Starting phenix.real_space_refine on Tue Jul 29 18:44:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rxg_24730/07_2025/7rxg_24730.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rxg_24730/07_2025/7rxg_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7rxg_24730/07_2025/7rxg_24730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rxg_24730/07_2025/7rxg_24730.map" model { file = "/net/cci-nas-00/data/ceres_data/7rxg_24730/07_2025/7rxg_24730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rxg_24730/07_2025/7rxg_24730.cif" } resolution = 2.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'TYR:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 1, 'HIS: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: {'TYR:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 1, 'HIS: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-2': 1, 'PGW:plan-3': 5} 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-2': 1, 'PGW:plan-3': 7} 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: 10.73, per 1000 atoms: 0.94 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: 2.69 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.95 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: 3.86 Time building geometry restraints manager: 3.20 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: 31.070 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: 0.320 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 31.590 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:17.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.260 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (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 TRP 0.028 0.002 TRP B 155 HIS 0.008 0.002 HIS A 619 PHE 0.018 0.002 PHE A 388 TYR 0.013 0.002 TYR B 352 ARG 0.004 0.000 ARG A 496 Details of bonding type rmsd hydrogen bonds : bond 0.11633 ( 722) hydrogen bonds : angle 5.47866 ( 2082) covalent geometry : bond 0.00803 (11490) covalent geometry : angle 1.26852 (15482) *********************** 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 : 1.255 Fit side-chains REVERT: B 34 LYS cc_start: 0.7068 (ttpt) cc_final: 0.6787 (mttt) REVERT: B 150 GLN cc_start: 0.7269 (tp40) cc_final: 0.7064 (mm-40) REVERT: B 417 THR cc_start: 0.2252 (OUTLIER) cc_final: 0.1545 (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: 0.6805 (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: 0.6996 (mm-40) REVERT: A 417 THR cc_start: 0.2234 (OUTLIER) cc_final: 0.1550 (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: 1.6999 time to fit residues: 328.1635 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 : 1.215 ------------------------------------------------------------------------------- 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 109 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.158492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.119575 restraints weight = 9700.954| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.06 r_work: 0.3084 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11490 Z= 0.131 Angle : 0.507 4.557 15482 Z= 0.271 Chirality : 0.039 0.154 1670 Planarity : 0.004 0.033 1902 Dihedral : 24.103 161.774 2036 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.88 % Allowed : 6.43 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.24), residues: 1288 helix: 1.62 (0.17), residues: 890 sheet: 0.36 (0.67), residues: 44 loop : -1.53 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 227 HIS 0.007 0.001 HIS B 619 PHE 0.011 0.001 PHE B 193 TYR 0.014 0.002 TYR A 180 ARG 0.003 0.001 ARG B 457 Details of bonding type rmsd hydrogen bonds : bond 0.05127 ( 722) hydrogen bonds : angle 4.43799 ( 2082) covalent geometry : bond 0.00259 (11490) covalent geometry : angle 0.50672 (15482) *********************** 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 160 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 LYS cc_start: 0.7676 (mmtp) cc_final: 0.7196 (mttm) REVERT: B 69 LYS cc_start: 0.7813 (mtmm) cc_final: 0.7600 (mttm) REVERT: B 305 GLU cc_start: 0.8205 (tp30) cc_final: 0.7886 (tm-30) REVERT: B 601 GLU cc_start: 0.6684 (mm-30) cc_final: 0.6088 (mm-30) REVERT: B 606 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.6606 (mtp85) REVERT: B 629 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7822 (ttm110) REVERT: B 707 MET cc_start: 0.7620 (mtp) cc_final: 0.7310 (mtp) REVERT: A 35 LYS cc_start: 0.7689 (mmtp) cc_final: 0.7212 (mttm) REVERT: A 42 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7667 (mm-30) REVERT: A 69 LYS cc_start: 0.7785 (mtmm) cc_final: 0.7581 (mttm) REVERT: A 305 GLU cc_start: 0.8210 (tp30) cc_final: 0.7914 (tm-30) REVERT: A 601 GLU cc_start: 0.6776 (mm-30) cc_final: 0.6137 (mm-30) REVERT: A 606 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.6581 (mtp85) REVERT: A 629 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7830 (ttm110) REVERT: A 707 MET cc_start: 0.7585 (mtp) cc_final: 0.7367 (mtp) outliers start: 21 outliers final: 10 residues processed: 150 average time/residue: 1.5541 time to fit residues: 249.0196 Evaluate side-chains 139 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 1.219 ------------------------------------------------------------------------------- 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 162 SER 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 102 GLN Chi-restraints excluded: chain A residue 162 SER 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 73 optimal weight: 0.7980 chunk 4 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- 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 B 639 ASN A 58 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN A 639 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.151987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.113007 restraints weight = 9684.671| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.05 r_work: 0.2993 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 11490 Z= 0.261 Angle : 0.689 5.675 15482 Z= 0.368 Chirality : 0.049 0.214 1670 Planarity : 0.006 0.043 1902 Dihedral : 23.539 176.300 2034 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.32 % Allowed : 7.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.24), residues: 1288 helix: 1.65 (0.17), residues: 890 sheet: 0.74 (0.70), residues: 44 loop : -1.42 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 227 HIS 0.014 0.002 HIS A 619 PHE 0.023 0.003 PHE B 419 TYR 0.021 0.003 TYR B 352 ARG 0.006 0.001 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.06812 ( 722) hydrogen bonds : angle 4.78675 ( 2082) covalent geometry : bond 0.00570 (11490) covalent geometry : angle 0.68914 (15482) *********************** 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 162 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 1.289 Fit side-chains REVERT: B 69 LYS cc_start: 0.8016 (mtmm) cc_final: 0.7814 (mttm) REVERT: B 102 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.6563 (pm20) REVERT: B 145 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6728 (mp0) REVERT: B 305 GLU cc_start: 0.8224 (tp30) cc_final: 0.7944 (tm-30) REVERT: B 325 THR cc_start: 0.8090 (t) cc_final: 0.7746 (m) REVERT: B 601 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6232 (mm-30) REVERT: B 606 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.6769 (mtp85) REVERT: B 629 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7830 (ttm110) REVERT: A 42 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7701 (mm-30) REVERT: A 102 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.6552 (pm20) REVERT: A 145 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6713 (mp0) REVERT: A 305 GLU cc_start: 0.8207 (tp30) cc_final: 0.7924 (tm-30) REVERT: A 325 THR cc_start: 0.8086 (t) cc_final: 0.7736 (m) REVERT: A 601 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6249 (mm-30) REVERT: A 606 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.6715 (mtp85) REVERT: A 629 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7825 (ttm110) outliers start: 26 outliers final: 10 residues processed: 143 average time/residue: 1.7527 time to fit residues: 268.7593 Evaluate side-chains 148 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 1.330 ------------------------------------------------------------------------------- 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 162 SER Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 326 ILE 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 162 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 606 ARG 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 65 optimal weight: 10.0000 chunk 127 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.154047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.115385 restraints weight = 9683.538| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.05 r_work: 0.3026 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3214 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= 0.166 Angle : 0.544 4.847 15482 Z= 0.295 Chirality : 0.041 0.178 1670 Planarity : 0.004 0.038 1902 Dihedral : 21.955 168.883 2034 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.86 % Allowed : 7.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.24), residues: 1288 helix: 2.04 (0.17), residues: 890 sheet: 0.83 (0.75), residues: 44 loop : -1.25 (0.36), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 227 HIS 0.010 0.001 HIS B 619 PHE 0.013 0.002 PHE B 223 TYR 0.016 0.002 TYR B 589 ARG 0.003 0.001 ARG B 170 Details of bonding type rmsd hydrogen bonds : bond 0.05704 ( 722) hydrogen bonds : angle 4.50117 ( 2082) covalent geometry : bond 0.00354 (11490) covalent geometry : angle 0.54370 (15482) *********************** 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 164 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 1.152 Fit side-chains REVERT: B 69 LYS cc_start: 0.8000 (mtmm) cc_final: 0.7782 (mttm) REVERT: B 102 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.6570 (pm20) REVERT: B 145 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6769 (mp0) REVERT: B 305 GLU cc_start: 0.8135 (tp30) cc_final: 0.7844 (tm-30) REVERT: B 325 THR cc_start: 0.8078 (t) cc_final: 0.7770 (m) REVERT: B 504 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8107 (mm-30) REVERT: B 601 GLU cc_start: 0.6847 (mm-30) cc_final: 0.6162 (mm-30) REVERT: B 606 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6710 (mtp85) REVERT: B 629 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7827 (ttm110) REVERT: B 647 ARG cc_start: 0.8539 (ttp80) cc_final: 0.7711 (tpt170) REVERT: A 42 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7670 (mm-30) REVERT: A 102 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.6540 (pm20) REVERT: A 145 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6765 (mp0) REVERT: A 305 GLU cc_start: 0.8122 (tp30) cc_final: 0.7828 (tm-30) REVERT: A 325 THR cc_start: 0.8067 (t) cc_final: 0.7760 (m) REVERT: A 544 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8624 (tp) REVERT: A 601 GLU cc_start: 0.6847 (mm-30) cc_final: 0.6179 (mm-30) REVERT: A 606 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.6695 (mtp85) REVERT: A 629 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7828 (ttm110) outliers start: 32 outliers final: 11 residues processed: 144 average time/residue: 1.6111 time to fit residues: 247.0068 Evaluate side-chains 153 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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 162 SER Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 504 GLU 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 162 SER 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 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 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 = 0.3688 r_free = 0.3688 target = 0.153262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.114667 restraints weight = 9685.440| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.05 r_work: 0.3023 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3384 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= 0.189 Angle : 0.580 4.952 15482 Z= 0.316 Chirality : 0.043 0.191 1670 Planarity : 0.005 0.039 1902 Dihedral : 21.201 161.255 2034 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.41 % Allowed : 8.57 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.24), residues: 1288 helix: 1.99 (0.17), residues: 890 sheet: 0.94 (0.77), residues: 44 loop : -1.29 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 227 HIS 0.010 0.001 HIS A 619 PHE 0.016 0.002 PHE B 419 TYR 0.017 0.002 TYR B 589 ARG 0.004 0.001 ARG B 170 Details of bonding type rmsd hydrogen bonds : bond 0.06146 ( 722) hydrogen bonds : angle 4.58176 ( 2082) covalent geometry : bond 0.00408 (11490) covalent geometry : angle 0.57968 (15482) *********************** 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: 27 poor density : 136 time to evaluate : 1.231 Fit side-chains REVERT: B 42 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7712 (mm-30) REVERT: B 69 LYS cc_start: 0.7991 (mtmm) cc_final: 0.7781 (mttm) REVERT: B 102 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.6573 (pm20) REVERT: B 145 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6767 (mp0) REVERT: B 305 GLU cc_start: 0.8139 (tp30) cc_final: 0.7856 (tm-30) REVERT: B 325 THR cc_start: 0.8133 (t) cc_final: 0.7858 (m) REVERT: B 504 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.8069 (mm-30) REVERT: B 601 GLU cc_start: 0.6856 (mm-30) cc_final: 0.6238 (mm-30) REVERT: B 629 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7811 (ttm110) REVERT: B 647 ARG cc_start: 0.8569 (ttp80) cc_final: 0.7741 (tpt170) REVERT: A 42 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7673 (mm-30) REVERT: A 100 LYS cc_start: 0.7210 (tptt) cc_final: 0.6744 (pttp) REVERT: A 102 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.6566 (pm20) REVERT: A 145 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6745 (mp0) REVERT: A 305 GLU cc_start: 0.8117 (tp30) cc_final: 0.7829 (tm-30) REVERT: A 325 THR cc_start: 0.8133 (t) cc_final: 0.7859 (m) REVERT: A 495 THR cc_start: 0.8263 (t) cc_final: 0.7969 (m) REVERT: A 544 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8652 (tt) REVERT: A 601 GLU cc_start: 0.6867 (mm-30) cc_final: 0.6254 (mm-30) REVERT: A 629 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7813 (ttm110) outliers start: 27 outliers final: 11 residues processed: 146 average time/residue: 1.5516 time to fit residues: 241.8703 Evaluate side-chains 156 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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 162 SER Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 504 GLU 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 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 544 LEU 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 65 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.153792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.115132 restraints weight = 9843.990| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.06 r_work: 0.3026 rms_B_bonded: 2.14 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: 0.8548 moved from start: 0.3455 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= 0.169 Angle : 0.541 4.912 15482 Z= 0.296 Chirality : 0.042 0.182 1670 Planarity : 0.005 0.038 1902 Dihedral : 20.284 150.637 2034 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.68 % Allowed : 8.39 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.24), residues: 1288 helix: 2.10 (0.17), residues: 890 sheet: 1.12 (0.79), residues: 44 loop : -1.28 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 227 HIS 0.010 0.001 HIS B 619 PHE 0.013 0.002 PHE B 223 TYR 0.016 0.002 TYR A 432 ARG 0.003 0.001 ARG B 170 Details of bonding type rmsd hydrogen bonds : bond 0.05763 ( 722) hydrogen bonds : angle 4.48322 ( 2082) covalent geometry : bond 0.00361 (11490) covalent geometry : angle 0.54140 (15482) *********************** 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 167 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 1.157 Fit side-chains REVERT: B 42 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7732 (mm-30) REVERT: B 69 LYS cc_start: 0.7997 (mtmm) cc_final: 0.7784 (mttm) REVERT: B 102 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.6569 (pm20) REVERT: B 145 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6742 (mp0) REVERT: B 232 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7935 (mt-10) REVERT: B 305 GLU cc_start: 0.8110 (tp30) cc_final: 0.7810 (tm-30) REVERT: B 325 THR cc_start: 0.8136 (t) cc_final: 0.7874 (m) REVERT: B 601 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6263 (mm-30) REVERT: B 606 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.6756 (mtp85) REVERT: B 629 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7832 (ttm110) REVERT: B 647 ARG cc_start: 0.8552 (ttp80) cc_final: 0.7726 (tpt170) REVERT: A 42 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7676 (mm-30) REVERT: A 100 LYS cc_start: 0.7149 (tptt) cc_final: 0.6713 (pttp) REVERT: A 102 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.6548 (pm20) REVERT: A 145 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: A 305 GLU cc_start: 0.8104 (tp30) cc_final: 0.7804 (tm-30) REVERT: A 325 THR cc_start: 0.8136 (t) cc_final: 0.7880 (m) REVERT: A 495 THR cc_start: 0.8268 (t) cc_final: 0.7983 (m) REVERT: A 544 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8612 (tp) REVERT: A 601 GLU cc_start: 0.6887 (mm-30) cc_final: 0.6276 (mm-30) REVERT: A 606 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.6749 (mtp85) REVERT: A 629 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7833 (ttm110) outliers start: 30 outliers final: 15 residues processed: 148 average time/residue: 1.6198 time to fit residues: 255.2832 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 : 1.098 ------------------------------------------------------------------------------- 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 162 SER Chi-restraints excluded: chain B residue 232 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 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 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 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 16 optimal weight: 7.9990 chunk 26 optimal weight: 0.0370 chunk 80 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 chunk 65 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 52 optimal weight: 0.0980 chunk 32 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 overall best weight: 1.0460 ------------------------------------------------------------------------------- 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 58 ASN A 135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.156074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.117550 restraints weight = 10006.744| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.07 r_work: 0.3061 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11490 Z= 0.113 Angle : 0.454 4.477 15482 Z= 0.249 Chirality : 0.038 0.155 1670 Planarity : 0.004 0.034 1902 Dihedral : 18.813 141.492 2034 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.88 % Allowed : 9.38 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.24), residues: 1288 helix: 2.43 (0.17), residues: 890 sheet: 1.23 (0.82), residues: 44 loop : -1.22 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 227 HIS 0.006 0.001 HIS A 619 PHE 0.009 0.001 PHE B 388 TYR 0.011 0.001 TYR A 432 ARG 0.002 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.04909 ( 722) hydrogen bonds : angle 4.22886 ( 2082) covalent geometry : bond 0.00226 (11490) covalent geometry : angle 0.45416 (15482) *********************** 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 158 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 1.548 Fit side-chains REVERT: B 69 LYS cc_start: 0.7977 (mtmm) cc_final: 0.7731 (mttm) REVERT: B 100 LYS cc_start: 0.7232 (tptt) cc_final: 0.6755 (pttp) REVERT: B 102 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.6576 (pm20) REVERT: B 145 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6769 (mp0) REVERT: B 305 GLU cc_start: 0.8065 (tp30) cc_final: 0.7780 (tm-30) REVERT: B 325 THR cc_start: 0.8131 (t) cc_final: 0.7842 (m) REVERT: B 599 ASN cc_start: 0.7183 (OUTLIER) cc_final: 0.6982 (m-40) REVERT: B 601 GLU cc_start: 0.6776 (mm-30) cc_final: 0.6115 (mm-30) REVERT: B 606 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.6701 (mtp85) REVERT: B 647 ARG cc_start: 0.8480 (ttp80) cc_final: 0.7658 (tpt170) REVERT: A 42 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7647 (mm-30) REVERT: A 100 LYS cc_start: 0.7192 (tptt) cc_final: 0.6782 (pttp) REVERT: A 102 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.6576 (pm20) REVERT: A 145 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6773 (mp0) REVERT: A 232 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7899 (mt-10) REVERT: A 305 GLU cc_start: 0.8066 (tp30) cc_final: 0.7774 (tm-30) REVERT: A 325 THR cc_start: 0.8131 (t) cc_final: 0.7852 (m) REVERT: A 495 THR cc_start: 0.8251 (t) cc_final: 0.7967 (m) REVERT: A 599 ASN cc_start: 0.7181 (OUTLIER) cc_final: 0.6981 (m-40) REVERT: A 601 GLU cc_start: 0.6788 (mm-30) cc_final: 0.6128 (mm-30) REVERT: A 606 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.6703 (mtp85) outliers start: 21 outliers final: 10 residues processed: 147 average time/residue: 1.9911 time to fit residues: 311.0807 Evaluate side-chains 154 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 599 ASN Chi-restraints excluded: chain B residue 606 ARG Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 232 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 599 ASN Chi-restraints excluded: chain A residue 606 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 73 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN A 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.152648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.113317 restraints weight = 9782.390| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.09 r_work: 0.2991 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 11490 Z= 0.216 Angle : 0.608 5.155 15482 Z= 0.329 Chirality : 0.045 0.201 1670 Planarity : 0.005 0.037 1902 Dihedral : 19.711 146.160 2034 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.14 % Allowed : 9.02 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.24), residues: 1288 helix: 2.09 (0.17), residues: 890 sheet: 1.29 (0.81), residues: 44 loop : -1.34 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 227 HIS 0.012 0.002 HIS B 619 PHE 0.016 0.002 PHE B 419 TYR 0.021 0.003 TYR B 432 ARG 0.005 0.001 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.06291 ( 722) hydrogen bonds : angle 4.59534 ( 2082) covalent geometry : bond 0.00469 (11490) covalent geometry : angle 0.60776 (15482) *********************** 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 163 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 1.276 Fit side-chains REVERT: B 42 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7757 (mm-30) REVERT: B 69 LYS cc_start: 0.7993 (mtmm) cc_final: 0.7790 (mttm) REVERT: B 100 LYS cc_start: 0.7255 (tptt) cc_final: 0.6729 (pttp) REVERT: B 102 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.6584 (pm20) REVERT: B 145 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6745 (mp0) REVERT: B 305 GLU cc_start: 0.8176 (tp30) cc_final: 0.7891 (tm-30) REVERT: B 325 THR cc_start: 0.8165 (t) cc_final: 0.7912 (m) REVERT: B 544 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8645 (tp) REVERT: B 601 GLU cc_start: 0.6891 (mm-30) cc_final: 0.6275 (mm-30) REVERT: B 606 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.6818 (mtp85) REVERT: B 629 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7845 (ttm110) REVERT: B 647 ARG cc_start: 0.8597 (ttp80) cc_final: 0.7758 (tpt170) REVERT: B 703 GLU cc_start: 0.7090 (mm-30) cc_final: 0.6557 (tp30) REVERT: A 42 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7695 (mm-30) REVERT: A 100 LYS cc_start: 0.7227 (tptt) cc_final: 0.6707 (pttp) REVERT: A 102 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.6620 (pm20) REVERT: A 145 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6768 (mp0) REVERT: A 305 GLU cc_start: 0.8165 (tp30) cc_final: 0.7883 (tm-30) REVERT: A 325 THR cc_start: 0.8172 (t) cc_final: 0.7922 (m) REVERT: A 495 THR cc_start: 0.8245 (t) cc_final: 0.7966 (m) REVERT: A 544 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8685 (tp) REVERT: A 601 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6275 (mm-30) REVERT: A 606 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.6808 (mtp85) REVERT: A 629 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7841 (ttm110) outliers start: 24 outliers final: 11 residues processed: 146 average time/residue: 1.7258 time to fit residues: 268.5993 Evaluate side-chains 160 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 1.267 ------------------------------------------------------------------------------- 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 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 65 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 86 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.152928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.113640 restraints weight = 9860.694| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.10 r_work: 0.3005 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11490 Z= 0.192 Angle : 0.578 5.151 15482 Z= 0.314 Chirality : 0.043 0.190 1670 Planarity : 0.005 0.037 1902 Dihedral : 19.207 146.914 2034 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.96 % Allowed : 9.38 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.24), residues: 1288 helix: 2.07 (0.17), residues: 890 sheet: 1.31 (0.80), residues: 44 loop : -1.37 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 227 HIS 0.011 0.002 HIS A 619 PHE 0.015 0.002 PHE B 223 TYR 0.020 0.002 TYR A 432 ARG 0.003 0.001 ARG B 170 Details of bonding type rmsd hydrogen bonds : bond 0.06045 ( 722) hydrogen bonds : angle 4.54764 ( 2082) covalent geometry : bond 0.00415 (11490) covalent geometry : angle 0.57794 (15482) *********************** 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 161 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 1.152 Fit side-chains REVERT: B 69 LYS cc_start: 0.7991 (mtmm) cc_final: 0.7768 (mttm) REVERT: B 100 LYS cc_start: 0.7198 (tptt) cc_final: 0.6683 (pttp) REVERT: B 102 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.6609 (pm20) REVERT: B 145 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6721 (mp0) REVERT: B 305 GLU cc_start: 0.8132 (tp30) cc_final: 0.7832 (tm-30) REVERT: B 325 THR cc_start: 0.8150 (t) cc_final: 0.7904 (m) REVERT: B 544 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8645 (tp) REVERT: B 599 ASN cc_start: 0.7225 (OUTLIER) cc_final: 0.6868 (t0) REVERT: B 601 GLU cc_start: 0.6855 (mm-30) cc_final: 0.6247 (mm-30) REVERT: B 606 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.6770 (mtp85) REVERT: B 629 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7852 (ttm110) REVERT: B 647 ARG cc_start: 0.8582 (ttp80) cc_final: 0.7731 (tpt170) REVERT: B 703 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6369 (tp30) REVERT: A 100 LYS cc_start: 0.7194 (tptt) cc_final: 0.6662 (pttp) REVERT: A 102 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.6609 (pm20) REVERT: A 145 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6754 (mp0) REVERT: A 305 GLU cc_start: 0.8115 (tp30) cc_final: 0.7821 (tm-30) REVERT: A 325 THR cc_start: 0.8155 (t) cc_final: 0.7917 (m) REVERT: A 495 THR cc_start: 0.8247 (t) cc_final: 0.7980 (m) REVERT: A 599 ASN cc_start: 0.7226 (OUTLIER) cc_final: 0.6886 (t0) REVERT: A 601 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6246 (mm-30) REVERT: A 606 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.6757 (mtp85) REVERT: A 629 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7853 (ttm110) REVERT: A 703 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6454 (tp30) outliers start: 22 outliers final: 10 residues processed: 148 average time/residue: 1.6785 time to fit residues: 264.2503 Evaluate side-chains 158 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 1.152 ------------------------------------------------------------------------------- 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 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 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 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 28 optimal weight: 10.0000 chunk 117 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 127 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 60 optimal weight: 0.0970 chunk 115 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 chunk 75 optimal weight: 0.0020 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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 B 539 ASN B 599 ASN A 58 ASN A 135 ASN A 539 ASN A 599 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.155789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.116735 restraints weight = 9885.294| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.10 r_work: 0.3050 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11490 Z= 0.106 Angle : 0.463 4.658 15482 Z= 0.257 Chirality : 0.038 0.151 1670 Planarity : 0.004 0.035 1902 Dihedral : 18.292 144.061 2034 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.43 % Allowed : 10.18 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.24), residues: 1288 helix: 2.34 (0.17), residues: 890 sheet: 1.34 (0.83), residues: 44 loop : -1.29 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 227 HIS 0.004 0.001 HIS B 619 PHE 0.010 0.001 PHE A 419 TYR 0.013 0.001 TYR A 432 ARG 0.002 0.000 ARG A 647 Details of bonding type rmsd hydrogen bonds : bond 0.04946 ( 722) hydrogen bonds : angle 4.27572 ( 2082) covalent geometry : bond 0.00198 (11490) covalent geometry : angle 0.46273 (15482) ********************** 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 155 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 1.217 Fit side-chains REVERT: B 69 LYS cc_start: 0.7983 (mtmm) cc_final: 0.7765 (mttm) REVERT: B 100 LYS cc_start: 0.7174 (tptt) cc_final: 0.6675 (pttp) REVERT: B 102 GLN cc_start: 0.7444 (OUTLIER) cc_final: 0.6537 (pm20) REVERT: B 145 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6742 (mp0) REVERT: B 305 GLU cc_start: 0.8071 (tp30) cc_final: 0.7764 (tm-30) REVERT: B 325 THR cc_start: 0.8147 (t) cc_final: 0.7877 (m) REVERT: B 495 THR cc_start: 0.8195 (t) cc_final: 0.7899 (m) REVERT: B 599 ASN cc_start: 0.7390 (OUTLIER) cc_final: 0.7066 (t0) REVERT: B 601 GLU cc_start: 0.6868 (mm-30) cc_final: 0.6224 (mm-30) REVERT: B 606 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.6668 (mtp85) REVERT: B 629 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7850 (ttm110) REVERT: B 647 ARG cc_start: 0.8510 (ttp80) cc_final: 0.7670 (tpt170) REVERT: A 100 LYS cc_start: 0.7227 (tptt) cc_final: 0.6688 (pttp) REVERT: A 102 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.6587 (pm20) REVERT: A 145 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6712 (mp0) REVERT: A 305 GLU cc_start: 0.8065 (tp30) cc_final: 0.7758 (tm-30) REVERT: A 325 THR cc_start: 0.8164 (t) cc_final: 0.7902 (m) REVERT: A 495 THR cc_start: 0.8237 (t) cc_final: 0.7970 (m) REVERT: A 599 ASN cc_start: 0.7383 (OUTLIER) cc_final: 0.7099 (t0) REVERT: A 601 GLU cc_start: 0.6852 (mm-30) cc_final: 0.6215 (mm-30) REVERT: A 606 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.6656 (mtp85) REVERT: A 703 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6445 (tp30) outliers start: 16 outliers final: 6 residues processed: 145 average time/residue: 1.7241 time to fit residues: 265.2640 Evaluate side-chains 154 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 599 ASN Chi-restraints excluded: chain A residue 606 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 61 optimal weight: 4.9990 chunk 121 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.154897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.115864 restraints weight = 9869.696| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.10 r_work: 0.3043 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.184 11490 Z= 0.251 Angle : 0.982 59.199 15482 Z= 0.600 Chirality : 0.042 0.166 1670 Planarity : 0.004 0.035 1902 Dihedral : 18.333 144.139 2034 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.52 % Allowed : 9.91 % Favored : 88.57 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.24), residues: 1288 helix: 2.33 (0.17), residues: 890 sheet: 1.34 (0.83), residues: 44 loop : -1.30 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 227 HIS 0.006 0.001 HIS B 619 PHE 0.011 0.002 PHE A 223 TYR 0.013 0.002 TYR B 589 ARG 0.004 0.001 ARG A 237 Details of bonding type rmsd hydrogen bonds : bond 0.05181 ( 722) hydrogen bonds : angle 4.28313 ( 2082) covalent geometry : bond 0.00503 (11490) covalent geometry : angle 0.98217 (15482) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12891.47 seconds wall clock time: 224 minutes 4.59 seconds (13444.59 seconds total)