Starting phenix.real_space_refine on Thu Jul 2 15:35:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tpp_41480/07_2026/8tpp_41480.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tpp_41480/07_2026/8tpp_41480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tpp_41480/07_2026/8tpp_41480.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tpp_41480/07_2026/8tpp_41480.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tpp_41480/07_2026/8tpp_41480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tpp_41480/07_2026/8tpp_41480.map" } resolution = 3.64 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= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 38 5.16 5 C 5968 2.51 5 N 1524 2.21 5 O 1582 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9116 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4556 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 23, 'TRANS': 560} Chain breaks: 8 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ASN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 6, 'PHE:plan': 4, 'TRP:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 145 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Restraints were copied for chains: B Time building chain proxies: 2.96, per 1000 atoms: 0.32 Number of scatterers: 9116 At special positions: 0 Unit cell: (86.45, 139.23, 100.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 38 16.00 O 1582 8.00 N 1524 7.00 C 5968 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: 0.73 Conformation dependent library (CDL) restraints added in 256.6 milliseconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2220 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 74.1% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 32 through 47 Processing helix chain 'A' and resid 72 through 90 removed outlier: 3.552A pdb=" N PHE A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.728A pdb=" N ASP A 107 " --> pdb=" O GLN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 125 Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 152 through 164 Processing helix chain 'A' and resid 170 through 182 removed outlier: 3.701A pdb=" N ILE A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 199 removed outlier: 3.841A pdb=" N ALA A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 212 Processing helix chain 'A' and resid 217 through 246 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.637A pdb=" N ARG A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 319 removed outlier: 3.614A pdb=" N PHE A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 358 Proline residue: A 341 - end of helix Processing helix chain 'A' and resid 362 through 392 removed outlier: 5.143A pdb=" N ALA A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 408 Processing helix chain 'A' and resid 431 through 451 removed outlier: 3.923A pdb=" N ASN A 435 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR A 443 " --> pdb=" O TYR A 439 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE A 449 " --> pdb=" O GLN A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 465 removed outlier: 3.658A pdb=" N TYR A 457 " --> pdb=" O VAL A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 493 Processing helix chain 'A' and resid 500 through 518 removed outlier: 3.766A pdb=" N SER A 518 " --> pdb=" O VAL A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 545 removed outlier: 3.564A pdb=" N CYS A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG A 537 " --> pdb=" O TRP A 533 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 585 removed outlier: 3.626A pdb=" N ALA A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A 585 " --> pdb=" O TYR A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 625 Processing helix chain 'A' and resid 630 through 642 Processing helix chain 'A' and resid 701 through 715 Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'B' and resid 32 through 47 Processing helix chain 'B' and resid 72 through 90 removed outlier: 3.551A pdb=" N PHE B 76 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.728A pdb=" N ASP B 107 " --> pdb=" O GLN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 125 Processing helix chain 'B' and resid 126 through 130 Processing helix chain 'B' and resid 152 through 164 Processing helix chain 'B' and resid 170 through 182 removed outlier: 3.700A pdb=" N ILE B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 199 removed outlier: 3.841A pdb=" N ALA B 186 " --> pdb=" O GLY B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 Processing helix chain 'B' and resid 217 through 246 Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.637A pdb=" N ARG B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 319 removed outlier: 3.614A pdb=" N PHE B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 358 Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 362 through 392 removed outlier: 5.144A pdb=" N ALA B 385 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 408 Processing helix chain 'B' and resid 431 through 451 removed outlier: 3.922A pdb=" N ASN B 435 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR B 443 " --> pdb=" O TYR B 439 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA B 444 " --> pdb=" O PHE B 440 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE B 449 " --> pdb=" O GLN B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 465 removed outlier: 3.658A pdb=" N TYR B 457 " --> pdb=" O VAL B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 493 Processing helix chain 'B' and resid 500 through 518 removed outlier: 3.766A pdb=" N SER B 518 " --> pdb=" O VAL B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 545 removed outlier: 3.565A pdb=" N CYS B 527 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG B 537 " --> pdb=" O TRP B 533 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 585 removed outlier: 3.625A pdb=" N ALA B 564 " --> pdb=" O PRO B 560 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN B 585 " --> pdb=" O TYR B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 625 Processing helix chain 'B' and resid 630 through 642 Processing helix chain 'B' and resid 701 through 715 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 59 Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 267 removed outlier: 4.010A pdb=" N HIS A 265 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A 267 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 59 Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 267 removed outlier: 4.010A pdb=" N HIS B 265 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B 267 " --> pdb=" O VAL B 276 " (cutoff:3.500A) 648 hydrogen bonds defined for protein. 1902 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: 1.13 Time building geometry restraints manager: 0.97 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: 2860 1.34 - 1.46: 2385 1.46 - 1.58: 4035 1.58 - 1.70: 0 1.70 - 1.82: 62 Bond restraints: 9342 Sorted by residual: bond pdb=" C ILE B 201 " pdb=" N PRO B 202 " ideal model delta sigma weight residual 1.335 1.355 -0.020 1.28e-02 6.10e+03 2.44e+00 bond pdb=" C ILE A 201 " pdb=" N PRO A 202 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.28e-02 6.10e+03 2.31e+00 bond pdb=" C ILE A 394 " pdb=" N PRO A 395 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.20e-02 6.94e+03 2.20e+00 bond pdb=" C ILE B 394 " pdb=" N PRO B 395 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.20e-02 6.94e+03 2.17e+00 bond pdb=" CB GLU B 62 " pdb=" CG GLU B 62 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.11e+00 ... (remaining 9337 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 12366 1.36 - 2.72: 266 2.72 - 4.07: 50 4.07 - 5.43: 13 5.43 - 6.79: 11 Bond angle restraints: 12706 Sorted by residual: angle pdb=" N THR A 340 " pdb=" CA THR A 340 " pdb=" C THR A 340 " ideal model delta sigma weight residual 109.81 116.05 -6.24 2.21e+00 2.05e-01 7.98e+00 angle pdb=" N THR B 340 " pdb=" CA THR B 340 " pdb=" C THR B 340 " ideal model delta sigma weight residual 109.81 116.00 -6.19 2.21e+00 2.05e-01 7.85e+00 angle pdb=" CA GLU A 62 " pdb=" CB GLU A 62 " pdb=" CG GLU A 62 " ideal model delta sigma weight residual 114.10 118.87 -4.77 2.00e+00 2.50e-01 5.70e+00 angle pdb=" CA GLU B 62 " pdb=" CB GLU B 62 " pdb=" CG GLU B 62 " ideal model delta sigma weight residual 114.10 118.87 -4.77 2.00e+00 2.50e-01 5.69e+00 angle pdb=" N GLU A 264 " pdb=" CA GLU A 264 " pdb=" C GLU A 264 " ideal model delta sigma weight residual 112.93 109.97 2.96 1.33e+00 5.65e-01 4.94e+00 ... (remaining 12701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 4668 17.46 - 34.92: 594 34.92 - 52.38: 139 52.38 - 69.84: 23 69.84 - 87.30: 8 Dihedral angle restraints: 5432 sinusoidal: 2026 harmonic: 3406 Sorted by residual: dihedral pdb=" CG ARG B 490 " pdb=" CD ARG B 490 " pdb=" NE ARG B 490 " pdb=" CZ ARG B 490 " ideal model delta sinusoidal sigma weight residual 90.00 134.09 -44.09 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CG ARG A 490 " pdb=" CD ARG A 490 " pdb=" NE ARG A 490 " pdb=" CZ ARG A 490 " ideal model delta sinusoidal sigma weight residual 90.00 134.03 -44.03 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CG ARG B 284 " pdb=" CD ARG B 284 " pdb=" NE ARG B 284 " pdb=" CZ ARG B 284 " ideal model delta sinusoidal sigma weight residual 90.00 132.71 -42.71 2 1.50e+01 4.44e-03 9.81e+00 ... (remaining 5429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1159 0.045 - 0.091: 234 0.091 - 0.136: 49 0.136 - 0.181: 2 0.181 - 0.226: 2 Chirality restraints: 1446 Sorted by residual: chirality pdb=" CB VAL B 134 " pdb=" CA VAL B 134 " pdb=" CG1 VAL B 134 " pdb=" CG2 VAL B 134 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB VAL A 134 " pdb=" CA VAL A 134 " pdb=" CG1 VAL A 134 " pdb=" CG2 VAL A 134 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA THR A 340 " pdb=" N THR A 340 " pdb=" C THR A 340 " pdb=" CB THR A 340 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 1443 not shown) Planarity restraints: 1592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 62 " -0.007 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" CD GLU A 62 " 0.026 2.00e-02 2.50e+03 pdb=" OE1 GLU A 62 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU A 62 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 62 " 0.007 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" CD GLU B 62 " -0.026 2.00e-02 2.50e+03 pdb=" OE1 GLU B 62 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU B 62 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 201 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO B 202 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 202 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 202 " -0.021 5.00e-02 4.00e+02 ... (remaining 1589 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1617 2.76 - 3.30: 8695 3.30 - 3.83: 15211 3.83 - 4.37: 15299 4.37 - 4.90: 28303 Nonbonded interactions: 69125 Sorted by model distance: nonbonded pdb=" OH TYR B 188 " pdb=" OD2 ASP B 539 " model vdw 2.227 3.040 nonbonded pdb=" OH TYR A 188 " pdb=" OD2 ASP A 539 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR B 26 " pdb=" O ALA B 36 " model vdw 2.253 3.040 nonbonded pdb=" OH TYR A 26 " pdb=" O ALA A 36 " model vdw 2.253 3.040 nonbonded pdb=" OG1 THR B 555 " pdb=" O SER B 557 " model vdw 2.349 3.040 ... (remaining 69120 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 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: 9.390 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 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 0.032 9342 Z= 0.128 Angle : 0.526 6.790 12706 Z= 0.281 Chirality : 0.038 0.226 1446 Planarity : 0.004 0.036 1592 Dihedral : 16.551 87.300 3212 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.11 % Allowed : 23.92 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.18 (0.26), residues: 1132 helix: 2.43 (0.18), residues: 800 sheet: -0.42 (0.82), residues: 44 loop : -1.19 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 710 TYR 0.008 0.001 TYR A 188 PHE 0.014 0.001 PHE A 379 TRP 0.009 0.001 TRP A 235 HIS 0.002 0.001 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 9342) covalent geometry : angle 0.52646 / 0.28 (12706) hydrogen bonds : bond 0.13660 / 8.65 ( 648) hydrogen bonds : angle 5.53900 / 3.90 ( 1902) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.370 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.0752 time to fit residues: 8.4491 Evaluate side-chains 68 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.0980 chunk 100 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 ASN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 ASN A 698 GLN B 58 HIS B 359 ASN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.129664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.104182 restraints weight = 13970.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.106287 restraints weight = 9224.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.107395 restraints weight = 7163.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.108393 restraints weight = 6190.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.108583 restraints weight = 5621.382| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 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 0.037 9342 Z= 0.133 Angle : 0.514 6.834 12706 Z= 0.265 Chirality : 0.038 0.154 1446 Planarity : 0.004 0.036 1592 Dihedral : 3.574 15.042 1238 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.95 % Allowed : 22.62 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.68 (0.25), residues: 1132 helix: 2.78 (0.18), residues: 806 sheet: -0.12 (0.82), residues: 44 loop : -1.04 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 710 TYR 0.012 0.001 TYR A 188 PHE 0.013 0.001 PHE A 379 TRP 0.010 0.001 TRP A 235 HIS 0.003 0.001 HIS B 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 9342) covalent geometry : angle 0.51372 / 0.27 (12706) hydrogen bonds : bond 0.04570 / 3.08 ( 648) hydrogen bonds : angle 3.81179 / 2.72 ( 1902) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.293 Fit side-chains REVERT: A 114 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7776 (tm-30) REVERT: A 125 LYS cc_start: 0.7457 (ttmt) cc_final: 0.7208 (tppt) REVERT: B 125 LYS cc_start: 0.7418 (ttmt) cc_final: 0.7157 (tppt) outliers start: 18 outliers final: 12 residues processed: 96 average time/residue: 0.0738 time to fit residues: 10.6703 Evaluate side-chains 82 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 102 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 HIS A 359 ASN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 GLN A 714 GLN B 359 ASN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.128953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.103454 restraints weight = 13994.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.105526 restraints weight = 9314.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.106839 restraints weight = 7237.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.107682 restraints weight = 6219.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.107861 restraints weight = 5655.106| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9342 Z= 0.128 Angle : 0.501 6.280 12706 Z= 0.258 Chirality : 0.038 0.144 1446 Planarity : 0.003 0.033 1592 Dihedral : 3.591 14.494 1238 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.71 % Allowed : 22.73 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1132 helix: 2.71 (0.18), residues: 808 sheet: 0.10 (0.79), residues: 44 loop : -1.04 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 710 TYR 0.011 0.001 TYR A 188 PHE 0.013 0.001 PHE A 379 TRP 0.010 0.001 TRP A 235 HIS 0.003 0.001 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 9342) covalent geometry : angle 0.50111 / 0.26 (12706) hydrogen bonds : bond 0.04359 / 2.96 ( 648) hydrogen bonds : angle 3.56002 / 2.54 ( 1902) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.346 Fit side-chains REVERT: A 125 LYS cc_start: 0.7527 (ttmt) cc_final: 0.7273 (tppt) REVERT: A 482 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7737 (pm20) REVERT: B 125 LYS cc_start: 0.7509 (ttmt) cc_final: 0.7259 (tppt) outliers start: 25 outliers final: 13 residues processed: 93 average time/residue: 0.0589 time to fit residues: 8.9704 Evaluate side-chains 82 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 701 MET Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 70 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 0.0670 chunk 16 optimal weight: 0.7980 chunk 66 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 HIS A 359 ASN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 633 GLN B 714 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.129666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.104096 restraints weight = 14180.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.106234 restraints weight = 9368.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.107567 restraints weight = 7251.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.108247 restraints weight = 6213.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.108827 restraints weight = 5690.377| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9342 Z= 0.115 Angle : 0.487 6.274 12706 Z= 0.249 Chirality : 0.037 0.144 1446 Planarity : 0.003 0.033 1592 Dihedral : 3.565 14.895 1238 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.49 % Allowed : 23.05 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1132 helix: 2.73 (0.18), residues: 810 sheet: 0.26 (0.80), residues: 44 loop : -1.16 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 710 TYR 0.010 0.001 TYR A 188 PHE 0.012 0.001 PHE A 396 TRP 0.010 0.001 TRP A 235 HIS 0.003 0.001 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 9342) covalent geometry : angle 0.48747 / 0.25 (12706) hydrogen bonds : bond 0.04029 / 2.74 ( 648) hydrogen bonds : angle 3.39344 / 2.42 ( 1902) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.324 Fit side-chains REVERT: A 125 LYS cc_start: 0.7490 (ttmt) cc_final: 0.7247 (tppt) REVERT: A 482 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7780 (pm20) REVERT: B 125 LYS cc_start: 0.7503 (ttmt) cc_final: 0.7237 (tppt) outliers start: 23 outliers final: 17 residues processed: 92 average time/residue: 0.0638 time to fit residues: 9.1926 Evaluate side-chains 89 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 493 CYS Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 701 MET Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 8 optimal weight: 0.0970 chunk 87 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 44 optimal weight: 0.3980 chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 ASN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.128892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.103482 restraints weight = 14097.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.105514 restraints weight = 9299.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106847 restraints weight = 7237.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.107512 restraints weight = 6203.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.107761 restraints weight = 5690.604| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9342 Z= 0.127 Angle : 0.497 6.294 12706 Z= 0.254 Chirality : 0.038 0.145 1446 Planarity : 0.003 0.033 1592 Dihedral : 3.563 14.903 1238 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.14 % Allowed : 23.48 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1132 helix: 2.69 (0.18), residues: 810 sheet: 0.31 (0.82), residues: 44 loop : -1.26 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 710 TYR 0.010 0.001 TYR A 188 PHE 0.013 0.001 PHE A 396 TRP 0.010 0.001 TRP A 235 HIS 0.003 0.001 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 9342) covalent geometry : angle 0.49665 / 0.25 (12706) hydrogen bonds : bond 0.04146 / 2.82 ( 648) hydrogen bonds : angle 3.37676 / 2.41 ( 1902) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 0.271 Fit side-chains REVERT: A 125 LYS cc_start: 0.7486 (ttmt) cc_final: 0.7221 (tppt) REVERT: A 482 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7797 (pm20) REVERT: A 701 MET cc_start: 0.5475 (OUTLIER) cc_final: 0.4913 (mtt) REVERT: B 125 LYS cc_start: 0.7506 (ttmt) cc_final: 0.7263 (tppt) REVERT: B 380 MET cc_start: 0.7229 (OUTLIER) cc_final: 0.7028 (mtp) outliers start: 29 outliers final: 21 residues processed: 91 average time/residue: 0.0561 time to fit residues: 7.9947 Evaluate side-chains 95 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 701 MET Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 114 optimal weight: 0.0980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 ASN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 HIS B 359 ASN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.128155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.102659 restraints weight = 14122.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.104652 restraints weight = 9350.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105973 restraints weight = 7304.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.106545 restraints weight = 6284.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.107218 restraints weight = 5794.865| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9342 Z= 0.138 Angle : 0.505 6.304 12706 Z= 0.259 Chirality : 0.038 0.145 1446 Planarity : 0.003 0.034 1592 Dihedral : 3.591 14.993 1238 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.25 % Allowed : 23.92 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.43 (0.25), residues: 1132 helix: 2.62 (0.18), residues: 812 sheet: 0.46 (0.84), residues: 44 loop : -1.46 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 710 TYR 0.010 0.001 TYR A 188 PHE 0.014 0.001 PHE A 396 TRP 0.010 0.001 TRP A 235 HIS 0.004 0.001 HIS B 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 9342) covalent geometry : angle 0.50544 / 0.26 (12706) hydrogen bonds : bond 0.04298 / 2.92 ( 648) hydrogen bonds : angle 3.38510 / 2.42 ( 1902) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 75 time to evaluate : 0.296 Fit side-chains REVERT: A 125 LYS cc_start: 0.7511 (ttmt) cc_final: 0.7293 (tppt) REVERT: A 482 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7836 (pm20) REVERT: B 125 LYS cc_start: 0.7524 (ttmt) cc_final: 0.7292 (tppt) outliers start: 30 outliers final: 23 residues processed: 96 average time/residue: 0.0565 time to fit residues: 8.8096 Evaluate side-chains 94 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 516 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 701 MET Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 68 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 ASN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.126181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.100638 restraints weight = 14221.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.102649 restraints weight = 9564.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.103751 restraints weight = 7486.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.104672 restraints weight = 6496.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.104852 restraints weight = 5921.345| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9342 Z= 0.177 Angle : 0.548 6.318 12706 Z= 0.282 Chirality : 0.039 0.146 1446 Planarity : 0.004 0.034 1592 Dihedral : 3.714 15.099 1238 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.11 % Allowed : 23.38 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.25 (0.25), residues: 1132 helix: 2.50 (0.18), residues: 812 sheet: 0.56 (0.84), residues: 44 loop : -1.59 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 710 TYR 0.010 0.001 TYR A 188 PHE 0.017 0.001 PHE A 396 TRP 0.009 0.001 TRP B 159 HIS 0.004 0.001 HIS B 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 ( 9342) covalent geometry : angle 0.54836 / 0.28 (12706) hydrogen bonds : bond 0.04795 / 3.26 ( 648) hydrogen bonds : angle 3.47509 / 2.49 ( 1902) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 75 time to evaluate : 0.340 Fit side-chains REVERT: A 125 LYS cc_start: 0.7547 (ttmt) cc_final: 0.7333 (tppt) REVERT: A 482 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7897 (pm20) outliers start: 38 outliers final: 32 residues processed: 103 average time/residue: 0.0670 time to fit residues: 10.8390 Evaluate side-chains 101 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 68 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 141 TRP Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 516 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 701 MET Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 89 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 ASN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.127569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.101946 restraints weight = 14209.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.103926 restraints weight = 9428.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105017 restraints weight = 7403.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.105977 restraints weight = 6441.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.106221 restraints weight = 5870.217| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9342 Z= 0.133 Angle : 0.523 6.244 12706 Z= 0.267 Chirality : 0.038 0.145 1446 Planarity : 0.003 0.038 1592 Dihedral : 3.701 15.155 1238 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.33 % Allowed : 23.16 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.32 (0.25), residues: 1132 helix: 2.55 (0.18), residues: 810 sheet: 0.59 (0.85), residues: 44 loop : -1.50 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 710 TYR 0.011 0.001 TYR B 188 PHE 0.014 0.001 PHE A 396 TRP 0.011 0.001 TRP A 235 HIS 0.003 0.001 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 9342) covalent geometry : angle 0.52332 / 0.27 (12706) hydrogen bonds : bond 0.04394 / 2.99 ( 648) hydrogen bonds : angle 3.40402 / 2.43 ( 1902) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 69 time to evaluate : 0.305 Fit side-chains REVERT: A 125 LYS cc_start: 0.7491 (ttmt) cc_final: 0.7270 (tppt) REVERT: A 263 TRP cc_start: 0.8019 (OUTLIER) cc_final: 0.7353 (p-90) REVERT: A 482 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7870 (pm20) outliers start: 40 outliers final: 35 residues processed: 101 average time/residue: 0.0630 time to fit residues: 10.3442 Evaluate side-chains 106 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 69 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 141 TRP Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 516 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 701 MET Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 111 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 61 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 ASN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.127863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.103100 restraints weight = 14096.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.104971 restraints weight = 9670.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.106019 restraints weight = 7677.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.106882 restraints weight = 6694.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.107229 restraints weight = 6123.321| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9342 Z= 0.144 Angle : 0.527 6.269 12706 Z= 0.269 Chirality : 0.038 0.145 1446 Planarity : 0.003 0.038 1592 Dihedral : 3.704 15.143 1238 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.55 % Allowed : 22.94 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.29 (0.25), residues: 1132 helix: 2.52 (0.18), residues: 810 sheet: 0.61 (0.85), residues: 44 loop : -1.54 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 710 TYR 0.010 0.001 TYR B 188 PHE 0.015 0.001 PHE B 396 TRP 0.011 0.001 TRP A 235 HIS 0.004 0.001 HIS B 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 9342) covalent geometry : angle 0.52746 / 0.27 (12706) hydrogen bonds : bond 0.04440 / 3.02 ( 648) hydrogen bonds : angle 3.41043 / 2.44 ( 1902) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 69 time to evaluate : 0.280 Fit side-chains REVERT: A 263 TRP cc_start: 0.8032 (OUTLIER) cc_final: 0.7376 (p-90) REVERT: B 263 TRP cc_start: 0.7989 (OUTLIER) cc_final: 0.7330 (p-90) outliers start: 42 outliers final: 35 residues processed: 103 average time/residue: 0.0607 time to fit residues: 10.0750 Evaluate side-chains 105 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 68 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 141 TRP Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 263 TRP Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 516 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 701 MET Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 83 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 45 optimal weight: 0.0980 chunk 104 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 ASN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.128390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.102930 restraints weight = 14046.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.104900 restraints weight = 9339.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.106209 restraints weight = 7321.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106884 restraints weight = 6314.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.107175 restraints weight = 5786.013| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9342 Z= 0.120 Angle : 0.517 6.417 12706 Z= 0.263 Chirality : 0.038 0.150 1446 Planarity : 0.003 0.038 1592 Dihedral : 3.679 15.007 1238 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.68 % Allowed : 23.70 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.35 (0.25), residues: 1132 helix: 2.60 (0.18), residues: 810 sheet: 0.63 (0.86), residues: 44 loop : -1.62 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 710 TYR 0.011 0.001 TYR B 188 PHE 0.012 0.001 PHE B 396 TRP 0.012 0.001 TRP B 235 HIS 0.003 0.001 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 9342) covalent geometry : angle 0.51723 / 0.26 (12706) hydrogen bonds : bond 0.04118 / 2.81 ( 648) hydrogen bonds : angle 3.35205 / 2.40 ( 1902) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 73 time to evaluate : 0.344 Fit side-chains REVERT: A 263 TRP cc_start: 0.8035 (OUTLIER) cc_final: 0.7319 (p-90) REVERT: B 263 TRP cc_start: 0.7972 (OUTLIER) cc_final: 0.7236 (p-90) outliers start: 34 outliers final: 30 residues processed: 98 average time/residue: 0.0628 time to fit residues: 9.7992 Evaluate side-chains 100 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 141 TRP Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 263 TRP Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 516 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 701 MET Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 0.3980 chunk 10 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 77 optimal weight: 0.0470 chunk 87 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 105 optimal weight: 0.4980 chunk 91 optimal weight: 2.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 ASN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.129526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.104193 restraints weight = 13902.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.106192 restraints weight = 9249.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.107479 restraints weight = 7224.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.108119 restraints weight = 6252.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.108119 restraints weight = 5743.516| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9342 Z= 0.111 Angle : 0.518 6.445 12706 Z= 0.262 Chirality : 0.037 0.152 1446 Planarity : 0.003 0.038 1592 Dihedral : 3.635 14.846 1238 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.03 % Allowed : 24.35 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.42 (0.25), residues: 1132 helix: 2.64 (0.18), residues: 814 sheet: 0.56 (0.87), residues: 44 loop : -1.59 (0.34), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 710 TYR 0.011 0.001 TYR B 383 PHE 0.010 0.001 PHE A 396 TRP 0.013 0.001 TRP B 235 HIS 0.002 0.001 HIS B 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 9342) covalent geometry : angle 0.51803 / 0.26 (12706) hydrogen bonds : bond 0.03847 / 2.62 ( 648) hydrogen bonds : angle 3.31643 / 2.37 ( 1902) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1315.18 seconds wall clock time: 23 minutes 26.24 seconds (1406.24 seconds total)