Starting phenix.real_space_refine on Wed Sep 17 12:09:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ikv_60660/09_2025/9ikv_60660.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ikv_60660/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ikv_60660/09_2025/9ikv_60660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ikv_60660/09_2025/9ikv_60660.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ikv_60660/09_2025/9ikv_60660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ikv_60660/09_2025/9ikv_60660.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.19, per 1000 atoms: 0.25 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: 0.70 Conformation dependent library (CDL) restraints added in 259.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.30 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: 1.45 Time building geometry restraints manager: 0.92 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.670 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.430 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.800 ------------------------------------------------------------------------------- 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 : 5.64 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG B 29 TYR 0.015 0.001 TYR B 320 PHE 0.018 0.001 PHE B 251 TRP 0.011 0.001 TRP B 27 HIS 0.004 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8840) covalent geometry : angle 0.61091 (12028) hydrogen bonds : bond 0.14960 ( 517) hydrogen bonds : angle 5.56008 ( 1524) *********************** 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 : 0.277 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: 0.0926 time to fit residues: 12.1411 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 : 0.358 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3237 r_free = 0.3237 target = 0.112743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.088683 restraints weight = 6146.769| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.10 r_work: 0.2803 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.0710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8840 Z= 0.131 Angle : 0.531 6.152 12028 Z= 0.275 Chirality : 0.041 0.128 1452 Planarity : 0.004 0.038 1472 Dihedral : 5.253 54.797 1204 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.21 % Allowed : 12.92 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.26), residues: 1112 helix: 1.27 (0.20), residues: 724 sheet: -0.51 (0.86), residues: 32 loop : -1.75 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 368 TYR 0.014 0.001 TYR B 320 PHE 0.012 0.001 PHE A 581 TRP 0.016 0.001 TRP B 27 HIS 0.004 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8840) covalent geometry : angle 0.53126 (12028) hydrogen bonds : bond 0.04440 ( 517) hydrogen bonds : angle 4.12911 ( 1524) *********************** 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 108 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 251 PHE cc_start: 0.7841 (m-10) cc_final: 0.7565 (m-10) REVERT: B 481 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8017 (mtmt) outliers start: 21 outliers final: 13 residues processed: 97 average time/residue: 0.0900 time to fit residues: 12.1827 Evaluate side-chains 94 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 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 271 PHE 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 90 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3321 r_free = 0.3321 target = 0.117130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.092311 restraints weight = 6363.519| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.23 r_work: 0.2870 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1041 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= 0.106 Angle : 0.490 6.916 12028 Z= 0.252 Chirality : 0.040 0.128 1452 Planarity : 0.003 0.037 1472 Dihedral : 4.760 55.247 1198 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.63 % Allowed : 12.82 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.26), residues: 1112 helix: 1.48 (0.20), residues: 730 sheet: -0.13 (0.88), residues: 32 loop : -1.73 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 368 TYR 0.011 0.001 TYR B 320 PHE 0.011 0.001 PHE B 581 TRP 0.012 0.001 TRP B 27 HIS 0.004 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8840) covalent geometry : angle 0.48952 (12028) hydrogen bonds : bond 0.03537 ( 517) hydrogen bonds : angle 3.81520 ( 1524) *********************** 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 117 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.375 Fit side-chains REVERT: A 176 GLU cc_start: 0.8306 (tt0) cc_final: 0.8052 (mt-10) REVERT: A 251 PHE cc_start: 0.7584 (m-10) cc_final: 0.7286 (m-10) REVERT: B 481 LYS cc_start: 0.8228 (mtmt) cc_final: 0.7879 (ptpp) outliers start: 25 outliers final: 17 residues processed: 107 average time/residue: 0.0882 time to fit residues: 13.6930 Evaluate side-chains 106 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 271 PHE Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 310 THR 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 233 LEU Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 310 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 70 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 = 0.3267 r_free = 0.3267 target = 0.113225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.088065 restraints weight = 6140.490| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 1.20 r_work: 0.2690 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1018 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= 0.157 Angle : 0.534 7.469 12028 Z= 0.275 Chirality : 0.041 0.128 1452 Planarity : 0.004 0.034 1472 Dihedral : 4.905 59.586 1197 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 2.63 % Allowed : 13.66 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.26), residues: 1112 helix: 1.39 (0.19), residues: 734 sheet: -0.14 (0.88), residues: 32 loop : -1.79 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 253 TYR 0.012 0.001 TYR B 320 PHE 0.015 0.001 PHE B 581 TRP 0.012 0.001 TRP B 27 HIS 0.004 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8840) covalent geometry : angle 0.53399 (12028) hydrogen bonds : bond 0.04199 ( 517) hydrogen bonds : angle 3.88983 ( 1524) *********************** 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 110 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.331 Fit side-chains REVERT: A 251 PHE cc_start: 0.7572 (m-10) cc_final: 0.7213 (m-10) REVERT: B 481 LYS cc_start: 0.8310 (mtmt) cc_final: 0.7813 (mtmt) outliers start: 25 outliers final: 22 residues processed: 103 average time/residue: 0.0897 time to fit residues: 13.3689 Evaluate side-chains 106 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 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 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 303 ASN Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 407 CYS 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 29 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 87 optimal weight: 0.0870 chunk 91 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 0.0970 overall best weight: 0.4756 ------------------------------------------------------------------------------- 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 = 0.3337 r_free = 0.3337 target = 0.118294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.093554 restraints weight = 6048.993| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.19 r_work: 0.2894 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8840 Z= 0.093 Angle : 0.473 6.682 12028 Z= 0.243 Chirality : 0.039 0.172 1452 Planarity : 0.003 0.033 1472 Dihedral : 4.697 54.720 1197 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.21 % Allowed : 14.50 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.27), residues: 1112 helix: 1.68 (0.20), residues: 730 sheet: -0.40 (0.88), residues: 34 loop : -1.60 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 227 TYR 0.010 0.001 TYR A 320 PHE 0.011 0.001 PHE B 581 TRP 0.010 0.001 TRP B 27 HIS 0.003 0.000 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 8840) covalent geometry : angle 0.47254 (12028) hydrogen bonds : bond 0.03155 ( 517) hydrogen bonds : angle 3.68261 ( 1524) *********************** 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 117 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.366 Fit side-chains REVERT: A 60 GLN cc_start: 0.8674 (tt0) cc_final: 0.8441 (tt0) REVERT: A 176 GLU cc_start: 0.8298 (tt0) cc_final: 0.8004 (mt-10) REVERT: A 251 PHE cc_start: 0.7344 (m-10) cc_final: 0.7097 (m-10) REVERT: B 250 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7799 (tm-30) REVERT: B 481 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7802 (mtmt) outliers start: 21 outliers final: 17 residues processed: 108 average time/residue: 0.0851 time to fit residues: 13.2849 Evaluate side-chains 108 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 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 602 VAL Chi-restraints excluded: chain B residue 43 LEU 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 468 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 77 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3332 r_free = 0.3332 target = 0.118154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.093507 restraints weight = 6204.049| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.19 r_work: 0.2863 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8840 Z= 0.110 Angle : 0.489 6.319 12028 Z= 0.251 Chirality : 0.040 0.152 1452 Planarity : 0.003 0.033 1472 Dihedral : 4.624 49.198 1197 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.42 % Allowed : 14.39 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.26), residues: 1112 helix: 1.69 (0.20), residues: 730 sheet: -0.24 (0.89), residues: 34 loop : -1.60 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 29 TYR 0.010 0.001 TYR A 320 PHE 0.012 0.001 PHE B 581 TRP 0.010 0.001 TRP B 27 HIS 0.003 0.000 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 8840) covalent geometry : angle 0.48874 (12028) hydrogen bonds : bond 0.03469 ( 517) hydrogen bonds : angle 3.69910 ( 1524) *********************** 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 114 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.345 Fit side-chains REVERT: A 60 GLN cc_start: 0.8711 (tt0) cc_final: 0.8480 (tt0) REVERT: A 176 GLU cc_start: 0.8262 (tt0) cc_final: 0.7984 (mt-10) REVERT: A 251 PHE cc_start: 0.7409 (m-10) cc_final: 0.7100 (m-10) REVERT: B 43 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8908 (pp) REVERT: B 60 GLN cc_start: 0.8709 (tt0) cc_final: 0.8492 (tt0) REVERT: B 250 GLN cc_start: 0.8157 (tm-30) cc_final: 0.7917 (tm-30) REVERT: B 481 LYS cc_start: 0.8300 (mtmt) cc_final: 0.7837 (mtmt) outliers start: 23 outliers final: 20 residues processed: 107 average time/residue: 0.0889 time to fit residues: 13.6447 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 : 0.332 ------------------------------------------------------------------------------- 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 59 VAL 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 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 20 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3326 r_free = 0.3326 target = 0.117600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.092645 restraints weight = 6083.917| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.20 r_work: 0.2888 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1313 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 : 0.483 6.083 12028 Z= 0.249 Chirality : 0.040 0.143 1452 Planarity : 0.003 0.033 1472 Dihedral : 4.530 49.531 1197 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.84 % Allowed : 14.39 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.26), residues: 1112 helix: 1.76 (0.20), residues: 728 sheet: -0.23 (0.89), residues: 34 loop : -1.58 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 29 TYR 0.010 0.001 TYR A 320 PHE 0.011 0.001 PHE B 581 TRP 0.010 0.001 TRP B 27 HIS 0.003 0.000 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 8840) covalent geometry : angle 0.48335 (12028) hydrogen bonds : bond 0.03366 ( 517) hydrogen bonds : angle 3.66634 ( 1524) *********************** 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 117 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.350 Fit side-chains REVERT: A 60 GLN cc_start: 0.8708 (tt0) cc_final: 0.8470 (tt0) REVERT: A 176 GLU cc_start: 0.8287 (tt0) cc_final: 0.8003 (mt-10) REVERT: A 251 PHE cc_start: 0.7409 (m-10) cc_final: 0.7123 (m-10) REVERT: B 43 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8798 (pp) REVERT: B 60 GLN cc_start: 0.8699 (tt0) cc_final: 0.8473 (tt0) REVERT: B 250 GLN cc_start: 0.8210 (tm-30) cc_final: 0.7949 (tm-30) REVERT: B 481 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7845 (mtmt) outliers start: 27 outliers final: 21 residues processed: 108 average time/residue: 0.0870 time to fit residues: 13.6610 Evaluate side-chains 113 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 59 VAL 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 303 ASN 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 602 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 73 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3289 r_free = 0.3289 target = 0.114854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.089796 restraints weight = 6040.700| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.19 r_work: 0.2829 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1280 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= 0.123 Angle : 0.508 10.531 12028 Z= 0.258 Chirality : 0.040 0.128 1452 Planarity : 0.003 0.032 1472 Dihedral : 4.524 49.622 1197 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.84 % Allowed : 14.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.26), residues: 1112 helix: 1.71 (0.20), residues: 728 sheet: -0.19 (0.89), residues: 34 loop : -1.60 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 29 TYR 0.011 0.001 TYR A 320 PHE 0.012 0.001 PHE B 581 TRP 0.010 0.001 TRP B 27 HIS 0.003 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8840) covalent geometry : angle 0.50804 (12028) hydrogen bonds : bond 0.03645 ( 517) hydrogen bonds : angle 3.71142 ( 1524) *********************** 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 118 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.717 Fit side-chains REVERT: A 60 GLN cc_start: 0.8728 (tt0) cc_final: 0.8497 (tt0) REVERT: A 176 GLU cc_start: 0.8340 (tt0) cc_final: 0.8069 (mt-10) REVERT: A 251 PHE cc_start: 0.7426 (m-10) cc_final: 0.7142 (m-10) REVERT: A 481 LYS cc_start: 0.8371 (mtpp) cc_final: 0.8053 (mtpt) REVERT: B 43 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8724 (pp) REVERT: B 60 GLN cc_start: 0.8725 (tt0) cc_final: 0.8505 (tt0) REVERT: B 250 GLN cc_start: 0.8284 (tm-30) cc_final: 0.8025 (tm-30) REVERT: B 481 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7818 (mtmt) outliers start: 27 outliers final: 21 residues processed: 108 average time/residue: 0.0887 time to fit residues: 13.8286 Evaluate side-chains 112 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL 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 233 LEU Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 303 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 20 optimal weight: 0.0770 chunk 35 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 = 0.3329 r_free = 0.3329 target = 0.117825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.093002 restraints weight = 5964.392| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.18 r_work: 0.2836 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1369 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= 0.100 Angle : 0.488 9.949 12028 Z= 0.248 Chirality : 0.039 0.130 1452 Planarity : 0.003 0.032 1472 Dihedral : 4.455 50.273 1197 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.73 % Allowed : 14.50 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.26), residues: 1112 helix: 1.80 (0.20), residues: 728 sheet: -0.14 (0.90), residues: 34 loop : -1.54 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 144 TYR 0.010 0.001 TYR A 320 PHE 0.011 0.001 PHE B 581 TRP 0.009 0.001 TRP B 27 HIS 0.003 0.000 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 8840) covalent geometry : angle 0.48831 (12028) hydrogen bonds : bond 0.03309 ( 517) hydrogen bonds : angle 3.64870 ( 1524) *********************** 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 118 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.340 Fit side-chains REVERT: A 60 GLN cc_start: 0.8700 (tt0) cc_final: 0.8448 (tt0) REVERT: A 176 GLU cc_start: 0.8305 (tt0) cc_final: 0.8021 (mt-10) REVERT: A 251 PHE cc_start: 0.7340 (m-10) cc_final: 0.7059 (m-10) REVERT: A 481 LYS cc_start: 0.8326 (mtpp) cc_final: 0.8004 (mtpt) REVERT: B 43 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8688 (pp) REVERT: B 60 GLN cc_start: 0.8691 (tt0) cc_final: 0.8469 (tt0) REVERT: B 250 GLN cc_start: 0.8312 (tm-30) cc_final: 0.8071 (tm-30) REVERT: B 481 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7833 (mtmt) outliers start: 26 outliers final: 22 residues processed: 108 average time/residue: 0.0867 time to fit residues: 13.5949 Evaluate side-chains 114 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL 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 195 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 303 ASN 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 90 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 0.0770 chunk 64 optimal weight: 1.9990 chunk 10 optimal weight: 0.0030 chunk 80 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.9552 ------------------------------------------------------------------------------- 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 = 0.3219 r_free = 0.3219 target = 0.110991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.084318 restraints weight = 4918.723| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.20 r_work: 0.2830 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8840 Z= 0.113 Angle : 0.499 9.995 12028 Z= 0.253 Chirality : 0.040 0.135 1452 Planarity : 0.003 0.032 1472 Dihedral : 4.472 50.353 1197 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.84 % Allowed : 14.50 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.26), residues: 1112 helix: 1.77 (0.20), residues: 728 sheet: -0.08 (0.90), residues: 34 loop : -1.57 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 29 TYR 0.010 0.001 TYR A 320 PHE 0.012 0.001 PHE B 581 TRP 0.009 0.001 TRP B 27 HIS 0.003 0.000 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8840) covalent geometry : angle 0.49922 (12028) hydrogen bonds : bond 0.03509 ( 517) hydrogen bonds : angle 3.68084 ( 1524) ********************** 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 116 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.362 Fit side-chains REVERT: A 60 GLN cc_start: 0.8635 (tt0) cc_final: 0.8380 (tt0) REVERT: A 176 GLU cc_start: 0.8397 (tt0) cc_final: 0.8110 (mt-10) REVERT: A 251 PHE cc_start: 0.7249 (m-10) cc_final: 0.6913 (m-10) REVERT: B 43 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8660 (pp) REVERT: B 60 GLN cc_start: 0.8607 (tt0) cc_final: 0.8367 (tt0) REVERT: B 250 GLN cc_start: 0.8332 (tm-30) cc_final: 0.8035 (tm-30) REVERT: B 481 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7780 (mtmt) outliers start: 27 outliers final: 22 residues processed: 106 average time/residue: 0.0947 time to fit residues: 14.5199 Evaluate side-chains 113 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL 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 195 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 303 ASN 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 69 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 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 = 0.3176 r_free = 0.3176 target = 0.109314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.081832 restraints weight = 5773.679| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 1.33 r_work: 0.2758 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1438 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= 0.099 Angle : 0.487 9.748 12028 Z= 0.246 Chirality : 0.039 0.130 1452 Planarity : 0.003 0.032 1472 Dihedral : 4.431 50.525 1197 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.63 % Allowed : 14.71 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.26), residues: 1112 helix: 1.84 (0.20), residues: 728 sheet: -0.03 (0.90), residues: 34 loop : -1.50 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 144 TYR 0.011 0.001 TYR A 320 PHE 0.011 0.001 PHE B 581 TRP 0.009 0.001 TRP B 27 HIS 0.003 0.000 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 8840) covalent geometry : angle 0.48653 (12028) hydrogen bonds : bond 0.03272 ( 517) hydrogen bonds : angle 3.64170 ( 1524) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2130.55 seconds wall clock time: 37 minutes 20.58 seconds (2240.58 seconds total)