Starting phenix.real_space_refine on Sat Jul 26 12:39:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ikv_60660/07_2025/9ikv_60660.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ikv_60660/07_2025/9ikv_60660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ikv_60660/07_2025/9ikv_60660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ikv_60660/07_2025/9ikv_60660.map" model { file = "/net/cci-nas-00/data/ceres_data/9ikv_60660/07_2025/9ikv_60660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ikv_60660/07_2025/9ikv_60660.cif" } resolution = 3.1 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= 0.001 sd= 0.006 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 I 4 10.91 5 S 66 5.16 5 C 5684 2.51 5 N 1380 2.21 5 O 1520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8654 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4323 Classifications: {'peptide': 562} Link IDs: {'PTRANS': 21, 'TRANS': 540} Chain breaks: 2 Chain: "B" Number of atoms: 4323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4323 Classifications: {'peptide': 562} Link IDs: {'PTRANS': 21, 'TRANS': 540} Chain breaks: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {'IOD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {'IOD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 5.85, per 1000 atoms: 0.68 Number of scatterers: 8654 At special positions: 0 Unit cell: (98.007, 119.547, 104.469, 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) I 4 52.95 S 66 16.00 O 1520 8.00 N 1380 7.00 C 5684 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: 2.58 Conformation dependent library (CDL) restraints added in 1.1 seconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 4 sheets defined 69.8% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 21 through 31 Processing helix chain 'A' and resid 33 through 38 removed outlier: 3.680A pdb=" N TRP A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 72 removed outlier: 3.951A pdb=" N VAL A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN A 60 " --> pdb=" O MET A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 82 removed outlier: 3.910A pdb=" N LEU A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 94 removed outlier: 3.546A pdb=" N ILE A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 119 removed outlier: 3.502A pdb=" N SER A 108 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASN A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 124 removed outlier: 3.696A pdb=" N MET A 123 " --> pdb=" O PRO A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 165 removed outlier: 3.593A pdb=" N VAL A 147 " --> pdb=" O GLN A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 removed outlier: 3.775A pdb=" N THR A 171 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N PHE A 172 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL A 173 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 174 " --> pdb=" O THR A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 194 Processing helix chain 'A' and resid 194 through 200 Processing helix chain 'A' and resid 210 through 222 removed outlier: 3.750A pdb=" N TYR A 216 " --> pdb=" O PHE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 226 removed outlier: 3.965A pdb=" N VAL A 226 " --> pdb=" O ILE A 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 223 through 226' Processing helix chain 'A' and resid 227 through 251 removed outlier: 3.731A pdb=" N GLU A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 275 Processing helix chain 'A' and resid 301 through 307 removed outlier: 4.371A pdb=" N SER A 306 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 335 removed outlier: 3.719A pdb=" N TYR A 320 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 356 removed outlier: 3.560A pdb=" N LEU A 345 " --> pdb=" O ASN A 341 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE A 356 " --> pdb=" O ILE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 376 removed outlier: 3.517A pdb=" N THR A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 396 removed outlier: 3.691A pdb=" N SER A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N CYS A 387 " --> pdb=" O CYS A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 425 through 434 removed outlier: 4.093A pdb=" N LYS A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 451 Processing helix chain 'A' and resid 452 through 470 Processing helix chain 'A' and resid 512 through 514 No H-bonds generated for 'chain 'A' and resid 512 through 514' Processing helix chain 'A' and resid 515 through 526 removed outlier: 3.832A pdb=" N MET A 526 " --> pdb=" O ASP A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 600 Processing helix chain 'A' and resid 611 through 621 removed outlier: 3.606A pdb=" N LYS A 615 " --> pdb=" O ALA A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 642 Processing helix chain 'B' and resid 22 through 31 Processing helix chain 'B' and resid 33 through 38 removed outlier: 3.674A pdb=" N TRP B 37 " --> pdb=" O PRO B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 72 removed outlier: 3.939A pdb=" N VAL B 59 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN B 60 " --> pdb=" O MET B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 82 removed outlier: 4.212A pdb=" N GLY B 79 " --> pdb=" O HIS B 75 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU B 80 " --> pdb=" O PRO B 76 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR B 81 " --> pdb=" O VAL B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 94 removed outlier: 3.526A pdb=" N ILE B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 119 removed outlier: 3.515A pdb=" N SER B 108 " --> pdb=" O PHE B 104 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASN B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA B 114 " --> pdb=" O ILE B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 124 removed outlier: 3.672A pdb=" N MET B 123 " --> pdb=" O PRO B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 165 removed outlier: 3.639A pdb=" N VAL B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 194 Processing helix chain 'B' and resid 194 through 200 Processing helix chain 'B' and resid 210 through 222 removed outlier: 3.825A pdb=" N TYR B 216 " --> pdb=" O PHE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 226 removed outlier: 3.976A pdb=" N VAL B 226 " --> pdb=" O ILE B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 223 through 226' Processing helix chain 'B' and resid 227 through 251 removed outlier: 3.832A pdb=" N GLU B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 250 " --> pdb=" O GLU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 335 removed outlier: 3.816A pdb=" N TYR B 320 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 326 " --> pdb=" O ALA B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 356 removed outlier: 3.545A pdb=" N LEU B 345 " --> pdb=" O ASN B 341 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE B 356 " --> pdb=" O ILE B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 376 removed outlier: 3.620A pdb=" N THR B 369 " --> pdb=" O ALA B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 396 removed outlier: 3.725A pdb=" N SER B 386 " --> pdb=" O ALA B 382 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N CYS B 387 " --> pdb=" O CYS B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 417 Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 425 through 434 removed outlier: 4.049A pdb=" N LYS B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 451 Processing helix chain 'B' and resid 452 through 471 Processing helix chain 'B' and resid 515 through 526 removed outlier: 3.799A pdb=" N MET B 526 " --> pdb=" O ASP B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 600 Processing helix chain 'B' and resid 611 through 621 removed outlier: 3.731A pdb=" N LYS B 615 " --> pdb=" O ALA B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 642 Processing sheet with id=AA1, first strand: chain 'A' and resid 101 through 102 removed outlier: 3.517A pdb=" N ALA A 363 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 478 through 481 removed outlier: 4.349A pdb=" N ILE A 504 " --> pdb=" O LYS A 481 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AA4, first strand: chain 'B' and resid 478 through 481 removed outlier: 4.308A pdb=" N ILE B 504 " --> pdb=" O LYS B 481 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU B 572 " --> pdb=" O LEU B 605 " (cutoff:3.500A) 517 hydrogen bonds defined for protein. 1524 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: 2.24 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2642 1.35 - 1.46: 2145 1.46 - 1.58: 3949 1.58 - 1.70: 0 1.70 - 1.82: 104 Bond restraints: 8840 Sorted by residual: bond pdb=" CB GLU A 249 " pdb=" CG GLU A 249 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.09e+00 bond pdb=" CB GLU B 22 " pdb=" CG GLU B 22 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.05e+00 bond pdb=" CA LEU A 135 " pdb=" C LEU A 135 " ideal model delta sigma weight residual 1.532 1.521 0.011 1.12e-02 7.97e+03 9.63e-01 bond pdb=" CB GLU B 249 " pdb=" CG GLU B 249 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.23e-01 bond pdb=" CG GLU B 22 " pdb=" CD GLU B 22 " ideal model delta sigma weight residual 1.516 1.535 -0.019 2.50e-02 1.60e+03 5.80e-01 ... (remaining 8835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 11786 1.70 - 3.41: 185 3.41 - 5.11: 38 5.11 - 6.81: 16 6.81 - 8.51: 3 Bond angle restraints: 12028 Sorted by residual: angle pdb=" C LEU A 135 " pdb=" CA LEU A 135 " pdb=" CB LEU A 135 " ideal model delta sigma weight residual 116.34 110.27 6.07 1.40e+00 5.10e-01 1.88e+01 angle pdb=" N ILE B 397 " pdb=" CA ILE B 397 " pdb=" C ILE B 397 " ideal model delta sigma weight residual 111.91 108.67 3.24 8.90e-01 1.26e+00 1.33e+01 angle pdb=" N ILE A 397 " pdb=" CA ILE A 397 " pdb=" C ILE A 397 " ideal model delta sigma weight residual 111.91 109.17 2.74 8.90e-01 1.26e+00 9.48e+00 angle pdb=" C PHE B 93 " pdb=" N GLY B 94 " pdb=" CA GLY B 94 " ideal model delta sigma weight residual 122.66 119.78 2.88 9.80e-01 1.04e+00 8.66e+00 angle pdb=" N GLY A 136 " pdb=" CA GLY A 136 " pdb=" C GLY A 136 " ideal model delta sigma weight residual 115.80 110.78 5.02 1.74e+00 3.30e-01 8.31e+00 ... (remaining 12023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 4665 18.02 - 36.04: 428 36.04 - 54.07: 88 54.07 - 72.09: 12 72.09 - 90.11: 5 Dihedral angle restraints: 5198 sinusoidal: 1930 harmonic: 3268 Sorted by residual: dihedral pdb=" CA LEU B 165 " pdb=" C LEU B 165 " pdb=" N GLN B 166 " pdb=" CA GLN B 166 " ideal model delta harmonic sigma weight residual -180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA LEU A 165 " pdb=" C LEU A 165 " pdb=" N GLN A 166 " pdb=" CA GLN A 166 " ideal model delta harmonic sigma weight residual -180.00 -160.01 -19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA GLN A 292 " pdb=" C GLN A 292 " pdb=" N GLY A 293 " pdb=" CA GLY A 293 " ideal model delta harmonic sigma weight residual 180.00 -162.02 -17.98 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 5195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 660 0.025 - 0.051: 505 0.051 - 0.076: 201 0.076 - 0.102: 54 0.102 - 0.127: 32 Chirality restraints: 1452 Sorted by residual: chirality pdb=" CA ILE B 507 " pdb=" N ILE B 507 " pdb=" C ILE B 507 " pdb=" CB ILE B 507 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 chirality pdb=" CA ILE B 505 " pdb=" N ILE B 505 " pdb=" C ILE B 505 " pdb=" CB ILE B 505 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA ILE A 507 " pdb=" N ILE A 507 " pdb=" C ILE A 507 " pdb=" CB ILE A 507 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.70e-01 ... (remaining 1449 not shown) Planarity restraints: 1472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 300 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO A 301 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 301 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 301 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 360 " 0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO B 361 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 361 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 361 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 360 " -0.020 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO A 361 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 361 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 361 " -0.017 5.00e-02 4.00e+02 ... (remaining 1469 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.76: 1493 2.76 - 3.31: 8692 3.31 - 3.86: 14857 3.86 - 4.41: 18091 4.41 - 4.96: 30943 Nonbonded interactions: 74076 Sorted by model distance: nonbonded pdb=" OH TYR B 520 " pdb=" OD2 ASP B 596 " model vdw 2.208 3.040 nonbonded pdb=" OH TYR A 520 " pdb=" OD2 ASP A 596 " model vdw 2.237 3.040 nonbonded pdb=" O SER B 350 " pdb=" OG SER B 354 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR B 41 " pdb=" O ASN B 46 " model vdw 2.263 3.040 nonbonded pdb=" OG SER A 330 " pdb=" OH TYR A 336 " model vdw 2.270 3.040 ... (remaining 74071 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: 0.05 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.630 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 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 : 0.004 0.034 8840 Z= 0.161 Angle : 0.611 8.515 12028 Z= 0.342 Chirality : 0.041 0.127 1452 Planarity : 0.003 0.036 1472 Dihedral : 14.586 90.111 3094 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 1.16 % Allowed : 14.81 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.26), residues: 1112 helix: 0.88 (0.20), residues: 738 sheet: -0.77 (0.84), residues: 32 loop : -1.95 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 27 HIS 0.004 0.001 HIS B 347 PHE 0.018 0.001 PHE B 251 TYR 0.015 0.001 TYR B 320 ARG 0.001 0.000 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.14960 ( 517) hydrogen bonds : angle 5.56008 ( 1524) covalent geometry : bond 0.00362 ( 8840) covalent geometry : angle 0.61091 (12028) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 1.067 Fit side-chains REVERT: A 251 PHE cc_start: 0.8196 (m-10) cc_final: 0.7810 (m-10) REVERT: A 583 ASP cc_start: 0.8934 (p0) cc_final: 0.8622 (p0) REVERT: B 22 GLU cc_start: 0.5860 (pm20) cc_final: 0.5478 (pm20) outliers start: 11 outliers final: 10 residues processed: 91 average time/residue: 0.2049 time to fit residues: 26.6983 Evaluate side-chains 90 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 271 PHE Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 407 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 84 optimal weight: 0.3980 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.112219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.088527 restraints weight = 5204.397| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 0.99 r_work: 0.2772 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.0705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8840 Z= 0.154 Angle : 0.550 6.363 12028 Z= 0.286 Chirality : 0.042 0.128 1452 Planarity : 0.004 0.040 1472 Dihedral : 5.361 54.890 1204 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.52 % Allowed : 12.82 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.26), residues: 1112 helix: 1.17 (0.20), residues: 732 sheet: -0.58 (0.85), residues: 32 loop : -1.86 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 27 HIS 0.004 0.001 HIS A 97 PHE 0.013 0.001 PHE A 447 TYR 0.014 0.001 TYR B 320 ARG 0.002 0.000 ARG A 368 Details of bonding type rmsd hydrogen bonds : bond 0.04604 ( 517) hydrogen bonds : angle 4.16022 ( 1524) covalent geometry : bond 0.00367 ( 8840) covalent geometry : angle 0.54996 (12028) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: A 251 PHE cc_start: 0.7891 (m-10) cc_final: 0.7618 (m-10) REVERT: B 481 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7907 (mtmt) outliers start: 24 outliers final: 16 residues processed: 95 average time/residue: 0.2193 time to fit residues: 29.5015 Evaluate side-chains 96 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 271 PHE Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 602 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 59 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.110642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.086416 restraints weight = 6158.085| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 1.10 r_work: 0.2765 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8840 Z= 0.171 Angle : 0.551 7.516 12028 Z= 0.285 Chirality : 0.042 0.128 1452 Planarity : 0.004 0.037 1472 Dihedral : 5.003 55.030 1198 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 2.94 % Allowed : 12.82 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.26), residues: 1112 helix: 1.20 (0.19), residues: 732 sheet: -0.55 (0.86), residues: 32 loop : -1.93 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 27 HIS 0.004 0.001 HIS B 97 PHE 0.015 0.001 PHE B 581 TYR 0.013 0.001 TYR B 320 ARG 0.001 0.000 ARG B 368 Details of bonding type rmsd hydrogen bonds : bond 0.04571 ( 517) hydrogen bonds : angle 4.04213 ( 1524) covalent geometry : bond 0.00417 ( 8840) covalent geometry : angle 0.55110 (12028) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.994 Fit side-chains REVERT: A 251 PHE cc_start: 0.7746 (m-10) cc_final: 0.7392 (m-10) REVERT: A 589 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8679 (mmt) REVERT: B 251 PHE cc_start: 0.8030 (m-10) cc_final: 0.7681 (m-10) REVERT: B 481 LYS cc_start: 0.8344 (mtmt) cc_final: 0.7986 (mtmt) outliers start: 28 outliers final: 23 residues processed: 98 average time/residue: 0.1957 time to fit residues: 27.5126 Evaluate side-chains 105 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 271 PHE Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 602 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 0.0470 chunk 24 optimal weight: 2.9990 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 GLN B 509 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.116713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.091944 restraints weight = 6110.534| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 1.19 r_work: 0.2737 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8840 Z= 0.103 Angle : 0.484 7.368 12028 Z= 0.250 Chirality : 0.039 0.129 1452 Planarity : 0.003 0.035 1472 Dihedral : 4.827 59.097 1197 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.73 % Allowed : 13.34 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.26), residues: 1112 helix: 1.49 (0.20), residues: 730 sheet: -0.74 (0.87), residues: 34 loop : -1.73 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 27 HIS 0.003 0.000 HIS B 347 PHE 0.011 0.001 PHE B 581 TYR 0.011 0.001 TYR A 320 ARG 0.001 0.000 ARG A 144 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 517) hydrogen bonds : angle 3.77278 ( 1524) covalent geometry : bond 0.00229 ( 8840) covalent geometry : angle 0.48449 (12028) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.993 Fit side-chains REVERT: A 60 GLN cc_start: 0.8741 (tt0) cc_final: 0.8533 (tt0) REVERT: A 176 GLU cc_start: 0.8374 (tt0) cc_final: 0.8127 (mt-10) REVERT: A 251 PHE cc_start: 0.7435 (m-10) cc_final: 0.7115 (m-10) outliers start: 26 outliers final: 17 residues processed: 105 average time/residue: 0.1949 time to fit residues: 29.3694 Evaluate side-chains 105 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 271 PHE Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 602 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 96 optimal weight: 0.0170 chunk 80 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 110 optimal weight: 9.9990 chunk 58 optimal weight: 0.0270 chunk 12 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 509 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.117699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.093043 restraints weight = 5692.826| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 1.15 r_work: 0.2769 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8840 Z= 0.097 Angle : 0.483 6.715 12028 Z= 0.248 Chirality : 0.039 0.181 1452 Planarity : 0.003 0.033 1472 Dihedral : 4.723 56.113 1197 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.42 % Allowed : 13.45 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.27), residues: 1112 helix: 1.62 (0.20), residues: 730 sheet: -0.53 (0.87), residues: 34 loop : -1.65 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 27 HIS 0.003 0.000 HIS B 347 PHE 0.025 0.001 PHE B 251 TYR 0.011 0.001 TYR A 320 ARG 0.000 0.000 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.03288 ( 517) hydrogen bonds : angle 3.70769 ( 1524) covalent geometry : bond 0.00209 ( 8840) covalent geometry : angle 0.48253 (12028) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.968 Fit side-chains REVERT: A 176 GLU cc_start: 0.8248 (tt0) cc_final: 0.7989 (mt-10) REVERT: A 251 PHE cc_start: 0.7408 (m-10) cc_final: 0.7101 (m-10) outliers start: 23 outliers final: 21 residues processed: 107 average time/residue: 0.2006 time to fit residues: 30.8262 Evaluate side-chains 110 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 271 PHE Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 602 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 5 optimal weight: 0.6980 chunk 95 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 58 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 509 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.119217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.094524 restraints weight = 6025.531| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.18 r_work: 0.2895 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8840 Z= 0.100 Angle : 0.478 6.192 12028 Z= 0.246 Chirality : 0.039 0.155 1452 Planarity : 0.003 0.033 1472 Dihedral : 4.610 49.367 1197 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.84 % Allowed : 13.76 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.27), residues: 1112 helix: 1.56 (0.20), residues: 744 sheet: -0.23 (0.89), residues: 34 loop : -1.69 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 27 HIS 0.003 0.000 HIS B 347 PHE 0.011 0.001 PHE B 581 TYR 0.011 0.001 TYR A 320 ARG 0.001 0.000 ARG B 31 Details of bonding type rmsd hydrogen bonds : bond 0.03293 ( 517) hydrogen bonds : angle 3.66247 ( 1524) covalent geometry : bond 0.00223 ( 8840) covalent geometry : angle 0.47778 (12028) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.992 Fit side-chains REVERT: A 45 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7847 (pm20) REVERT: A 176 GLU cc_start: 0.8198 (tt0) cc_final: 0.7937 (mt-10) REVERT: A 251 PHE cc_start: 0.7390 (m-10) cc_final: 0.7092 (m-10) REVERT: B 43 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8893 (pp) outliers start: 27 outliers final: 22 residues processed: 112 average time/residue: 0.1930 time to fit residues: 31.4663 Evaluate side-chains 115 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 271 PHE Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 602 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 100 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 509 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.117858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.093245 restraints weight = 5669.464| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 1.13 r_work: 0.2778 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8840 Z= 0.121 Angle : 0.500 6.277 12028 Z= 0.257 Chirality : 0.040 0.131 1452 Planarity : 0.003 0.033 1472 Dihedral : 4.594 49.427 1197 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 3.26 % Allowed : 13.87 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.26), residues: 1112 helix: 1.64 (0.20), residues: 730 sheet: -0.18 (0.90), residues: 34 loop : -1.60 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 27 HIS 0.003 0.000 HIS B 347 PHE 0.013 0.001 PHE A 581 TYR 0.010 0.001 TYR A 320 ARG 0.001 0.000 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 517) hydrogen bonds : angle 3.70752 ( 1524) covalent geometry : bond 0.00286 ( 8840) covalent geometry : angle 0.50046 (12028) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.954 Fit side-chains REVERT: A 45 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7727 (pm20) REVERT: A 176 GLU cc_start: 0.8270 (tt0) cc_final: 0.8021 (mt-10) REVERT: A 251 PHE cc_start: 0.7380 (m-10) cc_final: 0.7094 (m-10) REVERT: B 43 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8808 (pp) REVERT: B 250 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7958 (tm-30) REVERT: B 476 MET cc_start: 0.9177 (mmm) cc_final: 0.8887 (mmm) outliers start: 31 outliers final: 24 residues processed: 114 average time/residue: 0.1838 time to fit residues: 30.3766 Evaluate side-chains 117 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 271 PHE Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 602 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 13 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 509 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.115929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.090628 restraints weight = 6510.376| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.24 r_work: 0.2841 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8840 Z= 0.104 Angle : 0.493 10.961 12028 Z= 0.251 Chirality : 0.040 0.131 1452 Planarity : 0.003 0.033 1472 Dihedral : 4.511 49.865 1197 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.94 % Allowed : 14.08 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.27), residues: 1112 helix: 1.61 (0.20), residues: 738 sheet: -0.13 (0.91), residues: 34 loop : -1.58 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 27 HIS 0.003 0.000 HIS B 347 PHE 0.011 0.001 PHE B 581 TYR 0.010 0.001 TYR A 320 ARG 0.001 0.000 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 517) hydrogen bonds : angle 3.66394 ( 1524) covalent geometry : bond 0.00235 ( 8840) covalent geometry : angle 0.49319 (12028) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.960 Fit side-chains REVERT: A 45 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7740 (pm20) REVERT: A 176 GLU cc_start: 0.8269 (tt0) cc_final: 0.8027 (mt-10) REVERT: A 251 PHE cc_start: 0.7375 (m-10) cc_final: 0.7089 (m-10) REVERT: A 481 LYS cc_start: 0.8332 (mtpp) cc_final: 0.8002 (mtpt) REVERT: B 43 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8702 (pp) REVERT: B 250 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7964 (tm-30) REVERT: B 476 MET cc_start: 0.9171 (mmm) cc_final: 0.8884 (mmm) outliers start: 28 outliers final: 24 residues processed: 113 average time/residue: 0.1815 time to fit residues: 29.7343 Evaluate side-chains 118 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 271 PHE Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 602 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 87 optimal weight: 0.0270 chunk 93 optimal weight: 0.1980 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 509 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.109968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.082506 restraints weight = 6016.405| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 1.34 r_work: 0.2768 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8840 Z= 0.095 Angle : 0.482 9.672 12028 Z= 0.245 Chirality : 0.039 0.138 1452 Planarity : 0.003 0.032 1472 Dihedral : 4.415 50.642 1197 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.94 % Allowed : 14.18 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.27), residues: 1112 helix: 1.69 (0.20), residues: 742 sheet: 0.08 (0.93), residues: 34 loop : -1.61 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 27 HIS 0.003 0.000 HIS B 347 PHE 0.011 0.001 PHE B 581 TYR 0.011 0.001 TYR A 320 ARG 0.000 0.000 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.03133 ( 517) hydrogen bonds : angle 3.60561 ( 1524) covalent geometry : bond 0.00210 ( 8840) covalent geometry : angle 0.48169 (12028) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.984 Fit side-chains REVERT: A 45 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7748 (pm20) REVERT: A 176 GLU cc_start: 0.8274 (tt0) cc_final: 0.8023 (mt-10) REVERT: A 251 PHE cc_start: 0.7226 (m-10) cc_final: 0.6944 (m-10) REVERT: A 481 LYS cc_start: 0.8310 (mtpp) cc_final: 0.7973 (mtpt) REVERT: B 43 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8655 (pp) REVERT: B 250 GLN cc_start: 0.8331 (tm-30) cc_final: 0.7992 (tm-30) REVERT: B 476 MET cc_start: 0.9152 (mmm) cc_final: 0.8854 (mmm) REVERT: B 481 LYS cc_start: 0.8255 (mtmt) cc_final: 0.8027 (ptpp) outliers start: 28 outliers final: 24 residues processed: 113 average time/residue: 0.1821 time to fit residues: 29.8243 Evaluate side-chains 118 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 271 PHE Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 602 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 38 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 61 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 509 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.106361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.079008 restraints weight = 5758.522| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 1.31 r_work: 0.2786 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8840 Z= 0.151 Angle : 0.540 10.401 12028 Z= 0.272 Chirality : 0.041 0.161 1452 Planarity : 0.003 0.033 1472 Dihedral : 4.566 50.044 1197 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.94 % Allowed : 14.60 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.26), residues: 1112 helix: 1.64 (0.19), residues: 732 sheet: -0.02 (0.92), residues: 34 loop : -1.60 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 27 HIS 0.003 0.001 HIS A 97 PHE 0.013 0.001 PHE B 581 TYR 0.011 0.001 TYR B 320 ARG 0.001 0.000 ARG A 474 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 517) hydrogen bonds : angle 3.75060 ( 1524) covalent geometry : bond 0.00368 ( 8840) covalent geometry : angle 0.54021 (12028) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 1.117 Fit side-chains REVERT: A 176 GLU cc_start: 0.8485 (tt0) cc_final: 0.8246 (mt-10) REVERT: A 251 PHE cc_start: 0.7314 (m-10) cc_final: 0.6984 (m-10) REVERT: B 43 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8668 (pp) REVERT: B 250 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7834 (tm-30) REVERT: B 481 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7936 (ptpp) outliers start: 28 outliers final: 24 residues processed: 108 average time/residue: 0.1921 time to fit residues: 29.9715 Evaluate side-chains 115 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 271 PHE Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 602 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 73 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 96 optimal weight: 0.4980 chunk 54 optimal weight: 0.0020 chunk 47 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 28 optimal weight: 0.0040 chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 overall best weight: 0.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 509 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.116139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.089401 restraints weight = 5793.133| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.30 r_work: 0.2873 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8840 Z= 0.090 Angle : 0.489 9.874 12028 Z= 0.245 Chirality : 0.039 0.133 1452 Planarity : 0.003 0.032 1472 Dihedral : 4.432 50.790 1197 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.42 % Allowed : 15.13 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.27), residues: 1112 helix: 1.72 (0.20), residues: 742 sheet: 0.07 (0.93), residues: 34 loop : -1.53 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 441 HIS 0.003 0.000 HIS B 347 PHE 0.010 0.001 PHE B 581 TYR 0.010 0.001 TYR A 320 ARG 0.001 0.000 ARG B 253 Details of bonding type rmsd hydrogen bonds : bond 0.03076 ( 517) hydrogen bonds : angle 3.59879 ( 1524) covalent geometry : bond 0.00188 ( 8840) covalent geometry : angle 0.48931 (12028) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4254.60 seconds wall clock time: 73 minutes 48.21 seconds (4428.21 seconds total)