ( 9462) covalent geometry : angle 0.52929 / 0.27 (12646) SS BOND : bond 0.00307 / 0.14 ( 4) SS BOND : angle 0.32636 / 0.18 ( 8) hydrogen bonds : bond 0.06091 / 4.01 ( 522) hydrogen bonds : angle 3.90368 / 2.81 ( 1536) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.198 Fit side-chains REVERT: B 38 ARG cc_start: 0.7250 (tpp-160) cc_final: 0.6905 (tmt170) REVERT: B 212 LYS cc_start: 0.8735 (mttm) cc_final: 0.7993 (mppt) outliers start: 5 outliers final: 4 residues processed: 67 average time/residue: 0.5811 time to fit residues: 41.4370 Evaluate side-chains 65 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 229 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 44 optimal weight: 0.0470 chunk 97 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 5 optimal weight: 0.5980 chunk 98 optimal weight: 0.0270 chunk 33 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.122319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.089170 restraints weight = 11747.301| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.61 r_work: 0.3036 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9466 Z= 0.129 Angle : 0.535 9.208 12654 Z= 0.270 Chirality : 0.039 0.308 1498 Planarity : 0.005 0.049 1418 Dihedral : 8.976 57.049 3150 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.77 % Favored : 99.03 % Rotamer: Outliers : 0.48 % Allowed : 12.89 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.66 (0.25), residues: 1034 helix: 2.39 (0.19), residues: 718 sheet: None (None), residues: 0 loop : 0.33 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 262 TYR 0.009 0.001 TYR B 492 PHE 0.015 0.001 PHE A 528 TRP 0.007 0.001 TRP B 242 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 ( 9462) covalent geometry : angle 0.53553 / 0.27 (12646) SS BOND : bond 0.00318 / 0.15 ( 4) SS BOND : angle 0.32949 / 0.18 ( 8) hydrogen bonds : bond 0.06150 / 4.05 ( 522) hydrogen bonds : angle 3.89769 / 2.80 ( 1536) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3670.83 seconds wall clock time: 63 minutes 7.96 seconds (3787.96 seconds total)