Starting phenix.real_space_refine on Sat Aug 23 06:44:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sh3_40479/08_2025/8sh3_40479.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sh3_40479/08_2025/8sh3_40479.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sh3_40479/08_2025/8sh3_40479.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sh3_40479/08_2025/8sh3_40479.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sh3_40479/08_2025/8sh3_40479.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sh3_40479/08_2025/8sh3_40479.map" } resolution = 2.8 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= -0.002 sd= 0.100 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: 6 Type Number sf(0) Gaussians I 4 10.91 5 P 6 5.49 5 S 36 5.16 5 C 7004 2.51 5 N 1542 2.21 5 O 1794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10386 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 4755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4755 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 24, 'TRANS': 588} Chain breaks: 3 Chain: "D" Number of atoms: 4755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4755 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 24, 'TRANS': 588} Chain breaks: 3 Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 438 Unusual residues: {'AV0': 2, 'CLR': 6, 'IOD': 2, 'LBN': 9} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 420 Unresolved non-hydrogen dihedrals: 351 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'LBN:plan-1': 7, 'LBN:plan-3': 7, 'LBN:plan-2': 6} Unresolved non-hydrogen planarities: 72 Chain: "D" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 438 Unusual residues: {'AV0': 2, 'CLR': 6, 'IOD': 2, 'LBN': 9} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 420 Unresolved non-hydrogen dihedrals: 351 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'LBN:plan-1': 7, 'LBN:plan-3': 7, 'LBN:plan-2': 6} Unresolved non-hydrogen planarities: 72 Time building chain proxies: 2.74, per 1000 atoms: 0.26 Number of scatterers: 10386 At special positions: 0 Unit cell: (85.078, 121.422, 105.728, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) I 4 52.95 S 36 16.00 P 6 15.00 O 1794 8.00 N 1542 7.00 C 7004 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 426.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 5 sheets defined 70.2% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'C' and resid 28 through 36 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 82 through 109 removed outlier: 4.050A pdb=" N SER C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU C 107 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU C 108 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 131 removed outlier: 3.596A pdb=" N TYR C 118 " --> pdb=" O GLY C 114 " (cutoff:3.500A) Proline residue: C 123 - end of helix removed outlier: 4.188A pdb=" N ILE C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N PHE C 130 " --> pdb=" O THR C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 156 removed outlier: 3.522A pdb=" N SER C 145 " --> pdb=" O PHE C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 162 Processing helix chain 'C' and resid 177 through 206 Processing helix chain 'C' and resid 210 through 215 removed outlier: 3.852A pdb=" N TYR C 214 " --> pdb=" O PHE C 210 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU C 215 " --> pdb=" O ILE C 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 210 through 215' Processing helix chain 'C' and resid 216 through 241 Processing helix chain 'C' and resid 251 through 264 Processing helix chain 'C' and resid 265 through 267 No H-bonds generated for 'chain 'C' and resid 265 through 267' Processing helix chain 'C' and resid 268 through 292 Processing helix chain 'C' and resid 301 through 318 Processing helix chain 'C' and resid 318 through 323 Processing helix chain 'C' and resid 342 through 348 removed outlier: 4.053A pdb=" N SER C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 376 removed outlier: 3.593A pdb=" N LYS C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 398 Processing helix chain 'C' and resid 406 through 416 Processing helix chain 'C' and resid 421 through 437 Processing helix chain 'C' and resid 446 through 458 removed outlier: 3.901A pdb=" N LEU C 450 " --> pdb=" O GLN C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 463 Processing helix chain 'C' and resid 466 through 475 removed outlier: 4.502A pdb=" N ARG C 470 " --> pdb=" O CYS C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 491 Processing helix chain 'C' and resid 493 through 515 Processing helix chain 'C' and resid 533 through 537 removed outlier: 4.194A pdb=" N LYS C 537 " --> pdb=" O THR C 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 533 through 537' Processing helix chain 'C' and resid 555 through 571 Processing helix chain 'C' and resid 573 through 585 Processing helix chain 'C' and resid 669 through 685 Processing helix chain 'C' and resid 696 through 706 Processing helix chain 'C' and resid 723 through 731 Processing helix chain 'D' and resid 28 through 36 Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 82 through 109 removed outlier: 4.144A pdb=" N SER D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU D 107 " --> pdb=" O MET D 103 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 131 removed outlier: 3.585A pdb=" N TYR D 118 " --> pdb=" O GLY D 114 " (cutoff:3.500A) Proline residue: D 123 - end of helix removed outlier: 4.227A pdb=" N ILE D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE D 130 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 156 removed outlier: 3.521A pdb=" N SER D 145 " --> pdb=" O PHE D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 162 Processing helix chain 'D' and resid 177 through 207 Processing helix chain 'D' and resid 210 through 215 removed outlier: 3.866A pdb=" N TYR D 214 " --> pdb=" O PHE D 210 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU D 215 " --> pdb=" O ILE D 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 210 through 215' Processing helix chain 'D' and resid 216 through 241 Processing helix chain 'D' and resid 251 through 264 Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 268 through 292 Processing helix chain 'D' and resid 301 through 318 Processing helix chain 'D' and resid 342 through 348 removed outlier: 4.067A pdb=" N SER D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 376 removed outlier: 3.652A pdb=" N SER D 355 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 398 Processing helix chain 'D' and resid 406 through 416 Processing helix chain 'D' and resid 421 through 437 Processing helix chain 'D' and resid 446 through 458 removed outlier: 3.867A pdb=" N LEU D 450 " --> pdb=" O GLN D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 463 Processing helix chain 'D' and resid 466 through 475 removed outlier: 4.305A pdb=" N ARG D 470 " --> pdb=" O CYS D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 491 Processing helix chain 'D' and resid 493 through 515 Processing helix chain 'D' and resid 533 through 537 removed outlier: 4.197A pdb=" N LYS D 537 " --> pdb=" O THR D 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 533 through 537' Processing helix chain 'D' and resid 555 through 571 Processing helix chain 'D' and resid 573 through 585 Processing helix chain 'D' and resid 669 through 685 Processing helix chain 'D' and resid 696 through 706 Processing helix chain 'D' and resid 723 through 731 Processing sheet with id=AA1, first strand: chain 'C' and resid 19 through 25 Processing sheet with id=AA2, first strand: chain 'C' and resid 138 through 139 Processing sheet with id=AA3, first strand: chain 'C' and resid 530 through 532 removed outlier: 4.273A pdb=" N ILE C 547 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N SER C 523 " --> pdb=" O VAL C 545 " (cutoff:3.500A) removed outlier: 12.667A pdb=" N VAL C 545 " --> pdb=" O SER C 523 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LYS C 546 " --> pdb=" O VAL C 659 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASP C 661 " --> pdb=" O LYS C 546 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU C 548 " --> pdb=" O ASP C 661 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N PHE C 719 " --> pdb=" O VAL C 690 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N PHE C 692 " --> pdb=" O PHE C 719 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 138 through 139 Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 532 removed outlier: 4.269A pdb=" N ILE D 547 " --> pdb=" O LEU D 521 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N SER D 523 " --> pdb=" O VAL D 545 " (cutoff:3.500A) removed outlier: 12.668A pdb=" N VAL D 545 " --> pdb=" O SER D 523 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE D 550 " --> pdb=" O ASP D 661 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N PHE D 719 " --> pdb=" O VAL D 690 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE D 692 " --> pdb=" O PHE D 719 " (cutoff:3.500A) 626 hydrogen bonds defined for protein. 1842 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: 1.51 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1531 1.32 - 1.44: 2634 1.44 - 1.57: 6373 1.57 - 1.69: 12 1.69 - 1.81: 56 Bond restraints: 10606 Sorted by residual: bond pdb=" O2 LBN C 813 " pdb=" P1 LBN C 813 " ideal model delta sigma weight residual 1.650 1.596 0.054 2.00e-02 2.50e+03 7.36e+00 bond pdb=" O2 LBN D 813 " pdb=" P1 LBN D 813 " ideal model delta sigma weight residual 1.650 1.596 0.054 2.00e-02 2.50e+03 7.34e+00 bond pdb=" O2 LBN C 811 " pdb=" P1 LBN C 811 " ideal model delta sigma weight residual 1.650 1.596 0.054 2.00e-02 2.50e+03 7.34e+00 bond pdb=" O2 LBN C 810 " pdb=" P1 LBN C 810 " ideal model delta sigma weight residual 1.650 1.596 0.054 2.00e-02 2.50e+03 7.34e+00 bond pdb=" O2 LBN D 810 " pdb=" P1 LBN D 810 " ideal model delta sigma weight residual 1.650 1.596 0.054 2.00e-02 2.50e+03 7.25e+00 ... (remaining 10601 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 14138 2.20 - 4.40: 220 4.40 - 6.60: 16 6.60 - 8.80: 2 8.80 - 11.00: 6 Bond angle restraints: 14382 Sorted by residual: angle pdb=" O1 LBN D 813 " pdb=" P1 LBN D 813 " pdb=" O2 LBN D 813 " ideal model delta sigma weight residual 93.45 104.45 -11.00 3.00e+00 1.11e-01 1.34e+01 angle pdb=" O1 LBN D 810 " pdb=" P1 LBN D 810 " pdb=" O2 LBN D 810 " ideal model delta sigma weight residual 93.45 104.17 -10.72 3.00e+00 1.11e-01 1.28e+01 angle pdb=" O1 LBN C 810 " pdb=" P1 LBN C 810 " pdb=" O2 LBN C 810 " ideal model delta sigma weight residual 93.45 104.14 -10.69 3.00e+00 1.11e-01 1.27e+01 angle pdb=" O1 LBN C 813 " pdb=" P1 LBN C 813 " pdb=" O2 LBN C 813 " ideal model delta sigma weight residual 93.45 104.04 -10.59 3.00e+00 1.11e-01 1.25e+01 angle pdb=" O1 LBN D 811 " pdb=" P1 LBN D 811 " pdb=" O2 LBN D 811 " ideal model delta sigma weight residual 93.45 103.76 -10.31 3.00e+00 1.11e-01 1.18e+01 ... (remaining 14377 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.53: 6833 34.53 - 69.07: 207 69.07 - 103.60: 45 103.60 - 138.14: 56 138.14 - 172.67: 9 Dihedral angle restraints: 7150 sinusoidal: 3600 harmonic: 3550 Sorted by residual: dihedral pdb=" CA VAL C 722 " pdb=" C VAL C 722 " pdb=" N HIS C 723 " pdb=" CA HIS C 723 " ideal model delta harmonic sigma weight residual 180.00 151.87 28.13 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA VAL D 722 " pdb=" C VAL D 722 " pdb=" N HIS D 723 " pdb=" CA HIS D 723 " ideal model delta harmonic sigma weight residual 180.00 151.87 28.13 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" C1 LBN D 810 " pdb=" O1 LBN D 810 " pdb=" P1 LBN D 810 " pdb=" O3 LBN D 810 " ideal model delta sinusoidal sigma weight residual 275.40 102.73 172.67 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 7147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.971: 1756 0.971 - 1.943: 0 1.943 - 2.914: 0 2.914 - 3.885: 0 3.885 - 4.856: 2 Chirality restraints: 1758 Sorted by residual: chirality pdb=" C2 LBN C 813 " pdb=" C1 LBN C 813 " pdb=" C3 LBN C 813 " pdb=" O7 LBN C 813 " both_signs ideal model delta sigma weight residual False -2.36 2.49 -4.86 2.00e-01 2.50e+01 5.90e+02 chirality pdb=" C2 LBN D 813 " pdb=" C1 LBN D 813 " pdb=" C3 LBN D 813 " pdb=" O7 LBN D 813 " both_signs ideal model delta sigma weight residual False -2.36 2.46 -4.83 2.00e-01 2.50e+01 5.82e+02 chirality pdb=" C2 LBN D 811 " pdb=" C1 LBN D 811 " pdb=" C3 LBN D 811 " pdb=" O7 LBN D 811 " both_signs ideal model delta sigma weight residual False -2.36 -2.60 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1755 not shown) Planarity restraints: 1638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C41 LBN C 813 " -0.100 2.00e-02 2.50e+03 2.28e-01 5.20e+02 pdb=" C42 LBN C 813 " 0.307 2.00e-02 2.50e+03 pdb=" C5 LBN C 813 " -0.307 2.00e-02 2.50e+03 pdb=" C8 LBN C 813 " 0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN D 813 " 0.217 2.00e-02 2.50e+03 2.17e-01 4.72e+02 pdb=" C42 LBN D 813 " -0.215 2.00e-02 2.50e+03 pdb=" C5 LBN D 813 " -0.219 2.00e-02 2.50e+03 pdb=" C8 LBN D 813 " 0.218 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN C 810 " 0.095 2.00e-02 2.50e+03 2.09e-01 4.35e+02 pdb=" C42 LBN C 810 " -0.279 2.00e-02 2.50e+03 pdb=" C5 LBN C 810 " 0.279 2.00e-02 2.50e+03 pdb=" C8 LBN C 810 " -0.095 2.00e-02 2.50e+03 ... (remaining 1635 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 813 2.74 - 3.30: 11017 3.30 - 3.85: 18599 3.85 - 4.41: 23383 4.41 - 4.96: 38834 Nonbonded interactions: 92646 Sorted by model distance: nonbonded pdb=" OH TYR D 78 " pdb=" OD2 ASP D 87 " model vdw 2.186 3.040 nonbonded pdb=" O PRO C 553 " pdb=" ND2 ASN C 558 " model vdw 2.196 3.120 nonbonded pdb=" O PRO D 553 " pdb=" ND2 ASN D 558 " model vdw 2.196 3.120 nonbonded pdb=" OH TYR C 78 " pdb=" OD2 ASP C 87 " model vdw 2.204 3.040 nonbonded pdb=" OH TYR C 247 " pdb=" OE1 GLU C 259 " model vdw 2.276 3.040 ... (remaining 92641 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.780 Find NCS groups from input model: 0.100 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:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 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 0.054 10607 Z= 0.202 Angle : 0.651 11.001 14382 Z= 0.310 Chirality : 0.169 4.856 1758 Planarity : 0.011 0.228 1638 Dihedral : 21.604 172.671 4862 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: 1.02 (0.25), residues: 1210 helix: 1.74 (0.19), residues: 802 sheet: 1.57 (0.77), residues: 36 loop : -1.88 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 185 TYR 0.012 0.001 TYR C 371 PHE 0.017 0.001 PHE D 141 TRP 0.009 0.001 TRP D 482 HIS 0.002 0.001 HIS D 656 Details of bonding type rmsd covalent geometry : bond 0.00415 (10606) covalent geometry : angle 0.65094 (14382) hydrogen bonds : bond 0.12536 ( 626) hydrogen bonds : angle 5.13263 ( 1842) Misc. bond : bond 0.00063 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.273 Fit side-chains REVERT: C 79 ARG cc_start: 0.6657 (mmm-85) cc_final: 0.6188 (mtp180) REVERT: C 440 LYS cc_start: 0.7426 (ttmm) cc_final: 0.6726 (mptt) REVERT: D 35 GLN cc_start: 0.7316 (tt0) cc_final: 0.7094 (tm-30) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.4734 time to fit residues: 68.3410 Evaluate side-chains 106 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 0.4980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 ASN D 241 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.171222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.136704 restraints weight = 6890.489| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.38 r_work: 0.3540 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10607 Z= 0.178 Angle : 0.690 11.093 14382 Z= 0.334 Chirality : 0.047 0.206 1758 Planarity : 0.005 0.077 1638 Dihedral : 19.512 179.051 2714 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.79 % Favored : 95.04 % Rotamer: Outliers : 1.53 % Allowed : 7.65 % Favored : 90.82 % 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: 0.79 (0.24), residues: 1210 helix: 1.38 (0.18), residues: 838 sheet: 1.49 (0.73), residues: 34 loop : -1.79 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 24 TYR 0.015 0.002 TYR C 371 PHE 0.021 0.002 PHE D 141 TRP 0.009 0.001 TRP C 74 HIS 0.003 0.001 HIS C 698 Details of bonding type rmsd covalent geometry : bond 0.00405 (10606) covalent geometry : angle 0.68969 (14382) hydrogen bonds : bond 0.05360 ( 626) hydrogen bonds : angle 4.44140 ( 1842) Misc. bond : bond 0.00146 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.382 Fit side-chains REVERT: C 35 GLN cc_start: 0.7692 (tt0) cc_final: 0.7234 (tm-30) REVERT: C 79 ARG cc_start: 0.6740 (mmm-85) cc_final: 0.6191 (mtp180) REVERT: C 307 THR cc_start: 0.8292 (m) cc_final: 0.8091 (p) REVERT: C 438 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8143 (mm) REVERT: C 440 LYS cc_start: 0.7485 (ttmm) cc_final: 0.6743 (mptt) REVERT: D 35 GLN cc_start: 0.7665 (tt0) cc_final: 0.7233 (tm-30) REVERT: D 38 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.7132 (ttt180) REVERT: D 307 THR cc_start: 0.8235 (m) cc_final: 0.8023 (p) REVERT: D 322 ASN cc_start: 0.7783 (m110) cc_final: 0.7502 (m110) REVERT: D 440 LYS cc_start: 0.7324 (ttmm) cc_final: 0.6584 (mptt) outliers start: 16 outliers final: 7 residues processed: 132 average time/residue: 0.5098 time to fit residues: 73.5662 Evaluate side-chains 117 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 721 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 96 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 70 optimal weight: 0.0770 chunk 120 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 73 optimal weight: 0.0770 chunk 28 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 ASN C 263 ASN D 241 ASN D 263 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.177568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.143237 restraints weight = 7905.508| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.49 r_work: 0.3588 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 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 : 0.003 0.053 10607 Z= 0.123 Angle : 0.592 7.638 14382 Z= 0.291 Chirality : 0.045 0.286 1758 Planarity : 0.005 0.078 1638 Dihedral : 17.202 173.783 2714 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.63 % Allowed : 9.66 % Favored : 88.72 % 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: 1.13 (0.25), residues: 1210 helix: 1.65 (0.18), residues: 830 sheet: 1.30 (0.70), residues: 34 loop : -1.59 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 185 TYR 0.012 0.001 TYR C 371 PHE 0.015 0.001 PHE D 141 TRP 0.009 0.001 TRP D 482 HIS 0.002 0.001 HIS D 656 Details of bonding type rmsd covalent geometry : bond 0.00262 (10606) covalent geometry : angle 0.59158 (14382) hydrogen bonds : bond 0.04478 ( 626) hydrogen bonds : angle 4.24940 ( 1842) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.482 Fit side-chains REVERT: C 35 GLN cc_start: 0.7472 (tt0) cc_final: 0.6999 (tm-30) REVERT: C 307 THR cc_start: 0.7924 (m) cc_final: 0.7668 (p) REVERT: C 385 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7464 (m-80) REVERT: C 440 LYS cc_start: 0.7285 (ttmm) cc_final: 0.6489 (mptt) REVERT: D 35 GLN cc_start: 0.7483 (tt0) cc_final: 0.7061 (tm-30) REVERT: D 38 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.6921 (ttt180) REVERT: D 307 THR cc_start: 0.7879 (m) cc_final: 0.7635 (p) REVERT: D 322 ASN cc_start: 0.7717 (m110) cc_final: 0.7360 (m110) REVERT: D 440 LYS cc_start: 0.7083 (ttmm) cc_final: 0.6295 (mptt) REVERT: D 689 HIS cc_start: 0.8266 (m-70) cc_final: 0.8049 (m90) outliers start: 17 outliers final: 5 residues processed: 131 average time/residue: 0.5286 time to fit residues: 75.5643 Evaluate side-chains 117 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 545 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.175619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.141709 restraints weight = 6594.324| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.34 r_work: 0.3586 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10607 Z= 0.141 Angle : 0.611 8.009 14382 Z= 0.301 Chirality : 0.047 0.354 1758 Planarity : 0.005 0.077 1638 Dihedral : 15.930 163.664 2714 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.71 % Rotamer: Outliers : 2.68 % Allowed : 9.66 % Favored : 87.67 % 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: 1.15 (0.25), residues: 1210 helix: 1.67 (0.18), residues: 826 sheet: 1.34 (0.70), residues: 34 loop : -1.55 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 185 TYR 0.014 0.001 TYR C 371 PHE 0.018 0.001 PHE D 141 TRP 0.008 0.001 TRP C 74 HIS 0.002 0.001 HIS D 656 Details of bonding type rmsd covalent geometry : bond 0.00309 (10606) covalent geometry : angle 0.61140 (14382) hydrogen bonds : bond 0.04726 ( 626) hydrogen bonds : angle 4.23812 ( 1842) Misc. bond : bond 0.00033 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.383 Fit side-chains REVERT: C 35 GLN cc_start: 0.7644 (tt0) cc_final: 0.7210 (tm-30) REVERT: C 307 THR cc_start: 0.8185 (m) cc_final: 0.7906 (p) REVERT: C 385 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.7707 (m-80) REVERT: C 440 LYS cc_start: 0.7433 (ttmm) cc_final: 0.6696 (mptt) REVERT: D 35 GLN cc_start: 0.7667 (tt0) cc_final: 0.7266 (tm-30) REVERT: D 38 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.7054 (ttt180) REVERT: D 318 ASN cc_start: 0.7463 (t0) cc_final: 0.6987 (t0) REVERT: D 322 ASN cc_start: 0.7745 (m110) cc_final: 0.7447 (m110) REVERT: D 385 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7825 (m-80) REVERT: D 440 LYS cc_start: 0.7285 (ttmm) cc_final: 0.6536 (mptt) outliers start: 28 outliers final: 9 residues processed: 140 average time/residue: 0.5059 time to fit residues: 77.4936 Evaluate side-chains 120 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 721 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 89 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 82 optimal weight: 0.0670 chunk 114 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 70 optimal weight: 0.3980 chunk 78 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 ASN D 241 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.175757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.141252 restraints weight = 7452.014| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.44 r_work: 0.3582 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10607 Z= 0.134 Angle : 0.597 7.999 14382 Z= 0.297 Chirality : 0.047 0.356 1758 Planarity : 0.005 0.082 1638 Dihedral : 15.029 155.253 2714 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.63 % Favored : 95.21 % Rotamer: Outliers : 2.01 % Allowed : 11.47 % Favored : 86.52 % 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: 1.19 (0.25), residues: 1210 helix: 1.70 (0.18), residues: 826 sheet: 1.29 (0.70), residues: 34 loop : -1.50 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 185 TYR 0.014 0.001 TYR C 323 PHE 0.016 0.001 PHE C 141 TRP 0.009 0.001 TRP C 482 HIS 0.002 0.001 HIS D 656 Details of bonding type rmsd covalent geometry : bond 0.00291 (10606) covalent geometry : angle 0.59710 (14382) hydrogen bonds : bond 0.04543 ( 626) hydrogen bonds : angle 4.21960 ( 1842) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.449 Fit side-chains REVERT: C 35 GLN cc_start: 0.7627 (tt0) cc_final: 0.7201 (tm-30) REVERT: C 79 ARG cc_start: 0.6993 (mmm160) cc_final: 0.6139 (mtp180) REVERT: C 307 THR cc_start: 0.8175 (m) cc_final: 0.7898 (p) REVERT: C 385 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.7495 (m-80) REVERT: C 440 LYS cc_start: 0.7443 (ttmm) cc_final: 0.6686 (mptt) REVERT: D 35 GLN cc_start: 0.7654 (tt0) cc_final: 0.7280 (tm-30) REVERT: D 38 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.7026 (ttt180) REVERT: D 307 THR cc_start: 0.8151 (m) cc_final: 0.7883 (p) REVERT: D 318 ASN cc_start: 0.7459 (t0) cc_final: 0.6936 (t0) REVERT: D 322 ASN cc_start: 0.7784 (m110) cc_final: 0.7459 (m110) REVERT: D 385 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7646 (m-80) REVERT: D 440 LYS cc_start: 0.7268 (ttmm) cc_final: 0.6511 (mptt) outliers start: 21 outliers final: 10 residues processed: 128 average time/residue: 0.5247 time to fit residues: 73.4663 Evaluate side-chains 125 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 721 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 28 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 80 optimal weight: 0.0870 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- 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 = 0.4004 r_free = 0.4004 target = 0.175130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.141383 restraints weight = 7027.757| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.38 r_work: 0.3574 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10607 Z= 0.139 Angle : 0.597 9.025 14382 Z= 0.298 Chirality : 0.046 0.339 1758 Planarity : 0.005 0.081 1638 Dihedral : 14.456 147.227 2714 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.71 % Rotamer: Outliers : 2.10 % Allowed : 11.95 % Favored : 85.95 % 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: 1.11 (0.24), residues: 1210 helix: 1.62 (0.18), residues: 826 sheet: 1.27 (0.69), residues: 34 loop : -1.48 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 185 TYR 0.014 0.001 TYR C 371 PHE 0.017 0.001 PHE C 141 TRP 0.008 0.001 TRP C 482 HIS 0.002 0.001 HIS D 656 Details of bonding type rmsd covalent geometry : bond 0.00313 (10606) covalent geometry : angle 0.59672 (14382) hydrogen bonds : bond 0.04640 ( 626) hydrogen bonds : angle 4.30093 ( 1842) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.390 Fit side-chains REVERT: C 35 GLN cc_start: 0.7503 (tt0) cc_final: 0.7037 (tm-30) REVERT: C 79 ARG cc_start: 0.6829 (mmm160) cc_final: 0.5960 (mtp180) REVERT: C 307 THR cc_start: 0.7968 (m) cc_final: 0.7661 (p) REVERT: C 318 ASN cc_start: 0.7296 (t0) cc_final: 0.6995 (t0) REVERT: C 385 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7266 (m-80) REVERT: C 440 LYS cc_start: 0.7318 (ttmm) cc_final: 0.6532 (mptt) REVERT: D 35 GLN cc_start: 0.7529 (tt0) cc_final: 0.7182 (tm-30) REVERT: D 38 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6953 (ttt180) REVERT: D 307 THR cc_start: 0.7952 (m) cc_final: 0.7657 (p) REVERT: D 318 ASN cc_start: 0.7248 (t0) cc_final: 0.6696 (t0) REVERT: D 322 ASN cc_start: 0.7743 (m110) cc_final: 0.7369 (m110) REVERT: D 385 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.7365 (m-80) REVERT: D 440 LYS cc_start: 0.7141 (ttmm) cc_final: 0.6362 (mptt) outliers start: 22 outliers final: 10 residues processed: 133 average time/residue: 0.4974 time to fit residues: 72.6972 Evaluate side-chains 127 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 721 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 23 optimal weight: 0.9990 chunk 109 optimal weight: 0.2980 chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 ASN D 689 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.172297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.137961 restraints weight = 7409.050| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.43 r_work: 0.3530 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 10607 Z= 0.159 Angle : 0.612 9.075 14382 Z= 0.309 Chirality : 0.046 0.287 1758 Planarity : 0.005 0.084 1638 Dihedral : 14.019 144.130 2714 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.96 % Favored : 94.88 % Rotamer: Outliers : 2.10 % Allowed : 12.33 % Favored : 85.56 % 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: 1.01 (0.24), residues: 1210 helix: 1.54 (0.18), residues: 826 sheet: 1.18 (0.71), residues: 34 loop : -1.53 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 185 TYR 0.015 0.002 TYR D 371 PHE 0.017 0.002 PHE C 141 TRP 0.008 0.001 TRP C 74 HIS 0.003 0.001 HIS C 656 Details of bonding type rmsd covalent geometry : bond 0.00370 (10606) covalent geometry : angle 0.61237 (14382) hydrogen bonds : bond 0.04915 ( 626) hydrogen bonds : angle 4.36594 ( 1842) Misc. bond : bond 0.00046 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.407 Fit side-chains REVERT: C 35 GLN cc_start: 0.7676 (tt0) cc_final: 0.7304 (tm-30) REVERT: C 79 ARG cc_start: 0.6983 (mmm160) cc_final: 0.6100 (mtp180) REVERT: C 307 THR cc_start: 0.8233 (m) cc_final: 0.7944 (p) REVERT: C 385 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.7540 (m-80) REVERT: C 440 LYS cc_start: 0.7477 (ttmm) cc_final: 0.6736 (mptt) REVERT: C 655 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7182 (mp) REVERT: D 35 GLN cc_start: 0.7630 (tt0) cc_final: 0.7308 (tm-30) REVERT: D 38 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.7111 (ttt180) REVERT: D 79 ARG cc_start: 0.6965 (mmm160) cc_final: 0.6155 (mtp180) REVERT: D 307 THR cc_start: 0.8185 (m) cc_final: 0.7873 (p) REVERT: D 318 ASN cc_start: 0.7445 (t0) cc_final: 0.6861 (t0) REVERT: D 322 ASN cc_start: 0.7811 (m110) cc_final: 0.7353 (m110) REVERT: D 385 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7579 (m-80) REVERT: D 440 LYS cc_start: 0.7319 (ttmm) cc_final: 0.6524 (mptt) outliers start: 22 outliers final: 12 residues processed: 129 average time/residue: 0.4994 time to fit residues: 70.6707 Evaluate side-chains 124 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 721 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 102 optimal weight: 0.0050 chunk 101 optimal weight: 0.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 689 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.174726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.140586 restraints weight = 7512.330| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.44 r_work: 0.3574 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10607 Z= 0.131 Angle : 0.581 9.940 14382 Z= 0.292 Chirality : 0.044 0.242 1758 Planarity : 0.005 0.085 1638 Dihedral : 13.495 140.381 2714 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.88 % Favored : 94.96 % Rotamer: Outliers : 2.01 % Allowed : 12.91 % Favored : 85.09 % 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: 1.15 (0.25), residues: 1210 helix: 1.63 (0.18), residues: 826 sheet: 1.21 (0.71), residues: 34 loop : -1.42 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 185 TYR 0.013 0.001 TYR C 371 PHE 0.017 0.001 PHE C 141 TRP 0.009 0.001 TRP C 482 HIS 0.002 0.001 HIS D 728 Details of bonding type rmsd covalent geometry : bond 0.00292 (10606) covalent geometry : angle 0.58116 (14382) hydrogen bonds : bond 0.04559 ( 626) hydrogen bonds : angle 4.28681 ( 1842) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.386 Fit side-chains REVERT: C 35 GLN cc_start: 0.7620 (tt0) cc_final: 0.7264 (tm-30) REVERT: C 79 ARG cc_start: 0.6949 (mmm160) cc_final: 0.6125 (mtp180) REVERT: C 307 THR cc_start: 0.8170 (m) cc_final: 0.7933 (p) REVERT: C 318 ASN cc_start: 0.7449 (t0) cc_final: 0.7189 (t0) REVERT: C 385 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.7473 (m-80) REVERT: C 440 LYS cc_start: 0.7434 (ttmm) cc_final: 0.6680 (mptt) REVERT: C 503 MET cc_start: 0.7553 (mmt) cc_final: 0.7289 (mmm) REVERT: C 655 ILE cc_start: 0.7495 (OUTLIER) cc_final: 0.7066 (mp) REVERT: D 35 GLN cc_start: 0.7569 (tt0) cc_final: 0.7286 (tm-30) REVERT: D 79 ARG cc_start: 0.6927 (mmm160) cc_final: 0.6116 (mtp180) REVERT: D 318 ASN cc_start: 0.7451 (t0) cc_final: 0.6940 (t0) REVERT: D 322 ASN cc_start: 0.7773 (m110) cc_final: 0.7438 (m110) REVERT: D 385 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.7410 (m-80) REVERT: D 440 LYS cc_start: 0.7317 (ttmm) cc_final: 0.6568 (mptt) outliers start: 21 outliers final: 13 residues processed: 132 average time/residue: 0.5010 time to fit residues: 72.4601 Evaluate side-chains 129 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 721 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 114 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 0.0270 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.175388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.141835 restraints weight = 6847.012| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.36 r_work: 0.3576 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10607 Z= 0.132 Angle : 0.577 9.835 14382 Z= 0.292 Chirality : 0.044 0.209 1758 Planarity : 0.005 0.084 1638 Dihedral : 13.028 137.861 2714 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.71 % Favored : 95.12 % Rotamer: Outliers : 1.53 % Allowed : 13.58 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.23 (0.24), residues: 1210 helix: 1.68 (0.18), residues: 814 sheet: 1.21 (0.70), residues: 34 loop : -1.25 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 185 TYR 0.014 0.001 TYR D 105 PHE 0.017 0.001 PHE C 141 TRP 0.009 0.001 TRP C 482 HIS 0.002 0.001 HIS D 656 Details of bonding type rmsd covalent geometry : bond 0.00296 (10606) covalent geometry : angle 0.57730 (14382) hydrogen bonds : bond 0.04553 ( 626) hydrogen bonds : angle 4.26948 ( 1842) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.386 Fit side-chains REVERT: C 35 GLN cc_start: 0.7638 (tt0) cc_final: 0.7269 (tm-30) REVERT: C 79 ARG cc_start: 0.6976 (mmm160) cc_final: 0.6112 (mtp180) REVERT: C 307 THR cc_start: 0.8191 (m) cc_final: 0.7941 (p) REVERT: C 318 ASN cc_start: 0.7480 (t0) cc_final: 0.7215 (t0) REVERT: C 385 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.7432 (m-80) REVERT: C 440 LYS cc_start: 0.7436 (ttmm) cc_final: 0.6685 (mptt) REVERT: C 503 MET cc_start: 0.7593 (mmt) cc_final: 0.7322 (mmm) REVERT: C 655 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.7066 (mp) REVERT: D 35 GLN cc_start: 0.7589 (tt0) cc_final: 0.7326 (tm-30) REVERT: D 79 ARG cc_start: 0.6945 (mmm160) cc_final: 0.6174 (mtp180) REVERT: D 318 ASN cc_start: 0.7444 (t0) cc_final: 0.6923 (t0) REVERT: D 322 ASN cc_start: 0.7792 (m110) cc_final: 0.7477 (m110) REVERT: D 385 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.7440 (m-80) REVERT: D 440 LYS cc_start: 0.7329 (ttmm) cc_final: 0.6582 (mptt) outliers start: 16 outliers final: 13 residues processed: 130 average time/residue: 0.5098 time to fit residues: 72.7159 Evaluate side-chains 129 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 721 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 84 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 241 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.170280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.135976 restraints weight = 7383.412| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.42 r_work: 0.3498 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 10607 Z= 0.196 Angle : 0.654 10.888 14382 Z= 0.331 Chirality : 0.047 0.206 1758 Planarity : 0.005 0.084 1638 Dihedral : 13.307 137.171 2714 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.04 % Favored : 94.79 % Rotamer: Outliers : 1.82 % Allowed : 13.96 % Favored : 84.23 % 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: 0.81 (0.24), residues: 1210 helix: 1.36 (0.18), residues: 826 sheet: 1.02 (0.70), residues: 34 loop : -1.50 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 581 TYR 0.018 0.002 TYR D 371 PHE 0.017 0.002 PHE C 401 TRP 0.008 0.001 TRP C 74 HIS 0.003 0.001 HIS C 698 Details of bonding type rmsd covalent geometry : bond 0.00468 (10606) covalent geometry : angle 0.65357 (14382) hydrogen bonds : bond 0.05306 ( 626) hydrogen bonds : angle 4.49097 ( 1842) Misc. bond : bond 0.00088 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.413 Fit side-chains REVERT: C 35 GLN cc_start: 0.7714 (tt0) cc_final: 0.7305 (tm-30) REVERT: C 79 ARG cc_start: 0.6907 (mmm160) cc_final: 0.6095 (mtp180) REVERT: C 318 ASN cc_start: 0.7476 (t0) cc_final: 0.7221 (t0) REVERT: C 385 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.7529 (m-80) REVERT: C 440 LYS cc_start: 0.7480 (ttmm) cc_final: 0.6746 (mptt) REVERT: C 503 MET cc_start: 0.7719 (mmt) cc_final: 0.7441 (mmm) REVERT: C 655 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.7128 (mp) REVERT: D 35 GLN cc_start: 0.7614 (tt0) cc_final: 0.7300 (tm-30) REVERT: D 79 ARG cc_start: 0.6907 (mmm160) cc_final: 0.6136 (mtp180) REVERT: D 318 ASN cc_start: 0.7436 (t0) cc_final: 0.6989 (t0) REVERT: D 322 ASN cc_start: 0.7786 (m110) cc_final: 0.7472 (m110) REVERT: D 385 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.7557 (m-80) REVERT: D 440 LYS cc_start: 0.7388 (ttmm) cc_final: 0.6643 (mptt) outliers start: 19 outliers final: 15 residues processed: 128 average time/residue: 0.5079 time to fit residues: 71.2772 Evaluate side-chains 130 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 721 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 82 optimal weight: 0.0070 chunk 7 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 = 0.3994 r_free = 0.3994 target = 0.174029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.140213 restraints weight = 7166.979| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.40 r_work: 0.3552 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10607 Z= 0.135 Angle : 0.593 10.888 14382 Z= 0.301 Chirality : 0.044 0.198 1758 Planarity : 0.005 0.085 1638 Dihedral : 12.767 134.668 2714 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.63 % Favored : 95.21 % Rotamer: Outliers : 1.53 % Allowed : 14.15 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.97 (0.24), residues: 1210 helix: 1.47 (0.18), residues: 826 sheet: 0.96 (0.69), residues: 34 loop : -1.42 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 185 TYR 0.015 0.001 TYR D 371 PHE 0.018 0.001 PHE C 141 TRP 0.010 0.001 TRP D 482 HIS 0.002 0.001 HIS D 656 Details of bonding type rmsd covalent geometry : bond 0.00300 (10606) covalent geometry : angle 0.59313 (14382) hydrogen bonds : bond 0.04660 ( 626) hydrogen bonds : angle 4.34484 ( 1842) Misc. bond : bond 0.00021 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3444.92 seconds wall clock time: 59 minutes 48.48 seconds (3588.48 seconds total)