Starting phenix.real_space_refine on Thu Mar 13 18:31:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tpp_41480/03_2025/8tpp_41480.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tpp_41480/03_2025/8tpp_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tpp_41480/03_2025/8tpp_41480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tpp_41480/03_2025/8tpp_41480.map" model { file = "/net/cci-nas-00/data/ceres_data/8tpp_41480/03_2025/8tpp_41480.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tpp_41480/03_2025/8tpp_41480.cif" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 6, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 11, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 145 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 8.62, per 1000 atoms: 0.95 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: 2.31 Conformation dependent library (CDL) restraints added in 993.2 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: 0.90 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: 2.56 Time building geometry restraints manager: 2.71 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: 0.04 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: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.190 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 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= 0.175 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (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 TRP 0.009 0.001 TRP A 235 HIS 0.002 0.001 HIS A 611 PHE 0.014 0.001 PHE A 379 TYR 0.008 0.001 TYR A 188 ARG 0.006 0.000 ARG A 710 *********************** 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 : 1.024 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.1799 time to fit residues: 20.0990 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 : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.3980 chunk 87 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.128873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.103358 restraints weight = 13872.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.105364 restraints weight = 9304.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.106661 restraints weight = 7312.308| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.0875 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= 0.217 Angle : 0.525 6.940 12706 Z= 0.271 Chirality : 0.039 0.161 1446 Planarity : 0.004 0.038 1592 Dihedral : 3.617 14.959 1238 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.16 % Allowed : 22.51 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.25), residues: 1132 helix: 2.73 (0.18), residues: 806 sheet: -0.11 (0.81), residues: 44 loop : -1.08 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 235 HIS 0.004 0.001 HIS B 611 PHE 0.014 0.001 PHE A 379 TYR 0.010 0.001 TYR A 188 ARG 0.006 0.000 ARG B 710 *********************** 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: 20 poor density : 80 time to evaluate : 0.928 Fit side-chains REVERT: A 114 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7856 (tm-30) REVERT: A 125 LYS cc_start: 0.7577 (ttmt) cc_final: 0.7274 (tppt) REVERT: B 125 LYS cc_start: 0.7519 (ttmt) cc_final: 0.7278 (tppt) outliers start: 20 outliers final: 12 residues processed: 96 average time/residue: 0.1722 time to fit residues: 24.9588 Evaluate side-chains 83 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 34 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 32 optimal weight: 0.0020 chunk 25 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS A 359 ASN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 ASN A 633 GLN A 714 GLN B 359 ASN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.128412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.103092 restraints weight = 14023.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.105077 restraints weight = 9309.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.106349 restraints weight = 7289.823| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1087 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= 0.201 Angle : 0.508 6.272 12706 Z= 0.262 Chirality : 0.038 0.145 1446 Planarity : 0.003 0.034 1592 Dihedral : 3.628 14.460 1238 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.60 % Allowed : 22.08 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.25), residues: 1132 helix: 2.70 (0.18), residues: 806 sheet: 0.09 (0.79), residues: 44 loop : -1.12 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 235 HIS 0.003 0.001 HIS A 611 PHE 0.013 0.001 PHE A 379 TYR 0.010 0.001 TYR A 188 ARG 0.007 0.000 ARG B 710 *********************** 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 102 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.956 Fit side-chains REVERT: A 114 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7812 (tm-30) REVERT: A 125 LYS cc_start: 0.7557 (ttmt) cc_final: 0.7280 (tppt) REVERT: B 125 LYS cc_start: 0.7537 (ttmt) cc_final: 0.7304 (tppt) outliers start: 24 outliers final: 14 residues processed: 93 average time/residue: 0.1491 time to fit residues: 21.9655 Evaluate side-chains 85 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 509 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 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 67 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 7 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 77 optimal weight: 0.0980 chunk 94 optimal weight: 0.0270 chunk 97 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 435 ASN B 633 GLN B 714 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.131384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.106147 restraints weight = 13783.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.108213 restraints weight = 9172.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.109404 restraints weight = 7168.844| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9342 Z= 0.139 Angle : 0.471 6.229 12706 Z= 0.240 Chirality : 0.037 0.144 1446 Planarity : 0.003 0.033 1592 Dihedral : 3.538 14.902 1238 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.06 % Allowed : 23.05 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.25), residues: 1132 helix: 2.78 (0.18), residues: 808 sheet: 0.28 (0.81), residues: 44 loop : -1.22 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 235 HIS 0.002 0.000 HIS A 611 PHE 0.010 0.001 PHE A 379 TYR 0.009 0.001 TYR A 188 ARG 0.005 0.000 ARG B 710 *********************** 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: 19 poor density : 79 time to evaluate : 1.037 Fit side-chains REVERT: A 125 LYS cc_start: 0.7485 (ttmt) cc_final: 0.7215 (tppt) REVERT: B 125 LYS cc_start: 0.7501 (ttmt) cc_final: 0.7225 (tppt) outliers start: 19 outliers final: 13 residues processed: 92 average time/residue: 0.1773 time to fit residues: 24.7223 Evaluate side-chains 86 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 HIS 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 493 CYS Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain B residue 153 HIS 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 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 110 optimal weight: 3.9990 chunk 87 optimal weight: 0.2980 chunk 40 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 72 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3591 r_free = 0.3591 target = 0.129549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.104411 restraints weight = 13949.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.106450 restraints weight = 9313.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.107773 restraints weight = 7277.917| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1374 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= 0.180 Angle : 0.489 6.316 12706 Z= 0.249 Chirality : 0.037 0.144 1446 Planarity : 0.003 0.033 1592 Dihedral : 3.516 14.945 1238 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.03 % Allowed : 23.92 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.25), residues: 1132 helix: 2.76 (0.18), residues: 810 sheet: 0.33 (0.83), residues: 44 loop : -1.24 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 235 HIS 0.003 0.001 HIS A 611 PHE 0.012 0.001 PHE A 396 TYR 0.009 0.001 TYR A 188 ARG 0.007 0.000 ARG B 710 *********************** 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 103 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 1.027 Fit side-chains REVERT: A 125 LYS cc_start: 0.7504 (ttmt) cc_final: 0.7247 (tppt) REVERT: A 380 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.7057 (mtp) REVERT: A 701 MET cc_start: 0.5549 (OUTLIER) cc_final: 0.4994 (mtt) REVERT: B 125 LYS cc_start: 0.7509 (ttmt) cc_final: 0.7272 (tppt) REVERT: B 380 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6994 (mtp) outliers start: 28 outliers final: 18 residues processed: 92 average time/residue: 0.1777 time to fit residues: 26.1167 Evaluate side-chains 94 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 HIS 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 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 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 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 35 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 92 optimal weight: 0.4980 chunk 66 optimal weight: 10.0000 chunk 102 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 29 optimal weight: 0.0370 chunk 48 optimal weight: 0.1980 chunk 80 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3610 r_free = 0.3610 target = 0.131137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.106226 restraints weight = 13763.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.108237 restraints weight = 9078.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.109585 restraints weight = 7086.062| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9342 Z= 0.140 Angle : 0.473 6.273 12706 Z= 0.240 Chirality : 0.037 0.144 1446 Planarity : 0.003 0.033 1592 Dihedral : 3.480 14.698 1238 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.81 % Allowed : 24.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.25), residues: 1132 helix: 2.84 (0.17), residues: 810 sheet: 0.39 (0.84), residues: 44 loop : -1.35 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 235 HIS 0.002 0.001 HIS A 611 PHE 0.011 0.001 PHE A 379 TYR 0.009 0.001 TYR A 188 ARG 0.006 0.000 ARG A 710 *********************** 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 102 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 1.106 Fit side-chains REVERT: A 125 LYS cc_start: 0.7384 (ttmt) cc_final: 0.7176 (tppt) REVERT: A 380 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.7009 (mtp) REVERT: B 125 LYS cc_start: 0.7471 (ttmt) cc_final: 0.7244 (tppt) REVERT: B 380 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.6958 (mtp) outliers start: 26 outliers final: 14 residues processed: 94 average time/residue: 0.1563 time to fit residues: 23.3217 Evaluate side-chains 89 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 168 THR 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 627 LEU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 384 MET 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 62 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 114 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3588 r_free = 0.3588 target = 0.129283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.103897 restraints weight = 14154.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.105942 restraints weight = 9415.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.107276 restraints weight = 7366.130| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9342 Z= 0.194 Angle : 0.496 6.349 12706 Z= 0.253 Chirality : 0.037 0.144 1446 Planarity : 0.003 0.033 1592 Dihedral : 3.489 14.655 1238 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.38 % Allowed : 25.11 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.25), residues: 1132 helix: 2.79 (0.17), residues: 810 sheet: 0.52 (0.85), residues: 44 loop : -1.44 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 235 HIS 0.003 0.001 HIS B 611 PHE 0.013 0.001 PHE A 396 TYR 0.009 0.001 TYR A 188 ARG 0.005 0.000 ARG A 710 *********************** 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 98 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 1.017 Fit side-chains REVERT: A 125 LYS cc_start: 0.7497 (ttmt) cc_final: 0.7264 (tppt) REVERT: A 380 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.7053 (mtp) REVERT: B 125 LYS cc_start: 0.7507 (ttmt) cc_final: 0.7282 (tppt) REVERT: B 380 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.7013 (mtp) outliers start: 22 outliers final: 16 residues processed: 89 average time/residue: 0.1662 time to fit residues: 22.8077 Evaluate side-chains 91 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 290 LEU 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 575 THR Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain B residue 153 HIS 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 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 23 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 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 = 0.3571 r_free = 0.3571 target = 0.127958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.102786 restraints weight = 14208.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.104790 restraints weight = 9457.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.106083 restraints weight = 7392.525| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1581 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= 0.223 Angle : 0.521 6.801 12706 Z= 0.265 Chirality : 0.038 0.145 1446 Planarity : 0.003 0.033 1592 Dihedral : 3.543 14.716 1238 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.46 % Allowed : 24.03 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.25), residues: 1132 helix: 2.73 (0.17), residues: 810 sheet: 0.58 (0.85), residues: 44 loop : -1.46 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 159 HIS 0.004 0.001 HIS B 611 PHE 0.015 0.001 PHE A 396 TYR 0.010 0.001 TYR B 360 ARG 0.008 0.000 ARG B 710 *********************** 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 108 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 76 time to evaluate : 1.645 Fit side-chains REVERT: A 125 LYS cc_start: 0.7501 (ttmt) cc_final: 0.7258 (tppt) REVERT: A 263 TRP cc_start: 0.8006 (OUTLIER) cc_final: 0.7312 (p-90) REVERT: B 125 LYS cc_start: 0.7495 (ttmt) cc_final: 0.7265 (tppt) outliers start: 32 outliers final: 27 residues processed: 100 average time/residue: 0.1724 time to fit residues: 27.7988 Evaluate side-chains 101 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 615 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 705 ILE 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 384 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 31 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3554 r_free = 0.3554 target = 0.126566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.101349 restraints weight = 14102.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.103171 restraints weight = 9461.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.104502 restraints weight = 7458.828| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9342 Z= 0.275 Angle : 0.550 6.369 12706 Z= 0.282 Chirality : 0.039 0.145 1446 Planarity : 0.004 0.034 1592 Dihedral : 3.632 15.053 1238 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.00 % Allowed : 23.38 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.25), residues: 1132 helix: 2.59 (0.18), residues: 810 sheet: 0.59 (0.85), residues: 44 loop : -1.57 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 159 HIS 0.005 0.001 HIS B 611 PHE 0.018 0.001 PHE B 396 TYR 0.011 0.001 TYR A 360 ARG 0.007 0.000 ARG B 710 *********************** 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: 37 poor density : 74 time to evaluate : 1.040 Fit side-chains REVERT: A 125 LYS cc_start: 0.7515 (ttmt) cc_final: 0.7306 (tppt) REVERT: A 263 TRP cc_start: 0.8012 (OUTLIER) cc_final: 0.7336 (p-90) REVERT: B 263 TRP cc_start: 0.8013 (OUTLIER) cc_final: 0.7308 (p-90) outliers start: 37 outliers final: 33 residues processed: 103 average time/residue: 0.1532 time to fit residues: 24.9341 Evaluate side-chains 105 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 70 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 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 255 GLN 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 615 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain B residue 111 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 263 TRP 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 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 56 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3567 r_free = 0.3567 target = 0.127667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.102364 restraints weight = 14252.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.104379 restraints weight = 9488.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.105692 restraints weight = 7397.868| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9342 Z= 0.200 Angle : 0.525 6.285 12706 Z= 0.267 Chirality : 0.038 0.145 1446 Planarity : 0.003 0.035 1592 Dihedral : 3.638 14.989 1238 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.00 % Allowed : 23.27 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.25), residues: 1132 helix: 2.62 (0.17), residues: 810 sheet: 0.60 (0.85), residues: 44 loop : -1.57 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 235 HIS 0.003 0.001 HIS B 611 PHE 0.014 0.001 PHE A 396 TYR 0.010 0.001 TYR A 188 ARG 0.007 0.000 ARG B 710 ********************** 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 109 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 72 time to evaluate : 0.952 Fit side-chains REVERT: A 62 GLU cc_start: 0.7105 (mp0) cc_final: 0.6666 (mp0) REVERT: A 125 LYS cc_start: 0.7491 (ttmt) cc_final: 0.7249 (tppt) REVERT: A 263 TRP cc_start: 0.8024 (OUTLIER) cc_final: 0.7366 (p-90) REVERT: B 263 TRP cc_start: 0.8000 (OUTLIER) cc_final: 0.7330 (p-90) outliers start: 37 outliers final: 34 residues processed: 101 average time/residue: 0.1485 time to fit residues: 23.9995 Evaluate side-chains 107 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 71 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 111 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 255 GLN 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 615 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 111 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 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 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 109 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3559 r_free = 0.3559 target = 0.127052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.101848 restraints weight = 14183.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.103862 restraints weight = 9478.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.105189 restraints weight = 7399.360| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9342 Z= 0.232 Angle : 0.539 6.322 12706 Z= 0.275 Chirality : 0.038 0.144 1446 Planarity : 0.004 0.037 1592 Dihedral : 3.661 15.038 1238 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.00 % Allowed : 23.27 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.25), residues: 1132 helix: 2.58 (0.17), residues: 810 sheet: 0.57 (0.85), residues: 44 loop : -1.58 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 235 HIS 0.004 0.001 HIS B 611 PHE 0.016 0.001 PHE A 396 TYR 0.010 0.001 TYR A 188 ARG 0.007 0.000 ARG B 710 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2523.38 seconds wall clock time: 45 minutes 40.06 seconds (2740.06 seconds total)