Starting phenix.real_space_refine on Wed Mar 4 06:38:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rxg_24730/03_2026/7rxg_24730.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rxg_24730/03_2026/7rxg_24730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rxg_24730/03_2026/7rxg_24730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rxg_24730/03_2026/7rxg_24730.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rxg_24730/03_2026/7rxg_24730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rxg_24730/03_2026/7rxg_24730.map" } resolution = 2.28 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= -0.000 sd= 0.004 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 P 20 5.49 5 S 38 5.16 5 C 7374 2.51 5 N 1766 2.21 5 O 2082 1.98 5 H 96 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11380 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 5258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5258 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 31, 'TRANS': 618} Chain breaks: 2 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "A" Number of atoms: 5258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5258 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 31, 'TRANS': 618} Chain breaks: 2 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 326 Unusual residues: {' CA': 2, 'PGW': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 204 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PGW:plan-3': 5, 'PGW:plan-2': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 394 Unusual residues: {' CA': 2, 'PGW': 12} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PGW:plan-3': 7, 'PGW:plan-2': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 72 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 72 Classifications: {'water': 24} Link IDs: {None: 23} Time building chain proxies: 2.70, per 1000 atoms: 0.24 Number of scatterers: 11380 At special positions: 0 Unit cell: (86.9241, 127.913, 100.351, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 4 19.99 S 38 16.00 P 20 15.00 O 2082 8.00 N 1766 7.00 C 7374 6.00 H 96 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 601.1 milliseconds 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2488 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 6 sheets defined 73.5% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'B' and resid 28 through 46 Processing helix chain 'B' and resid 68 through 86 Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 103 through 117 Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 144 through 156 Processing helix chain 'B' and resid 162 through 174 Processing helix chain 'B' and resid 174 through 191 Processing helix chain 'B' and resid 191 through 205 Processing helix chain 'B' and resid 209 through 238 Processing helix chain 'B' and resid 242 through 247 Processing helix chain 'B' and resid 272 through 281 Processing helix chain 'B' and resid 282 through 311 Processing helix chain 'B' and resid 317 through 350 removed outlier: 4.461A pdb=" N ILE B 323 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Proline residue: B 324 - end of helix Proline residue: B 333 - end of helix Processing helix chain 'B' and resid 354 through 384 removed outlier: 3.980A pdb=" N VAL B 368 " --> pdb=" O GLN B 364 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) Proline residue: B 377 - end of helix Processing helix chain 'B' and resid 392 through 403 removed outlier: 4.124A pdb=" N ASP B 397 " --> pdb=" O PRO B 394 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL B 398 " --> pdb=" O TYR B 395 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU B 401 " --> pdb=" O VAL B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 414 Processing helix chain 'B' and resid 424 through 435 Processing helix chain 'B' and resid 435 through 463 removed outlier: 4.735A pdb=" N VAL B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Proline residue: B 449 - end of helix Processing helix chain 'B' and resid 490 through 501 Processing helix chain 'B' and resid 507 through 526 removed outlier: 4.054A pdb=" N ASP B 511 " --> pdb=" O ASP B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 529 No H-bonds generated for 'chain 'B' and resid 527 through 529' Processing helix chain 'B' and resid 531 through 554 removed outlier: 3.787A pdb=" N ARG B 545 " --> pdb=" O TRP B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 591 removed outlier: 4.419A pdb=" N ASP B 571 " --> pdb=" O GLY B 567 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE B 582 " --> pdb=" O TRP B 578 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 634 removed outlier: 3.527A pdb=" N LYS B 634 " --> pdb=" O SER B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 658 Processing helix chain 'B' and resid 702 through 707 removed outlier: 3.829A pdb=" N TRP B 706 " --> pdb=" O THR B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 724 Processing helix chain 'A' and resid 28 through 46 Processing helix chain 'A' and resid 68 through 86 Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 103 through 117 Processing helix chain 'A' and resid 118 through 122 Processing helix chain 'A' and resid 144 through 156 Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 174 through 191 Processing helix chain 'A' and resid 191 through 205 Processing helix chain 'A' and resid 209 through 238 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 272 through 281 Processing helix chain 'A' and resid 282 through 311 Processing helix chain 'A' and resid 317 through 350 removed outlier: 4.462A pdb=" N ILE A 323 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Proline residue: A 324 - end of helix Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 354 through 384 removed outlier: 3.980A pdb=" N VAL A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 392 through 403 removed outlier: 4.124A pdb=" N ASP A 397 " --> pdb=" O PRO A 394 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL A 398 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 401 " --> pdb=" O VAL A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 414 Processing helix chain 'A' and resid 424 through 435 Processing helix chain 'A' and resid 435 through 463 removed outlier: 4.735A pdb=" N VAL A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Proline residue: A 449 - end of helix Processing helix chain 'A' and resid 490 through 501 Processing helix chain 'A' and resid 507 through 526 removed outlier: 4.055A pdb=" N ASP A 511 " --> pdb=" O ASP A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 529 No H-bonds generated for 'chain 'A' and resid 527 through 529' Processing helix chain 'A' and resid 531 through 554 removed outlier: 3.787A pdb=" N ARG A 545 " --> pdb=" O TRP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 591 removed outlier: 4.419A pdb=" N ASP A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 582 " --> pdb=" O TRP A 578 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 634 removed outlier: 3.527A pdb=" N LYS A 634 " --> pdb=" O SER A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 658 Processing helix chain 'A' and resid 702 through 707 removed outlier: 3.830A pdb=" N TRP A 706 " --> pdb=" O THR A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 724 Processing sheet with id=AA1, first strand: chain 'B' and resid 48 through 54 removed outlier: 3.765A pdb=" N ALA B 138 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASN B 23 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N VAL B 136 " --> pdb=" O ASN B 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 260 through 261 removed outlier: 4.118A pdb=" N GLU B 266 " --> pdb=" O ASP B 261 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 504 through 505 removed outlier: 6.672A pdb=" N GLU B 504 " --> pdb=" O LYS B 556 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 54 removed outlier: 3.765A pdb=" N ALA A 138 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASN A 23 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N VAL A 136 " --> pdb=" O ASN A 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 260 through 261 removed outlier: 4.119A pdb=" N GLU A 266 " --> pdb=" O ASP A 261 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 504 through 505 removed outlier: 6.671A pdb=" N GLU A 504 " --> pdb=" O LYS A 556 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 722 hydrogen bonds defined for protein. 2082 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: 1.84 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 96 1.03 - 1.22: 46 1.22 - 1.42: 4769 1.42 - 1.61: 6579 1.61 - 1.81: 96 Bond restraints: 11586 Sorted by residual: bond pdb=" C1 PGW B 809 " pdb=" O01 PGW B 809 " ideal model delta sigma weight residual 1.332 1.426 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" C1 PGW A1112 " pdb=" O01 PGW A1112 " ideal model delta sigma weight residual 1.332 1.426 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C1 PGW A1109 " pdb=" O01 PGW A1109 " ideal model delta sigma weight residual 1.332 1.422 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C1 PGW B 806 " pdb=" O01 PGW B 806 " ideal model delta sigma weight residual 1.332 1.422 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C1 PGW A1111 " pdb=" O01 PGW A1111 " ideal model delta sigma weight residual 1.332 1.422 -0.090 2.00e-02 2.50e+03 2.02e+01 ... (remaining 11581 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 14626 2.29 - 4.58: 622 4.58 - 6.87: 190 6.87 - 9.16: 30 9.16 - 11.45: 62 Bond angle restraints: 15530 Sorted by residual: angle pdb=" CA PHE B 419 " pdb=" C PHE B 419 " pdb=" O PHE B 419 " ideal model delta sigma weight residual 120.82 113.55 7.27 1.05e+00 9.07e-01 4.79e+01 angle pdb=" CA PHE A 419 " pdb=" C PHE A 419 " pdb=" O PHE A 419 " ideal model delta sigma weight residual 120.82 113.63 7.19 1.05e+00 9.07e-01 4.69e+01 angle pdb=" O PHE B 419 " pdb=" C PHE B 419 " pdb=" N SER B 420 " ideal model delta sigma weight residual 122.07 127.32 -5.25 1.03e+00 9.43e-01 2.60e+01 angle pdb=" O PHE A 419 " pdb=" C PHE A 419 " pdb=" N SER A 420 " ideal model delta sigma weight residual 122.07 127.24 -5.17 1.03e+00 9.43e-01 2.52e+01 angle pdb=" N VAL A 403 " pdb=" CA VAL A 403 " pdb=" C VAL A 403 " ideal model delta sigma weight residual 112.80 108.35 4.45 1.15e+00 7.56e-01 1.50e+01 ... (remaining 15525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.97: 6620 34.97 - 69.95: 270 69.95 - 104.92: 48 104.92 - 139.90: 10 139.90 - 174.87: 20 Dihedral angle restraints: 6968 sinusoidal: 3134 harmonic: 3834 Sorted by residual: dihedral pdb=" CA ALA A 389 " pdb=" C ALA A 389 " pdb=" N SER A 390 " pdb=" CA SER A 390 " ideal model delta harmonic sigma weight residual 180.00 153.89 26.11 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA ALA B 389 " pdb=" C ALA B 389 " pdb=" N SER B 390 " pdb=" CA SER B 390 " ideal model delta harmonic sigma weight residual 180.00 153.90 26.10 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" O01 PGW B 809 " pdb=" C01 PGW B 809 " pdb=" C02 PGW B 809 " pdb=" O03 PGW B 809 " ideal model delta sinusoidal sigma weight residual 59.30 -115.57 174.87 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 6965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1021 0.038 - 0.075: 468 0.075 - 0.113: 127 0.113 - 0.151: 32 0.151 - 0.189: 22 Chirality restraints: 1670 Sorted by residual: chirality pdb=" CA GLU B 418 " pdb=" N GLU B 418 " pdb=" C GLU B 418 " pdb=" CB GLU B 418 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.89e-01 chirality pdb=" CA GLU A 418 " pdb=" N GLU A 418 " pdb=" C GLU A 418 " pdb=" CB GLU A 418 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" C02 PGW A1102 " pdb=" C01 PGW A1102 " pdb=" C03 PGW A1102 " pdb=" O01 PGW A1102 " both_signs ideal model delta sigma weight residual False 2.36 2.54 -0.18 2.00e-01 2.50e+01 8.33e-01 ... (remaining 1667 not shown) Planarity restraints: 1902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 420 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C SER B 420 " 0.059 2.00e-02 2.50e+03 pdb=" O SER B 420 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE B 421 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 420 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C SER A 420 " -0.059 2.00e-02 2.50e+03 pdb=" O SER A 420 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE A 421 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 404 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.97e+00 pdb=" C ARG A 404 " 0.046 2.00e-02 2.50e+03 pdb=" O ARG A 404 " -0.017 2.00e-02 2.50e+03 pdb=" N PRO A 405 " -0.016 2.00e-02 2.50e+03 ... (remaining 1899 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.30: 62 2.30 - 2.87: 4097 2.87 - 3.45: 13704 3.45 - 4.02: 23759 4.02 - 4.60: 35187 Nonbonded interactions: 76809 Sorted by model distance: nonbonded pdb=" OG SER A 546 " pdb=" H1 HOH A2702 " model vdw 1.722 2.450 nonbonded pdb=" OG SER B 546 " pdb=" H1 HOH B2702 " model vdw 1.722 2.450 nonbonded pdb=" O LYS B 556 " pdb=" H1 HOH B2709 " model vdw 1.739 2.450 nonbonded pdb=" O LYS A 556 " pdb=" H1 HOH A2709 " model vdw 1.739 2.450 nonbonded pdb=" OH TYR A 621 " pdb=" H1 HOH A2705 " model vdw 1.739 2.450 ... (remaining 76804 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 'A' and (resid 12 through 724 or (resid 1105 and (name C01 or name C02 or \ name C03 or name C1 or name C10 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name \ C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or na \ me C30 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name \ O01 or name O02 or name O03 or name O04 or name O11)) or (resid 1106 and (name \ C01 or name C02 or name C03 or name C1 or name C19 or name C2 or name C20 or nam \ e C21 or name C22 or name O01 or name O02 or name O03 or name O04 or name O11 or \ name O12 or name O13 or name O14 or name P )) or (resid 1107 and (name C01 or n \ ame C02 or name C03 or name C19 or name C2 or name C3 or name C4 or name C5 or n \ ame C6 or name C7 or name C8 or name O01 or name O02 or name O03 or name O11 or \ name O12 or name O13 or name O14 or name P )) or (resid 1108 and (name C01 or na \ me C02 or name C03 or name C1 or name C15 or name C16 or name C17 or name C18 or \ name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C24 \ or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or name \ C30 or name C4 )) or (resid 1109 and (name C01 or name C02 or name C03 or name C \ 3 or name C4 or name C5 or name C6 or name O01 or name O02 or name O03 or name O \ 04 or name O11 or name O12 or name O13 or name O14 or name P )) or (resid 1110 a \ nd (name C01 or name C02 or name C03 or name C3 or name C4 or name C5 or name C6 \ or name C7 or name O01 or name O02 or name O03 or name O11 or name O12 or name \ O13 or name O14 or name P )) or (resid 1111 and (name C01 or name C02 or name C0 \ 3 or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name \ C24 or name O01 or name O02 or name O03 or name O04 or name O11 or name O12 or \ name O13 or name O14 or name P )) or resid 1112)) selection = (chain 'B' and (resid 12 through 724 or (resid 805 and (name C01 or name C02 or \ name C03 or name C1 or name C10 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C \ 24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or nam \ e C30 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name \ O01 or name O02 or name O03 or name O04 or name O11)) or (resid 806 and (name C0 \ 1 or name C02 or name C03 or name C1 or name C19 or name C2 or name C20 or name \ C21 or name C22 or name O01 or name O02 or name O03 or name O04 or name O11 or n \ ame O12 or name O13 or name O14 or name P )) or (resid 807 and (name C01 or name \ C02 or name C03 or name C19 or name C2 or name C3 or name C4 or name C5 or name \ C6 or name C7 or name C8 or name O01 or name O02 or name O03 or name O11 or nam \ e O12 or name O13 or name O14 or name P )) or (resid 808 and (name C01 or name C \ 02 or name C03 or name C1 or name C15 or name C16 or name C17 or name C18 or nam \ e C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or name C30 \ or name C4 )) or (resid 809 and (name C01 or name C02 or name C03 or name C3 or \ name C4 or name C5 or name C6 or name O01 or name O02 or name O03 or name O04 or \ name O11 or name O12 or name O13 or name O14 or name P )) or (resid 810 and (na \ me C01 or name C02 or name C03 or name C3 or name C4 or name C5 or name C6 or na \ me C7 or name O01 or name O02 or name O03 or name O11 or name O12 or name O13 or \ name O14 or name P )) or (resid 811 and (name C01 or name C02 or name C03 or na \ me C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C24 or \ name O01 or name O02 or name O03 or name O04 or name O11 or name O12 or name O1 \ 3 or name O14 or name P )) or (resid 812 and (name C01 or name C02 or name C03 o \ r name C1 or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 \ or name C24 or name C25 or name C26 or name C27 or name C3 or name C4 or name C \ 5 or name C6 or name O01 or name O02 or name O03 or name O04 or name O11 or name \ O12 or name O13 or name O14 or name P )))) } 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: 5.090 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: 0.110 Extract box with map and model: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.340 Find NCS groups from input model: 0.150 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:7.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 : 0.008 0.094 11490 Z= 0.409 Angle : 1.269 11.455 15482 Z= 0.549 Chirality : 0.049 0.189 1670 Planarity : 0.005 0.045 1902 Dihedral : 22.385 174.869 4480 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.48 % Favored : 97.36 % Rotamer: Outliers : 0.18 % Allowed : 2.32 % Favored : 97.50 % 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 are not related in a simple way. whole: -0.83 (0.21), residues: 1288 helix: 0.09 (0.16), residues: 884 sheet: -0.80 (0.56), residues: 54 loop : -1.95 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 496 TYR 0.013 0.002 TYR B 352 PHE 0.018 0.002 PHE A 388 TRP 0.028 0.002 TRP B 155 HIS 0.008 0.002 HIS A 619 Details of bonding type rmsd covalent geometry : bond 0.00803 (11490) covalent geometry : angle 1.26852 (15482) hydrogen bonds : bond 0.11633 ( 722) hydrogen bonds : angle 5.47866 ( 2082) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 180 time to evaluate : 0.415 Fit side-chains REVERT: B 34 LYS cc_start: 0.7068 (ttpt) cc_final: 0.6788 (mttt) REVERT: B 150 GLN cc_start: 0.7269 (tp40) cc_final: 0.7063 (mm-40) REVERT: B 417 THR cc_start: 0.2252 (OUTLIER) cc_final: 0.1547 (m) REVERT: B 601 GLU cc_start: 0.6389 (mm-30) cc_final: 0.5758 (mm-30) REVERT: B 703 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6617 (tp30) REVERT: A 34 LYS cc_start: 0.7095 (ttpt) cc_final: 0.6806 (mttt) REVERT: A 137 ASP cc_start: 0.7606 (t0) cc_final: 0.7175 (t70) REVERT: A 150 GLN cc_start: 0.7213 (tp40) cc_final: 0.6994 (mm-40) REVERT: A 417 THR cc_start: 0.2234 (OUTLIER) cc_final: 0.1553 (m) REVERT: A 601 GLU cc_start: 0.6342 (mm-30) cc_final: 0.5743 (mm-30) outliers start: 2 outliers final: 0 residues processed: 182 average time/residue: 0.7559 time to fit residues: 145.7261 Evaluate side-chains 132 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain A residue 417 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 129 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN B 78 GLN B 113 HIS B 148 ASN B 171 ASN B 283 GLN B 355 GLN B 370 ASN B 400 HIS B 438 GLN B 453 GLN B 593 ASN B 599 ASN A 58 ASN A 78 GLN A 113 HIS A 148 ASN A 171 ASN A 283 GLN A 355 GLN A 370 ASN A 400 HIS A 438 GLN A 453 GLN A 593 ASN A 599 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.160249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.121267 restraints weight = 9873.010| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.08 r_work: 0.3118 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11490 Z= 0.120 Angle : 0.484 4.583 15482 Z= 0.256 Chirality : 0.038 0.144 1670 Planarity : 0.004 0.030 1902 Dihedral : 23.693 162.751 2036 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.43 % Allowed : 6.61 % Favored : 91.96 % 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 are not related in a simple way. whole: 1.20 (0.24), residues: 1288 helix: 1.70 (0.17), residues: 890 sheet: 0.35 (0.68), residues: 44 loop : -1.50 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 21 TYR 0.015 0.001 TYR A 180 PHE 0.009 0.001 PHE B 193 TRP 0.021 0.002 TRP A 227 HIS 0.005 0.001 HIS A 619 Details of bonding type rmsd covalent geometry : bond 0.00234 (11490) covalent geometry : angle 0.48436 (15482) hydrogen bonds : bond 0.04821 ( 722) hydrogen bonds : angle 4.35121 ( 2082) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 LYS cc_start: 0.7635 (mmtp) cc_final: 0.7328 (mttm) REVERT: B 69 LYS cc_start: 0.7803 (mtmm) cc_final: 0.7590 (mttm) REVERT: B 150 GLN cc_start: 0.7699 (tp40) cc_final: 0.7429 (mm110) REVERT: B 305 GLU cc_start: 0.8192 (tp30) cc_final: 0.7856 (tm-30) REVERT: B 601 GLU cc_start: 0.6648 (mm-30) cc_final: 0.6048 (mm-30) REVERT: B 606 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.6568 (mtp85) REVERT: B 707 MET cc_start: 0.7607 (mtp) cc_final: 0.7111 (mtt) REVERT: A 35 LYS cc_start: 0.7637 (mmtp) cc_final: 0.7340 (mttm) REVERT: A 42 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7628 (mm-30) REVERT: A 69 LYS cc_start: 0.7759 (mtmm) cc_final: 0.7557 (mttm) REVERT: A 104 GLU cc_start: 0.7773 (tt0) cc_final: 0.7573 (tt0) REVERT: A 305 GLU cc_start: 0.8196 (tp30) cc_final: 0.7868 (tm-30) REVERT: A 601 GLU cc_start: 0.6737 (mm-30) cc_final: 0.6099 (mm-30) REVERT: A 606 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.6550 (mtp85) REVERT: A 707 MET cc_start: 0.7604 (mtp) cc_final: 0.7387 (mtp) outliers start: 16 outliers final: 7 residues processed: 148 average time/residue: 0.6968 time to fit residues: 109.7326 Evaluate side-chains 137 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 606 ARG Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 606 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 107 optimal weight: 7.9990 chunk 34 optimal weight: 0.3980 chunk 29 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN B 599 ASN A 58 ASN A 599 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.157087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.117942 restraints weight = 9776.042| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.07 r_work: 0.3060 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11490 Z= 0.119 Angle : 0.486 4.805 15482 Z= 0.262 Chirality : 0.038 0.150 1670 Planarity : 0.004 0.030 1902 Dihedral : 20.830 154.504 2034 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.23 % Allowed : 6.70 % Favored : 91.07 % 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 are not related in a simple way. whole: 1.96 (0.24), residues: 1288 helix: 2.22 (0.17), residues: 890 sheet: 0.26 (0.73), residues: 48 loop : -1.01 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 647 TYR 0.012 0.002 TYR A 212 PHE 0.011 0.001 PHE A 419 TRP 0.022 0.002 TRP B 227 HIS 0.008 0.001 HIS B 619 Details of bonding type rmsd covalent geometry : bond 0.00238 (11490) covalent geometry : angle 0.48610 (15482) hydrogen bonds : bond 0.05139 ( 722) hydrogen bonds : angle 4.29936 ( 2082) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.423 Fit side-chains REVERT: B 33 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7248 (pt) REVERT: B 35 LYS cc_start: 0.7681 (mmtp) cc_final: 0.7306 (mttm) REVERT: B 42 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7728 (mm-30) REVERT: B 145 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6820 (mp0) REVERT: B 305 GLU cc_start: 0.8110 (tp30) cc_final: 0.7794 (tm-30) REVERT: B 601 GLU cc_start: 0.6634 (mm-30) cc_final: 0.5948 (mm-30) REVERT: B 629 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7828 (ttm110) REVERT: B 707 MET cc_start: 0.7666 (mtp) cc_final: 0.7177 (mtt) REVERT: A 33 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7230 (pt) REVERT: A 35 LYS cc_start: 0.7710 (mmtp) cc_final: 0.7333 (mttm) REVERT: A 42 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7716 (mm-30) REVERT: A 145 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6808 (mp0) REVERT: A 150 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7563 (mm-40) REVERT: A 305 GLU cc_start: 0.8104 (tp30) cc_final: 0.7797 (tm-30) REVERT: A 504 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8090 (mm-30) REVERT: A 601 GLU cc_start: 0.6691 (mm-30) cc_final: 0.6025 (mm-30) REVERT: A 629 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7822 (ttm110) REVERT: A 647 ARG cc_start: 0.8473 (ttp80) cc_final: 0.7711 (tpt-90) REVERT: A 707 MET cc_start: 0.7649 (mtp) cc_final: 0.7185 (mtt) outliers start: 25 outliers final: 9 residues processed: 149 average time/residue: 0.7404 time to fit residues: 117.1595 Evaluate side-chains 146 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 629 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 118 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 639 ASN A 58 ASN A 639 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.153663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.114802 restraints weight = 9724.541| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.05 r_work: 0.3018 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11490 Z= 0.188 Angle : 0.577 4.828 15482 Z= 0.313 Chirality : 0.043 0.188 1670 Planarity : 0.005 0.036 1902 Dihedral : 21.133 174.393 2034 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.05 % Allowed : 7.32 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.24), residues: 1288 helix: 2.05 (0.17), residues: 890 sheet: 0.85 (0.74), residues: 44 loop : -1.12 (0.36), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 170 TYR 0.017 0.002 TYR A 352 PHE 0.015 0.002 PHE B 419 TRP 0.023 0.003 TRP A 227 HIS 0.011 0.002 HIS A 619 Details of bonding type rmsd covalent geometry : bond 0.00400 (11490) covalent geometry : angle 0.57655 (15482) hydrogen bonds : bond 0.06077 ( 722) hydrogen bonds : angle 4.56657 ( 2082) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.339 Fit side-chains REVERT: B 42 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7725 (mm-30) REVERT: B 102 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.6686 (pm20) REVERT: B 145 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6714 (mp0) REVERT: B 305 GLU cc_start: 0.8168 (tp30) cc_final: 0.7870 (tm-30) REVERT: B 325 THR cc_start: 0.8036 (t) cc_final: 0.7701 (m) REVERT: B 544 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8645 (tt) REVERT: B 601 GLU cc_start: 0.6811 (mm-30) cc_final: 0.6167 (mm-30) REVERT: B 606 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.6687 (mtp85) REVERT: B 629 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7799 (ttm110) REVERT: B 647 ARG cc_start: 0.8604 (ttp80) cc_final: 0.7750 (tpt170) REVERT: A 42 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7686 (mm-30) REVERT: A 102 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.6695 (pm20) REVERT: A 145 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6718 (mp0) REVERT: A 305 GLU cc_start: 0.8153 (tp30) cc_final: 0.7855 (tm-30) REVERT: A 325 THR cc_start: 0.8029 (t) cc_final: 0.7692 (m) REVERT: A 504 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8104 (mm-30) REVERT: A 544 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8651 (tt) REVERT: A 601 GLU cc_start: 0.6832 (mm-30) cc_final: 0.6182 (mm-30) REVERT: A 606 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.6696 (mtp85) REVERT: A 629 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7782 (ttm110) outliers start: 23 outliers final: 10 residues processed: 140 average time/residue: 0.7754 time to fit residues: 114.9049 Evaluate side-chains 154 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 599 ASN Chi-restraints excluded: chain B residue 606 ARG Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 599 ASN Chi-restraints excluded: chain A residue 606 ARG Chi-restraints excluded: chain A residue 629 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 102 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 73 optimal weight: 0.0040 chunk 47 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.156141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.117627 restraints weight = 9728.351| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.05 r_work: 0.3069 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11490 Z= 0.120 Angle : 0.465 4.558 15482 Z= 0.254 Chirality : 0.038 0.158 1670 Planarity : 0.004 0.031 1902 Dihedral : 19.415 172.060 2034 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.32 % Allowed : 7.14 % Favored : 90.54 % 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 are not related in a simple way. whole: 2.15 (0.24), residues: 1288 helix: 2.34 (0.17), residues: 890 sheet: 1.05 (0.78), residues: 44 loop : -0.99 (0.36), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.012 0.002 TYR B 432 PHE 0.009 0.001 PHE B 223 TRP 0.022 0.002 TRP A 227 HIS 0.007 0.001 HIS A 619 Details of bonding type rmsd covalent geometry : bond 0.00242 (11490) covalent geometry : angle 0.46517 (15482) hydrogen bonds : bond 0.05009 ( 722) hydrogen bonds : angle 4.27385 ( 2082) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.381 Fit side-chains REVERT: B 42 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7726 (mm-30) REVERT: B 145 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6782 (mp0) REVERT: B 305 GLU cc_start: 0.8073 (tp30) cc_final: 0.7784 (tm-30) REVERT: B 601 GLU cc_start: 0.6756 (mm-30) cc_final: 0.6093 (mm-30) REVERT: B 606 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.6629 (mtp85) REVERT: B 629 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7825 (ttm110) REVERT: A 42 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7671 (mm-30) REVERT: A 145 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6795 (mp0) REVERT: A 305 GLU cc_start: 0.8066 (tp30) cc_final: 0.7779 (tm-30) REVERT: A 601 GLU cc_start: 0.6743 (mm-30) cc_final: 0.6093 (mm-30) REVERT: A 606 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.6643 (mtp85) REVERT: A 629 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7825 (ttm110) REVERT: A 647 ARG cc_start: 0.8496 (ttp80) cc_final: 0.7709 (tpt-90) outliers start: 26 outliers final: 8 residues processed: 145 average time/residue: 0.7515 time to fit residues: 115.2614 Evaluate side-chains 146 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 606 ARG Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 606 ARG Chi-restraints excluded: chain A residue 629 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 18 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 89 optimal weight: 0.0270 chunk 40 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN B 599 ASN A 135 ASN A 599 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.154895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.116222 restraints weight = 9829.015| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.06 r_work: 0.3038 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11490 Z= 0.142 Angle : 0.502 4.804 15482 Z= 0.276 Chirality : 0.040 0.166 1670 Planarity : 0.004 0.033 1902 Dihedral : 18.628 153.918 2034 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.32 % Allowed : 7.77 % Favored : 89.91 % 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 are not related in a simple way. whole: 2.10 (0.24), residues: 1288 helix: 2.32 (0.17), residues: 890 sheet: 1.10 (0.79), residues: 44 loop : -1.06 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 129 TYR 0.015 0.002 TYR B 432 PHE 0.012 0.002 PHE B 223 TRP 0.022 0.002 TRP A 227 HIS 0.009 0.001 HIS A 619 Details of bonding type rmsd covalent geometry : bond 0.00293 (11490) covalent geometry : angle 0.50226 (15482) hydrogen bonds : bond 0.05499 ( 722) hydrogen bonds : angle 4.37763 ( 2082) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.300 Fit side-chains REVERT: B 42 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7706 (mm-30) REVERT: B 102 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.7285 (pm20) REVERT: B 145 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6789 (mp0) REVERT: B 305 GLU cc_start: 0.8067 (tp30) cc_final: 0.7778 (tm-30) REVERT: B 325 THR cc_start: 0.8126 (t) cc_final: 0.7774 (m) REVERT: B 544 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8632 (tt) REVERT: B 601 GLU cc_start: 0.6772 (mm-30) cc_final: 0.6119 (mm-30) REVERT: B 606 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.6678 (mtp85) REVERT: B 629 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7813 (ttm110) REVERT: A 42 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7690 (mm-30) REVERT: A 102 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.7317 (pm20) REVERT: A 145 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6817 (mp0) REVERT: A 305 GLU cc_start: 0.8079 (tp30) cc_final: 0.7754 (tm-30) REVERT: A 325 THR cc_start: 0.8118 (t) cc_final: 0.7774 (m) REVERT: A 495 THR cc_start: 0.8189 (t) cc_final: 0.7883 (m) REVERT: A 544 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8633 (tt) REVERT: A 601 GLU cc_start: 0.6796 (mm-30) cc_final: 0.6152 (mm-30) REVERT: A 606 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.6656 (mtp85) REVERT: A 629 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7813 (ttm110) REVERT: A 647 ARG cc_start: 0.8534 (ttp80) cc_final: 0.7702 (tpt170) outliers start: 26 outliers final: 12 residues processed: 144 average time/residue: 0.7748 time to fit residues: 118.0392 Evaluate side-chains 157 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 606 ARG Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 606 ARG Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 659 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 108 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN B 599 ASN A 599 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.153327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.114547 restraints weight = 9830.386| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.06 r_work: 0.3018 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11490 Z= 0.184 Angle : 0.571 5.024 15482 Z= 0.310 Chirality : 0.043 0.188 1670 Planarity : 0.005 0.036 1902 Dihedral : 19.024 152.826 2034 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.23 % Allowed : 8.12 % Favored : 89.64 % 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 are not related in a simple way. whole: 1.83 (0.24), residues: 1288 helix: 2.13 (0.17), residues: 890 sheet: 1.11 (0.79), residues: 44 loop : -1.22 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 129 TYR 0.020 0.002 TYR A 432 PHE 0.015 0.002 PHE B 419 TRP 0.023 0.003 TRP A 227 HIS 0.012 0.002 HIS B 619 Details of bonding type rmsd covalent geometry : bond 0.00395 (11490) covalent geometry : angle 0.57130 (15482) hydrogen bonds : bond 0.06021 ( 722) hydrogen bonds : angle 4.53616 ( 2082) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.452 Fit side-chains REVERT: B 42 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7715 (mm-30) REVERT: B 102 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.7289 (pm20) REVERT: B 145 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6755 (mp0) REVERT: B 305 GLU cc_start: 0.8135 (tp30) cc_final: 0.7818 (tm-30) REVERT: B 325 THR cc_start: 0.8134 (t) cc_final: 0.7827 (m) REVERT: B 544 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8626 (tp) REVERT: B 601 GLU cc_start: 0.6877 (mm-30) cc_final: 0.6239 (mm-30) REVERT: B 606 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.6717 (mtp85) REVERT: B 629 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7800 (ttm110) REVERT: B 647 ARG cc_start: 0.8565 (ttp80) cc_final: 0.7701 (tpt-90) REVERT: A 42 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7689 (mm-30) REVERT: A 102 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7303 (pm20) REVERT: A 145 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6744 (mp0) REVERT: A 305 GLU cc_start: 0.8118 (tp30) cc_final: 0.7805 (tm-30) REVERT: A 325 THR cc_start: 0.8134 (t) cc_final: 0.7833 (m) REVERT: A 495 THR cc_start: 0.8211 (t) cc_final: 0.7916 (m) REVERT: A 544 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8629 (tp) REVERT: A 601 GLU cc_start: 0.6890 (mm-30) cc_final: 0.6257 (mm-30) REVERT: A 606 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.6719 (mtp85) REVERT: A 629 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7800 (ttm110) outliers start: 25 outliers final: 10 residues processed: 144 average time/residue: 0.7410 time to fit residues: 113.2380 Evaluate side-chains 157 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 606 ARG Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 606 ARG Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 659 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 108 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN B 135 ASN A 135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.154755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.116133 restraints weight = 9880.798| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.06 r_work: 0.3039 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11490 Z= 0.136 Angle : 0.494 4.822 15482 Z= 0.271 Chirality : 0.040 0.165 1670 Planarity : 0.004 0.034 1902 Dihedral : 18.222 143.579 2034 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.14 % Allowed : 8.57 % Favored : 89.29 % 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 are not related in a simple way. whole: 2.06 (0.24), residues: 1288 helix: 2.32 (0.17), residues: 890 sheet: 1.16 (0.80), residues: 44 loop : -1.19 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 129 TYR 0.014 0.002 TYR A 432 PHE 0.011 0.001 PHE B 223 TRP 0.023 0.002 TRP B 227 HIS 0.008 0.001 HIS B 619 Details of bonding type rmsd covalent geometry : bond 0.00281 (11490) covalent geometry : angle 0.49411 (15482) hydrogen bonds : bond 0.05348 ( 722) hydrogen bonds : angle 4.35052 ( 2082) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.391 Fit side-chains REVERT: B 42 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7717 (mm-30) REVERT: B 100 LYS cc_start: 0.7172 (tptt) cc_final: 0.6657 (pttp) REVERT: B 102 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7317 (pm20) REVERT: B 145 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6732 (mp0) REVERT: B 305 GLU cc_start: 0.8084 (tp30) cc_final: 0.7791 (tm-30) REVERT: B 325 THR cc_start: 0.8094 (t) cc_final: 0.7787 (m) REVERT: B 544 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8595 (tp) REVERT: B 601 GLU cc_start: 0.6839 (mm-30) cc_final: 0.6208 (mm-30) REVERT: B 606 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.6679 (mtp85) REVERT: B 629 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7831 (ttm110) REVERT: A 42 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7679 (mm-30) REVERT: A 100 LYS cc_start: 0.7169 (tptt) cc_final: 0.6668 (pttp) REVERT: A 102 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.7320 (pm20) REVERT: A 145 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6744 (mp0) REVERT: A 305 GLU cc_start: 0.8088 (tp30) cc_final: 0.7802 (tm-30) REVERT: A 325 THR cc_start: 0.8093 (t) cc_final: 0.7796 (m) REVERT: A 495 THR cc_start: 0.8201 (t) cc_final: 0.7914 (m) REVERT: A 544 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8601 (tp) REVERT: A 601 GLU cc_start: 0.6847 (mm-30) cc_final: 0.6219 (mm-30) REVERT: A 606 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.6679 (mtp85) REVERT: A 629 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7832 (ttm110) REVERT: A 647 ARG cc_start: 0.8533 (ttp80) cc_final: 0.7699 (tpt170) outliers start: 24 outliers final: 10 residues processed: 149 average time/residue: 0.7810 time to fit residues: 123.1776 Evaluate side-chains 161 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 606 ARG Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 606 ARG Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 659 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN B 599 ASN A 599 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.153759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.115278 restraints weight = 9747.128| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.05 r_work: 0.3029 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11490 Z= 0.171 Angle : 0.547 4.999 15482 Z= 0.298 Chirality : 0.042 0.181 1670 Planarity : 0.005 0.035 1902 Dihedral : 18.554 143.740 2034 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.23 % Allowed : 8.57 % Favored : 89.20 % 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 are not related in a simple way. whole: 1.89 (0.24), residues: 1288 helix: 2.19 (0.17), residues: 890 sheet: 1.19 (0.80), residues: 44 loop : -1.27 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 129 TYR 0.018 0.002 TYR A 432 PHE 0.014 0.002 PHE A 419 TRP 0.023 0.002 TRP A 227 HIS 0.010 0.001 HIS B 619 Details of bonding type rmsd covalent geometry : bond 0.00365 (11490) covalent geometry : angle 0.54692 (15482) hydrogen bonds : bond 0.05856 ( 722) hydrogen bonds : angle 4.48536 ( 2082) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.351 Fit side-chains REVERT: B 42 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7701 (mm-30) REVERT: B 100 LYS cc_start: 0.7191 (tptt) cc_final: 0.6688 (pttp) REVERT: B 102 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.7291 (pm20) REVERT: B 145 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6705 (mp0) REVERT: B 305 GLU cc_start: 0.8123 (tp30) cc_final: 0.7802 (tm-30) REVERT: B 325 THR cc_start: 0.8142 (t) cc_final: 0.7843 (m) REVERT: B 544 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8614 (tp) REVERT: B 599 ASN cc_start: 0.7195 (OUTLIER) cc_final: 0.6872 (t0) REVERT: B 601 GLU cc_start: 0.6872 (mm-30) cc_final: 0.6246 (mm-30) REVERT: B 606 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.6720 (mtp85) REVERT: B 629 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7803 (ttm110) REVERT: B 647 ARG cc_start: 0.8564 (ttp80) cc_final: 0.7704 (tpt-90) REVERT: B 703 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6401 (tp30) REVERT: A 42 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7681 (mm-30) REVERT: A 100 LYS cc_start: 0.7192 (tptt) cc_final: 0.6693 (pttp) REVERT: A 102 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.7278 (pm20) REVERT: A 145 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6743 (mp0) REVERT: A 305 GLU cc_start: 0.8092 (tp30) cc_final: 0.7771 (tm-30) REVERT: A 325 THR cc_start: 0.8148 (t) cc_final: 0.7857 (m) REVERT: A 495 THR cc_start: 0.8214 (t) cc_final: 0.7931 (m) REVERT: A 544 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8616 (tp) REVERT: A 599 ASN cc_start: 0.7208 (OUTLIER) cc_final: 0.6892 (t0) REVERT: A 601 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6247 (mm-30) REVERT: A 606 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.6716 (mtp85) REVERT: A 629 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7804 (ttm110) outliers start: 25 outliers final: 12 residues processed: 147 average time/residue: 0.7537 time to fit residues: 117.4961 Evaluate side-chains 163 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 599 ASN Chi-restraints excluded: chain B residue 606 ARG Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 599 ASN Chi-restraints excluded: chain A residue 606 ARG Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 659 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 48 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.153795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.115137 restraints weight = 9882.424| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.06 r_work: 0.3025 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.213 11490 Z= 0.219 Angle : 1.018 59.199 15482 Z= 0.614 Chirality : 0.042 0.182 1670 Planarity : 0.004 0.035 1902 Dihedral : 18.554 143.730 2034 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.14 % Allowed : 8.30 % Favored : 89.55 % 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 are not related in a simple way. whole: 1.89 (0.24), residues: 1288 helix: 2.19 (0.17), residues: 890 sheet: 1.18 (0.80), residues: 44 loop : -1.28 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 129 TYR 0.017 0.002 TYR A 432 PHE 0.014 0.002 PHE A 419 TRP 0.023 0.002 TRP A 227 HIS 0.010 0.001 HIS A 619 Details of bonding type rmsd covalent geometry : bond 0.00454 (11490) covalent geometry : angle 1.01831 (15482) hydrogen bonds : bond 0.05800 ( 722) hydrogen bonds : angle 4.48024 ( 2082) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.420 Fit side-chains REVERT: B 100 LYS cc_start: 0.7188 (tptt) cc_final: 0.6677 (pttp) REVERT: B 102 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7294 (pm20) REVERT: B 145 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6703 (mp0) REVERT: B 305 GLU cc_start: 0.8123 (tp30) cc_final: 0.7805 (tm-30) REVERT: B 325 THR cc_start: 0.8142 (t) cc_final: 0.7845 (m) REVERT: B 544 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8615 (tp) REVERT: B 601 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6242 (mm-30) REVERT: B 606 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.6712 (mtp85) REVERT: B 629 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7806 (ttm110) REVERT: B 647 ARG cc_start: 0.8554 (ttp80) cc_final: 0.7690 (tpt-90) REVERT: B 703 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6395 (tp30) REVERT: A 42 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7671 (mm-30) REVERT: A 100 LYS cc_start: 0.7182 (tptt) cc_final: 0.6676 (pttp) REVERT: A 102 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.7284 (pm20) REVERT: A 145 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6735 (mp0) REVERT: A 305 GLU cc_start: 0.8094 (tp30) cc_final: 0.7776 (tm-30) REVERT: A 325 THR cc_start: 0.8150 (t) cc_final: 0.7861 (m) REVERT: A 495 THR cc_start: 0.8212 (t) cc_final: 0.7932 (m) REVERT: A 544 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8635 (tt) REVERT: A 601 GLU cc_start: 0.6865 (mm-30) cc_final: 0.6245 (mm-30) REVERT: A 606 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.6704 (mtp85) REVERT: A 629 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7808 (ttm110) outliers start: 24 outliers final: 14 residues processed: 145 average time/residue: 0.7820 time to fit residues: 120.3585 Evaluate side-chains 161 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 606 ARG Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 606 ARG Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 659 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 0.0870 chunk 49 optimal weight: 0.0060 chunk 2 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.154305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.115716 restraints weight = 9845.587| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.06 r_work: 0.3029 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11490 Z= 0.126 Angle : 0.995 58.871 15482 Z= 0.580 Chirality : 0.039 0.165 1670 Planarity : 0.004 0.036 1902 Dihedral : 18.490 143.650 2034 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.14 % Allowed : 8.21 % Favored : 89.64 % 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 are not related in a simple way. whole: 1.92 (0.24), residues: 1288 helix: 2.21 (0.17), residues: 890 sheet: 1.17 (0.81), residues: 44 loop : -1.25 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 53 TYR 0.015 0.002 TYR A 432 PHE 0.013 0.001 PHE A 419 TRP 0.023 0.002 TRP A 227 HIS 0.008 0.001 HIS A 619 Details of bonding type rmsd covalent geometry : bond 0.00240 (11490) covalent geometry : angle 0.99505 (15482) hydrogen bonds : bond 0.05605 ( 722) hydrogen bonds : angle 4.45412 ( 2082) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5269.20 seconds wall clock time: 90 minutes 10.04 seconds (5410.04 seconds total)