Starting phenix.real_space_refine on Sat Nov 16 04:32:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh3_40479/11_2024/8sh3_40479.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh3_40479/11_2024/8sh3_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh3_40479/11_2024/8sh3_40479.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh3_40479/11_2024/8sh3_40479.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh3_40479/11_2024/8sh3_40479.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh3_40479/11_2024/8sh3_40479.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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-2': 6, 'LBN:plan-3': 7, 'LBN:plan-1': 7} 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-2': 6, 'LBN:plan-3': 7, 'LBN:plan-1': 7} Unresolved non-hydrogen planarities: 72 Time building chain proxies: 7.15, per 1000 atoms: 0.69 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: 2.67 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.05 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: 3.47 Time building geometry restraints manager: 3.03 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: 0.00 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: 2.100 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: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 26.470 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 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:14.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.750 ------------------------------------------------------------------------------- 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 10606 Z= 0.260 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (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 TRP 0.009 0.001 TRP D 482 HIS 0.002 0.001 HIS D 656 PHE 0.017 0.001 PHE D 141 TYR 0.012 0.001 TYR C 371 ARG 0.002 0.000 ARG D 185 *********************** 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 : 1.101 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: 0.9745 time to fit residues: 141.6183 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 : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10606 Z= 0.280 Angle : 0.699 11.112 14382 Z= 0.339 Chirality : 0.047 0.205 1758 Planarity : 0.005 0.076 1638 Dihedral : 19.504 178.167 2714 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.79 % Favored : 95.04 % Rotamer: Outliers : 1.63 % Allowed : 7.74 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.24), residues: 1210 helix: 1.36 (0.18), residues: 838 sheet: 1.48 (0.73), residues: 34 loop : -1.79 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 74 HIS 0.003 0.001 HIS C 698 PHE 0.021 0.002 PHE D 141 TYR 0.016 0.002 TYR D 371 ARG 0.004 0.000 ARG C 24 *********************** 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: 17 poor density : 123 time to evaluate : 1.222 Fit side-chains REVERT: C 35 GLN cc_start: 0.7474 (tt0) cc_final: 0.7101 (tm-30) REVERT: C 79 ARG cc_start: 0.6756 (mmm-85) cc_final: 0.6309 (mtp180) REVERT: C 307 THR cc_start: 0.8146 (m) cc_final: 0.7878 (p) REVERT: C 440 LYS cc_start: 0.7394 (ttmm) cc_final: 0.6743 (mptt) REVERT: D 35 GLN cc_start: 0.7463 (tt0) cc_final: 0.7116 (tm-30) REVERT: D 38 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.6886 (ttt180) REVERT: D 307 THR cc_start: 0.8118 (m) cc_final: 0.7827 (p) REVERT: D 322 ASN cc_start: 0.7699 (m110) cc_final: 0.7453 (m110) REVERT: D 440 LYS cc_start: 0.7331 (ttmm) cc_final: 0.6677 (mptt) outliers start: 17 outliers final: 7 residues processed: 133 average time/residue: 1.0245 time to fit residues: 149.9768 Evaluate side-chains 117 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 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 61 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 10606 Z= 0.212 Angle : 0.619 8.174 14382 Z= 0.307 Chirality : 0.046 0.261 1758 Planarity : 0.005 0.083 1638 Dihedral : 17.688 173.038 2714 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.79 % Favored : 95.04 % Rotamer: Outliers : 1.72 % Allowed : 9.18 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.24), residues: 1210 helix: 1.53 (0.18), residues: 826 sheet: 1.06 (0.70), residues: 34 loop : -1.72 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 74 HIS 0.002 0.001 HIS D 656 PHE 0.018 0.001 PHE C 141 TYR 0.014 0.002 TYR C 371 ARG 0.003 0.000 ARG C 185 *********************** 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: 18 poor density : 121 time to evaluate : 1.119 Fit side-chains REVERT: C 35 GLN cc_start: 0.7479 (tt0) cc_final: 0.7118 (tm-30) REVERT: C 79 ARG cc_start: 0.6806 (mmm-85) cc_final: 0.6380 (mtp180) REVERT: C 307 THR cc_start: 0.8124 (m) cc_final: 0.7838 (p) REVERT: C 440 LYS cc_start: 0.7450 (ttmm) cc_final: 0.6799 (mptt) REVERT: C 655 ILE cc_start: 0.7270 (OUTLIER) cc_final: 0.6992 (mp) REVERT: D 35 GLN cc_start: 0.7495 (tt0) cc_final: 0.7187 (tm-30) REVERT: D 38 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6867 (ttt180) REVERT: D 318 ASN cc_start: 0.7471 (t0) cc_final: 0.7090 (t0) REVERT: D 440 LYS cc_start: 0.7323 (ttmm) cc_final: 0.6667 (mptt) outliers start: 18 outliers final: 8 residues processed: 132 average time/residue: 0.9818 time to fit residues: 142.7568 Evaluate side-chains 121 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 288 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 655 ILE 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 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 83 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 12 optimal weight: 0.0770 chunk 52 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10606 Z= 0.197 Angle : 0.604 7.652 14382 Z= 0.298 Chirality : 0.046 0.363 1758 Planarity : 0.005 0.082 1638 Dihedral : 16.012 162.793 2714 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.79 % Favored : 95.04 % Rotamer: Outliers : 3.06 % Allowed : 9.46 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.24), residues: 1210 helix: 1.62 (0.18), residues: 826 sheet: 0.98 (0.70), residues: 34 loop : -1.57 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 482 HIS 0.002 0.001 HIS D 656 PHE 0.018 0.001 PHE D 141 TYR 0.013 0.001 TYR C 371 ARG 0.002 0.000 ARG C 185 *********************** 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 156 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 1.039 Fit side-chains REVERT: C 35 GLN cc_start: 0.7488 (tt0) cc_final: 0.7138 (tm-30) REVERT: C 307 THR cc_start: 0.8114 (m) cc_final: 0.7830 (p) REVERT: C 385 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.7480 (m-80) REVERT: C 440 LYS cc_start: 0.7451 (ttmm) cc_final: 0.6800 (mptt) REVERT: C 655 ILE cc_start: 0.7265 (OUTLIER) cc_final: 0.6953 (mp) REVERT: D 35 GLN cc_start: 0.7487 (tt0) cc_final: 0.7195 (tm-30) REVERT: D 307 THR cc_start: 0.8058 (m) cc_final: 0.7749 (p) REVERT: D 440 LYS cc_start: 0.7329 (ttmm) cc_final: 0.6675 (mptt) outliers start: 32 outliers final: 11 residues processed: 143 average time/residue: 0.9810 time to fit residues: 155.0355 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 : 1.189 ------------------------------------------------------------------------------- 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 288 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 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 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 66 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 0.0070 chunk 105 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 39 optimal weight: 0.0770 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 ASN D 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10606 Z= 0.160 Angle : 0.583 8.092 14382 Z= 0.289 Chirality : 0.046 0.353 1758 Planarity : 0.005 0.077 1638 Dihedral : 14.981 154.607 2714 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.53 % Allowed : 12.05 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.25), residues: 1210 helix: 1.71 (0.18), residues: 826 sheet: 0.95 (0.69), residues: 34 loop : -1.48 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 482 HIS 0.002 0.001 HIS D 728 PHE 0.016 0.001 PHE D 141 TYR 0.015 0.001 TYR C 323 ARG 0.002 0.000 ARG C 185 *********************** 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 137 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 1.144 Fit side-chains REVERT: C 35 GLN cc_start: 0.7454 (tt0) cc_final: 0.7145 (tm-30) REVERT: C 307 THR cc_start: 0.8065 (m) cc_final: 0.7824 (p) REVERT: C 385 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.7415 (m-80) REVERT: C 440 LYS cc_start: 0.7428 (ttmm) cc_final: 0.6781 (mptt) REVERT: C 655 ILE cc_start: 0.7241 (OUTLIER) cc_final: 0.6878 (mp) REVERT: D 35 GLN cc_start: 0.7509 (tt0) cc_final: 0.7233 (tm-30) REVERT: D 307 THR cc_start: 0.8004 (m) cc_final: 0.7726 (p) REVERT: D 440 LYS cc_start: 0.7307 (ttmm) cc_final: 0.6659 (mptt) outliers start: 16 outliers final: 9 residues processed: 131 average time/residue: 0.9945 time to fit residues: 143.1837 Evaluate side-chains 122 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 1.276 ------------------------------------------------------------------------------- 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 288 LEU 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 655 ILE Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 545 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 241 ASN D 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 10606 Z= 0.210 Angle : 0.606 8.379 14382 Z= 0.304 Chirality : 0.047 0.358 1758 Planarity : 0.005 0.081 1638 Dihedral : 14.545 147.733 2714 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.88 % Favored : 94.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.24), residues: 1210 helix: 1.62 (0.18), residues: 826 sheet: 0.91 (0.70), residues: 34 loop : -1.55 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 74 HIS 0.002 0.001 HIS D 656 PHE 0.017 0.001 PHE C 141 TYR 0.014 0.001 TYR C 371 ARG 0.002 0.000 ARG D 185 *********************** 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 139 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 1.299 Fit side-chains REVERT: C 35 GLN cc_start: 0.7484 (tt0) cc_final: 0.7151 (tm-30) REVERT: C 79 ARG cc_start: 0.7051 (mmm160) cc_final: 0.6303 (mtp180) REVERT: C 307 THR cc_start: 0.8095 (m) cc_final: 0.7790 (p) REVERT: C 385 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7384 (m-80) REVERT: C 440 LYS cc_start: 0.7446 (ttmm) cc_final: 0.6794 (mptt) REVERT: C 655 ILE cc_start: 0.7214 (OUTLIER) cc_final: 0.6819 (mp) REVERT: D 35 GLN cc_start: 0.7518 (tt0) cc_final: 0.7234 (tm-30) REVERT: D 318 ASN cc_start: 0.7521 (t0) cc_final: 0.7220 (t0) REVERT: D 385 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7554 (m-80) REVERT: D 440 LYS cc_start: 0.7332 (ttmm) cc_final: 0.6682 (mptt) outliers start: 22 outliers final: 12 residues processed: 133 average time/residue: 0.9767 time to fit residues: 143.3599 Evaluate side-chains 123 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 288 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 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 721 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 73 optimal weight: 0.4980 chunk 71 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 ASN D 322 ASN D 689 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10606 Z= 0.210 Angle : 0.600 9.111 14382 Z= 0.304 Chirality : 0.046 0.288 1758 Planarity : 0.005 0.082 1638 Dihedral : 13.952 143.666 2714 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.71 % Rotamer: Outliers : 2.29 % Allowed : 12.33 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.24), residues: 1210 helix: 1.57 (0.18), residues: 826 sheet: 0.96 (0.71), residues: 34 loop : -1.54 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 482 HIS 0.002 0.001 HIS D 728 PHE 0.017 0.001 PHE D 141 TYR 0.014 0.002 TYR D 371 ARG 0.003 0.000 ARG C 185 *********************** 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 143 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 1.075 Fit side-chains REVERT: C 35 GLN cc_start: 0.7475 (tt0) cc_final: 0.7141 (tm-30) REVERT: C 79 ARG cc_start: 0.7115 (mmm160) cc_final: 0.6358 (mtp180) REVERT: C 283 MET cc_start: 0.7408 (mmt) cc_final: 0.6990 (mmt) REVERT: C 307 THR cc_start: 0.8099 (m) cc_final: 0.7808 (p) REVERT: C 385 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7315 (m-80) REVERT: C 440 LYS cc_start: 0.7432 (ttmm) cc_final: 0.6785 (mptt) REVERT: C 655 ILE cc_start: 0.7217 (OUTLIER) cc_final: 0.6829 (mp) REVERT: D 35 GLN cc_start: 0.7411 (tt0) cc_final: 0.7202 (tm-30) REVERT: D 79 ARG cc_start: 0.7042 (mmm160) cc_final: 0.6303 (mtp180) REVERT: D 318 ASN cc_start: 0.7492 (t0) cc_final: 0.7169 (t0) REVERT: D 385 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7364 (m-80) REVERT: D 440 LYS cc_start: 0.7342 (ttmm) cc_final: 0.6685 (mptt) outliers start: 24 outliers final: 13 residues processed: 134 average time/residue: 0.9939 time to fit residues: 146.5066 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 : 1.153 ------------------------------------------------------------------------------- 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 288 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 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 721 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 322 ASN D 689 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10606 Z= 0.197 Angle : 0.595 10.352 14382 Z= 0.300 Chirality : 0.045 0.242 1758 Planarity : 0.005 0.081 1638 Dihedral : 13.526 140.527 2714 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.88 % Favored : 94.96 % Rotamer: Outliers : 2.20 % Allowed : 13.19 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.24), residues: 1210 helix: 1.58 (0.18), residues: 826 sheet: 0.98 (0.71), residues: 34 loop : -1.47 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 482 HIS 0.002 0.001 HIS D 728 PHE 0.017 0.001 PHE C 141 TYR 0.014 0.001 TYR D 371 ARG 0.002 0.000 ARG C 185 *********************** 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 146 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 1.121 Fit side-chains REVERT: C 35 GLN cc_start: 0.7485 (tt0) cc_final: 0.7228 (tm-30) REVERT: C 79 ARG cc_start: 0.7097 (mmm160) cc_final: 0.6367 (mtp180) REVERT: C 307 THR cc_start: 0.8082 (m) cc_final: 0.7804 (p) REVERT: C 318 ASN cc_start: 0.7467 (t0) cc_final: 0.7212 (t0) REVERT: C 385 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7211 (m-80) REVERT: C 440 LYS cc_start: 0.7427 (ttmm) cc_final: 0.6781 (mptt) REVERT: C 503 MET cc_start: 0.6931 (mmt) cc_final: 0.6707 (mmm) REVERT: C 655 ILE cc_start: 0.7185 (OUTLIER) cc_final: 0.6798 (mp) REVERT: D 79 ARG cc_start: 0.7076 (mmm160) cc_final: 0.6351 (mtp180) REVERT: D 307 THR cc_start: 0.8048 (m) cc_final: 0.7756 (p) REVERT: D 318 ASN cc_start: 0.7469 (t0) cc_final: 0.7195 (t0) REVERT: D 385 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.7269 (m-80) REVERT: D 440 LYS cc_start: 0.7389 (ttmm) cc_final: 0.6741 (mptt) outliers start: 23 outliers final: 14 residues processed: 138 average time/residue: 0.9404 time to fit residues: 143.8743 Evaluate side-chains 133 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 288 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 D residue 100 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 556 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 0.0970 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 D 322 ASN D 689 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10606 Z= 0.185 Angle : 0.586 11.002 14382 Z= 0.297 Chirality : 0.044 0.223 1758 Planarity : 0.005 0.081 1638 Dihedral : 12.991 137.729 2714 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.79 % Favored : 95.04 % Rotamer: Outliers : 2.01 % Allowed : 13.86 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.24), residues: 1210 helix: 1.60 (0.18), residues: 826 sheet: 1.03 (0.72), residues: 34 loop : -1.47 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 482 HIS 0.002 0.001 HIS D 728 PHE 0.017 0.001 PHE D 141 TYR 0.013 0.001 TYR D 105 ARG 0.003 0.000 ARG D 185 *********************** 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 139 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.976 Fit side-chains REVERT: C 35 GLN cc_start: 0.7479 (tt0) cc_final: 0.7228 (tm-30) REVERT: C 79 ARG cc_start: 0.7101 (mmm160) cc_final: 0.6350 (mtp180) REVERT: C 307 THR cc_start: 0.8074 (m) cc_final: 0.7810 (p) REVERT: C 318 ASN cc_start: 0.7454 (t0) cc_final: 0.7197 (t0) REVERT: C 385 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7203 (m-80) REVERT: C 440 LYS cc_start: 0.7431 (ttmm) cc_final: 0.6786 (mptt) REVERT: C 503 MET cc_start: 0.6956 (mmt) cc_final: 0.6745 (mmm) REVERT: C 655 ILE cc_start: 0.7229 (OUTLIER) cc_final: 0.6830 (mp) REVERT: D 79 ARG cc_start: 0.7027 (mmm160) cc_final: 0.6328 (mtp180) REVERT: D 307 THR cc_start: 0.8034 (m) cc_final: 0.7758 (p) REVERT: D 318 ASN cc_start: 0.7487 (t0) cc_final: 0.7220 (t0) REVERT: D 385 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7270 (m-80) REVERT: D 440 LYS cc_start: 0.7379 (ttmm) cc_final: 0.6732 (mptt) outliers start: 21 outliers final: 15 residues processed: 128 average time/residue: 0.9781 time to fit residues: 137.6630 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 : 1.057 ------------------------------------------------------------------------------- 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 288 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 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 70 optimal weight: 0.0470 chunk 54 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10606 Z= 0.186 Angle : 0.584 11.083 14382 Z= 0.296 Chirality : 0.044 0.227 1758 Planarity : 0.005 0.080 1638 Dihedral : 12.504 134.689 2714 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.79 % Favored : 95.04 % Rotamer: Outliers : 1.82 % Allowed : 14.63 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.24), residues: 1210 helix: 1.62 (0.18), residues: 826 sheet: 1.07 (0.71), residues: 34 loop : -1.47 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 482 HIS 0.002 0.001 HIS D 656 PHE 0.018 0.001 PHE C 141 TYR 0.015 0.001 TYR D 105 ARG 0.002 0.000 ARG D 185 ********************** 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 138 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 1.171 Fit side-chains REVERT: C 35 GLN cc_start: 0.7482 (tt0) cc_final: 0.7220 (tm-30) REVERT: C 79 ARG cc_start: 0.7092 (mmm160) cc_final: 0.6319 (mtp180) REVERT: C 307 THR cc_start: 0.8086 (m) cc_final: 0.7806 (p) REVERT: C 318 ASN cc_start: 0.7462 (t0) cc_final: 0.7178 (t0) REVERT: C 385 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7216 (m-80) REVERT: C 440 LYS cc_start: 0.7431 (ttmm) cc_final: 0.6784 (mptt) REVERT: C 503 MET cc_start: 0.6916 (mmt) cc_final: 0.6707 (mmm) REVERT: C 655 ILE cc_start: 0.7223 (OUTLIER) cc_final: 0.6834 (mp) REVERT: D 79 ARG cc_start: 0.7020 (mmm160) cc_final: 0.6317 (mtp180) REVERT: D 318 ASN cc_start: 0.7466 (t0) cc_final: 0.7207 (t0) REVERT: D 385 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.7289 (m-80) REVERT: D 440 LYS cc_start: 0.7377 (ttmm) cc_final: 0.6731 (mptt) outliers start: 19 outliers final: 14 residues processed: 129 average time/residue: 1.0741 time to fit residues: 153.4021 Evaluate side-chains 135 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 288 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 12 optimal weight: 0.0470 chunk 17 optimal weight: 0.9990 chunk 85 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 241 ASN D 322 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 = 0.175632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.141863 restraints weight = 7351.508| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.43 r_work: 0.3589 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10606 Z= 0.185 Angle : 0.583 11.164 14382 Z= 0.297 Chirality : 0.044 0.223 1758 Planarity : 0.005 0.081 1638 Dihedral : 12.351 133.460 2714 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.88 % Favored : 94.96 % Rotamer: Outliers : 2.10 % Allowed : 14.34 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.24), residues: 1210 helix: 1.60 (0.18), residues: 826 sheet: 1.10 (0.72), residues: 34 loop : -1.47 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 482 HIS 0.002 0.001 HIS D 728 PHE 0.017 0.001 PHE C 141 TYR 0.016 0.001 TYR D 105 ARG 0.002 0.000 ARG C 185 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3302.97 seconds wall clock time: 60 minutes 43.98 seconds (3643.98 seconds total)